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Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1.4 to 0.1.5 #513

Open

gxydevbot wants to merge 1 commit into galaxyproject:main from planemo-autoupdate:workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7

Contributor

gxydevbot commented Aug 22, 2024

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1

The workflow release number has been updated from 0.1.4 to 0.1.5.

Contributor Author

gxydevbot commented Aug 26, 2024

There are new updates, if you want to integrate them, close the PR and delete branch.

4 similar comments

Contributor Author

gxydevbot commented Sep 2, 2024

There are new updates, if you want to integrate them, close the PR and delete branch.

Contributor Author

gxydevbot commented Sep 9, 2024

There are new updates, if you want to integrate them, close the PR and delete branch.

Contributor Author

gxydevbot commented Sep 16, 2024

There are new updates, if you want to integrate them, close the PR and delete branch.

Contributor Author

gxydevbot commented Sep 23, 2024

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1.4 to 0.1.5~~ Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1.4 to 0.1.5

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 branch from c7dc8f3 to c230e11 Compare

September 23, 2024 14:03

Contributor Author

gxydevbot commented Sep 23, 2024

There are new updates, they have been integrated to the PR, check the file diff.

1 similar comment

Contributor Author

gxydevbot commented Sep 24, 2024

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 branch from c230e11 to d79bfac Compare

September 24, 2024 13:40

Contributor Author

gxydevbot commented Oct 14, 2024

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 branch from d79bfac to b342e74 Compare

October 14, 2024 04:31

github-actions bot commented Oct 14, 2024

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Scaffolding-BioNano-VGP7.ga_0

Problems:

Output with path /tmp/tmpo_ja3k7r/Bionano scaffolds reconciliated (GFA)__15a68f74-e91b-4142-82bd-095a44417d7d different than expected
Expected 67+-0 lines in the output found 66

Output with path /tmp/tmpev53b2cr/gfastats on data 12 stats__264cc922-e7f5-455d-970f-ef27f32ca133 different than expected
Expected line '# scaffolds	24' in output ('Expected genome size	11,748,793
# scaffolds	23
Total scaffold length	22,664,609
Average scaffold length	985,417.78
Scaffold N50	1,153,303
Scaffold auN	1,499,118.36
Scaffold L50	6
Scaffold NG50	2,181,178
Scaffold auNG	2,891,950.81
Scaffold LG50	3
Largest scaffold	3,064,584
Smallest scaffold	85,850
# contigs	32
Total contig length	22,664,492
Average contig length	708,265.38
Contig N50	923,452
Contig auN	903,816.25
Contig L50	10
Contig NG50	1,090,521
Contig auNG	1,743,543.88
Contig LG50	5
Largest contig	1,532,843
Smallest contig	85,850
# gaps in scaffolds	9
Total gap length in scaffolds	117
Average gap length in scaffolds	13.00
Gap N50 in scaffolds	13
Gap auN in scaffolds	13.00
Gap L50 in scaffolds	5
Largest gap in scaffolds	13
Smallest gap in scaffolds	13
Base composition (A:C:G:T)	7,010,241:4,337,484:4,330,387:6,986,380
GC content %	38.24
# soft-masked bases	0
# segments	33
Total segment length	23,447,265
Average segment length	710,523.18
# gaps	9
# paths	23
Scaffold N10	3,064,584
Scaffold N20	2,181,538
Scaffold N30	2,181,178
Scaffold N40	1,334,105
Scaffold N50	1,153,303
Scaffold N60	1,077,964
Scaffold N70	923,452
Scaffold N80	876,026
Scaffold N90	744,844
Scaffold N100	85,850
Scaffold L10	1
Scaffold L20	2
Scaffold L30	3
Scaffold L40	5
Scaffold L50	6
Scaffold L60	8
Scaffold L70	11
Scaffold L80	13
Scaffold L90	16
Scaffold L100	23
Scaffold NG10	3,064,584
Scaffold NG20	3,064,584
Scaffold NG30	2,181,538
Scaffold NG40	2,181,538
Scaffold NG50	2,181,178
Scaffold NG60	2,181,178
Scaffold NG70	1,626,363
Scaffold NG80	1,334,105
Scaffold NG90	1,153,303
Scaffold NG100	1,122,470
Scaffold LG10	1
Scaffold LG20	1
Scaffold LG30	2
Scaffold LG40	2
Scaffold LG50	3
Scaffold LG60	3
Scaffold LG70	4
Scaffold LG80	5
Scaffold LG90	6
Scaffold LG100	7
Contig N10	1,531,728
Contig N20	1,091,004
Contig N30	1,089,326
Contig N40	1,076,779
Contig N50	923,452
Contig N60	813,039
Contig N70	744,844
Contig N80	576,755
Contig N90	436,172
Contig N100	85,850
Contig L10	2
Contig L20	4
Contig L30	6
Contig L40	8
Contig L50	10
Contig L60	13
Contig L70	16
Contig L80	19
Contig L90	24
Contig L100	32
Contig NG10	1,532,843
Contig NG20	1,531,728
Contig NG30	1,091,839
Contig NG40	1,091,004
Contig NG50	1,090,521
Contig NG60	1,089,326
Contig NG70	1,077,964
Contig NG80	1,076,779
Contig NG90	923,452
Contig NG100	922,430
Contig LG10	1
Contig LG20	2
Contig LG30	3
Contig LG40	4
Contig LG50	5
Contig LG60	6
Contig LG70	7
Contig LG80	8
Contig LG90	10
Contig LG100	11
Gap N10	13
Gap N20	13
Gap N30	13
Gap N40	13
Gap N50	13
Gap N60	13
Gap N70	13
Gap N80	13
Gap N90	13
Gap N100	13
Gap L10	1
Gap L20	2
Gap L30	3
Gap L40	4
Gap L50	5
Gap L60	6
Gap L70	7
Gap L80	8
Gap L90	9
Gap L100	9
')

Output with path /tmp/tmp5ud3m6uc/gfastats on data 12 edited sequences__a77648e4-8a2d-47bc-8329-6eaba8a9fe8d different than expected
Expected 390825+-0 lines in the output found 377777

Workflow invocation details

Invocation Messages

Steps

Step 1: Bionano Data:
- step_state: scheduled
Step 2: Estimated genome size - Parameter File:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5oo0tnpd/files/1/5/a/dataset_15a68f74-e91b-4142-82bd-095a44417d7d.dat' --out-size s   --tabular > '/tmp/tmp5oo0tnpd/job_working_directory/000/9/outputs/dataset_9df9aeda-2de2-4e7b-8baa-5a1a8e266b8b.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp5oo0tnpd/job_working_directory/000/16/outputs/dataset_688baab8-1eb5-4034-b4f2-8cfc63db79c4.dat' -g     '#' 'Number of' '/tmp/tmp5oo0tnpd/files/2/6/4/dataset_264cc922-e7f5-455d-970f-ef27f32ca133.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 13: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp5oo0tnpd/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp5oo0tnpd/files/9/d/f/dataset_9df9aeda-2de2-4e7b-8baa-5a1a8e266b8b.dat' --output='/tmp/tmp5oo0tnpd/job_working_directory/000/10/outputs/dataset_7d6422bf-b12a-40a5-99ce-3106c7b5a122.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp5oo0tnpd/job_working_directory/000/11/configs/tmpmi392pum' '/tmp/tmp5oo0tnpd/files/7/d/6/dataset_7d6422bf-b12a-40a5-99ce-3106c7b5a122.dat' > '/tmp/tmp5oo0tnpd/job_working_directory/000/11/outputs/dataset_dc64ec1f-600d-4d4a-ad81-cd7cf6615be0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp5oo0tnpd/files/d/c/6/dataset_dc64ec1f-600d-4d4a-ad81-cd7cf6615be0.dat > '/tmp/tmp5oo0tnpd/job_working_directory/000/12/outputs/dataset_bce52862-4492-46d2-bab3-dc5e194c9db5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5oo0tnpd/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp5oo0tnpd/files/d/c/6/dataset_dc64ec1f-600d-4d4a-ad81-cd7cf6615be0.dat' '/tmp/tmp5oo0tnpd/job_working_directory/000/13/outputs/dataset_93603b9b-e26c-4ee7-a1b2-a7fa54e7da1c.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "22664609", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp5oo0tnpd/job_working_directory/000/18/configs/tmpzi_ckuuh' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp5oo0tnpd/files/9/3/6/dataset_93603b9b-e26c-4ee7-a1b2-a7fa54e7da1c.dat' '/tmp/tmp5oo0tnpd/job_working_directory/000/18/outputs/dataset_cf1b50c8-ca10-405e-869f-f6f6fa17c6e1.dat'

Exit Code:

```
0
```

Standard Output:

c3/22664609
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/22664609;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 23 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bd89e511efb621000d3acfb034"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/22664609"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 14: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5oo0tnpd/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5oo0tnpd/files/c/f/1/dataset_cf1b50c8-ca10-405e-869f-f6f6fa17c6e1.dat' 'c5,c6' T '/tmp/tmp5oo0tnpd/job_working_directory/000/19/outputs/dataset_edf2fd66-5bb2-4e14-9400-913cf6bcc867.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 15: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5oo0tnpd/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5oo0tnpd/files/c/f/1/dataset_cf1b50c8-ca10-405e-869f-f6f6fa17c6e1.dat' 'c4,c7' T '/tmp/tmp5oo0tnpd/job_working_directory/000/20/outputs/dataset_892d3917-690e-414f-a4d7-7dbf870d196b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp5oo0tnpd/job_working_directory/000/21/configs/tmpb0yz7kye' && Rscript '/tmp/tmp5oo0tnpd/job_working_directory/000/21/configs/tmpb0yz7kye'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp5oo0tnpd/files/e/d/f/dataset_edf2fd66-5bb2-4e14-9400-913cf6bcc867.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp5oo0tnpd/job_working_directory/000/21/outputs/dataset_f8ac6a55-e0e3-4dec-ae3d-8b7195524a54.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp5oo0tnpd/job_working_directory/000/22/configs/tmplxnzrrzl' && Rscript '/tmp/tmp5oo0tnpd/job_working_directory/000/22/configs/tmplxnzrrzl'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp5oo0tnpd/files/8/9/2/dataset_892d3917-690e-414f-a4d7-7dbf870d196b.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp5oo0tnpd/job_working_directory/000/22/outputs/dataset_73339cbe-8373-446f-9a6a-2fc3433f59f0.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 3: Input GFA:
- step_state: scheduled
Step 4: Conflict resolution files:
- step_state: scheduled

Step 5: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5oo0tnpd/files/7/c/7/dataset_7c76e5ae-6d15-4c7d-980b-b28af013d093.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 33
Total scaffold length: 23447265
Average scaffold length: 710523.18
Scaffold N50: 922430
Scaffold auN: 899775.29
Scaffold L50: 11
Largest scaffold: 1532843
Smallest scaffold: 85850
# contigs: 33
Total contig length: 23447265
Average contig length: 710523.18
Contig N50: 922430
Contig auN: 899775.29
Contig L50: 11
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 7251315:4489171:4481349:7225430
GC content %: 38.26
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 0
# paths: 33

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp5oo0tnpd/files/5/b/b/dataset_5bb94046-cc0a-49f6-a27d-9136dc581b33.dat' ./ngs.fasta && cp '/tmp/tmp5oo0tnpd/files/b/7/8/dataset_b78c5770-dffe-49c2-b92c-4c960db49d3c.dat' ./bionano.cmap && export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && export SLOTS=$(( ${GALAXY_SLOTS:-2} > 2 ? ${GALAXY_SLOTS:-2} : 2 )) && cp '/tmp/tmp5oo0tnpd/job_working_directory/000/6/configs/tmpaydholye' ./config.xml && sed -i "s|__MEMORY__|$GALAXY_MEMORY_GB|" ./config.xml && sed -i "s|__CORES__|$SLOTS|" ./config.xml && cat ./config.xml && perl '/HybridScaffold/hybridScaffold.pl' -n ./ngs.fasta -b ./bionano.cmap -c ./config.xml -r /RefAligner/RefAligner -B 3 -N 3 -f -z results.zip -o ./ && export PATH=/opt/conda/bin/:$PATH && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' && touch hybrid_scaffolds/temp_cut.txt && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt

Exit Code:

```
0
```

Standard Error:

cannot remove path when cwd is /tmp/tmp5oo0tnpd/job_working_directory/000/6/working for /tmp/tmp5oo0tnpd/job_working_directory/000/6/working:  at /HybridScaffold/hybridScaffold.pl line 1952.

Standard Output:

                <hybridScaffold>
                    <version>
                        <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
                    </version>
                    <global>
                        <flag attr="maxmem" val0="8" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
                        <flag attr="maxthreads" val0="2" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
                        <flag attr="maxvirtmem" val0="8"/>
                        <flag attr="RAmem" val0="3" val1="1"/>
                    </global>
                    <fasta2cmap>
                        <flag attr="enzyme" val0="CTTAAG" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
                        <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
                        <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
                        <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
                    </fasta2cmap>
                    <align0>
                        <flag attr="M" val0="1" val1="3"/>
                        <flag attr="ScaleDelta" val0="0.02" val1="15"/>
                        <flag attr="ScaleDeltaBPP"/>
                        <flag attr="hashScaleDelta" val0="2"/>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align0>
                    <align1>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align1>
                    <assignAlignType>
                        <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
                        <flag attr="max_overhang" val0="5" display=""/>
                    </assignAlignType>
                    <cut_conflicts>
                        <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
                        <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
                        <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
                    </cut_conflicts>
                    <mergeNGS_BN>
                        <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
                        <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
                        <flag attr="max_merge_rounds" val0="40" display=""/>
                        <flag attr="endoutlier" val0="1e-4" display=""/>
                        <flag attr="outlier" val0="1e-4" display=""/>
                        <flag attr="biaswt" val0="0" display=""/>
                        <flag attr="sd" val0="0.1" display=""/>
                        <flag attr="res" val0="2.9" display=""/>
                        <flag attr="mres" val0="2.9" display=""/>
                        <flag attr="sf" val0="0.2" display=""/>
                        <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
                        <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
                        <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
                        <flag attr="maxmem" val0="8" display=""/>
                        <flag attr="pairmergeRepeat"/>
                        <flag attr="NoBpp"/>
                        <flag attr="first" val0="-1" display=""/>
                        <flag attr="f"/>
                    </mergeNGS_BN>
                    <align_final_1st_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_1st_pass>
                    <align_final_2nd_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="50"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_2nd_pass>
                    <align_final_BNG>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="6"/>
                        <flag attr="deltaY" val0="6"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="14"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="BestRef" val0="1"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align_final_BNG>
                    <refineFinal1>
                        
..


Beginning FASTA header conversion...
Running command: /usr/bin/perl scripts/fa_key_convert.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/ngs.fasta /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in no time.

New FASTA with CMAP Ids as headers: /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Beginning initial NGS CMAP to BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/bionano.cmap -o align0 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -M 1 3 -ScaleDelta 0.02 15 -ScaleDeltaBPP -hashScaleDelta 2 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial alignment complete in 17 seconds.

Rescaling BioNano CMAP...
Running command: /RefAligner/RefAligner -merge -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/bionano.cmap -o /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust -readparameters /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/align0.errbin -stdout -stderr
Rescaling complete in no time.

Beginning initial NGS CMAP to rescaled BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -o align1 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial rescaled alignment complete in 1 second.

32 alignments found between /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/ngs.fasta and /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Beginning AssignAlignType...
Running command: /usr/bin/perl ./scripts/AssignAlignType.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1.xmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1_r.cmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1_q.cmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType.xmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap 11 5 /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/conflicts.txt 30
AssignAlignType complete in no time.
0 BNG contigs have been flagged as conflicting
0 NGS contigs have been flagged as conflicting

Beginning cut_conflicts...
Running command: /usr/bin/perl ./scripts/cut_conflicts.pl -align1XmapFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1.xmap -align1GMFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1_q.cmap -align1SeqFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -oriSeqFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -conflictFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/conflicts.txt -outDir /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/cut_conflicts -outGMFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/cut_conflicts/bionano_bppAdjust_cut.cmap -outSeqFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/cut_conflicts/ngs_CTTAAG_0kb_0labels_cut.cmap -windowSize 10000 -qScoreThreshold 35 -covThreshold 10 -refAligner /RefAligner/RefAligner
cut_conflicts complete in no time.
16 BNG contigs are found after the cut-conflict step
33 NGS contigs are found after the cut-conflict step

Beginning MergeNGS_BN...
*Using non-conflicting-only BioNano and non-conflicting-only sequence CMAP*
Running command: /usr/bin/perl ./scripts/MergeNGS_BN.pl -outputDir /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/mergeNGS_BN -refaligner /RefAligner/RefAligner -logFile mergeNGS_BN_script.log -ngs_cmap_fn /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -bng_cmap_fn /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -id_shift 100000 -readparameters /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align1/align1.errbin -xmlFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/config.xml
MergeNGS_BN complete in 1 second.

Beginning extraction of used and not used NGS contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_ngs.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /RefAligner/RefAligner
Extraction of NGS contigs complete in no time.

Beginning alignment of NGS cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_seq_two_passes.pl -outDir /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/config.xml -seqFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -scaffoldFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 1 second.

Beginning extraction of used and not used BNG contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_bn.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /RefAligner/RefAligner
Extraction of BNG contigs complete in no time.

Beginning alignment of BNG cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_bng.pl -outDir /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/config.xml -bngFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -scaffoldFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in no time.

Merging Hybrid CMAP with NGS not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_ngs.cmap -o HYBRID_SCAFFOLD_notUsedNGS_merged -merge -minsites 0 -stdout -stderr
Merging Hybrid CMAP with naive NGS CMAP complete in no time.

Merging Hybrid CMAP with BNG CMAP not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_bng.cmap -o HYBRID_SCAFFOLD_notUsedBNG_merged -merge -stdout -stderr
Merging Hybrid CMAP with naive BNG CMAP complete in no time.

Beginnning construction of AGP and FASTA file of the scaffolded and unscaffolded sequences...
Running command: /usr/bin/perl scripts/ExportAGP.pl -i /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/agp_fasta -m /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt -s /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs.fasta -e CTTAAG 1
AGP and FASTA generation complete in 1 second.

Calculating statistics...

Original BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/bionano.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.030

Bpp-adjusted BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Original NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

Before merge: BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Before merge: NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

BNG Genome Map in hybrid scaffold statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

NGS sequences in hybrid scaffold (CMAP) statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 32
Min length (Mbp) = 0.185
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.730
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.361

Hybrid scaffold Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final/step2.hybrid.cmap

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 0.764
Mean length (Mbp) = 0.755
N50 length (Mbp) = 0.924
Max length (Mbp) = 1.532
Total length (Mbp) = 12.072

NGS FASTA sequence in hybrid scaffold statistics:
Running command: /usr/bin/perl scripts/calc_scaffolded_seq_fasta_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/ngs.fasta /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 25
Min length (Mbp) = 0.231
Median length (Mbp) = 0.746
Mean length (Mbp) = 0.764
N50 length (Mbp) = 0.923
Max length (Mbp) = 1.533
Total length (Mbp) = 19.109

Hybrid scaffold FASTA statistics:
Running command: /usr/bin/perl scripts/calc_fasta_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 1.012
Mean length (Mbp) = 1.194
N50 length (Mbp) = 1.334
Max length (Mbp) = 3.065
Total length (Mbp) = 19.109

Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics:
Running command: /usr/bin/perl scripts/calc_hybrid_scaffold_not_scaffolded_seq_fasta_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 24
Min length (Mbp) = 0.086
Median length (Mbp) = 0.899
Mean length (Mbp) = 0.977
N50 length (Mbp) = 1.122
Max length (Mbp) = 3.065
Total length (Mbp) = 23.447


Calculating CMAP statistics complete in no time.

Calculating XMAP statistics...
Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	1599388	799694	98.36
7	1078752.8	2090973.6	1045486.8	96.92
26	562548.0	1041912	520956	92.61
2	231313.0	419334	209667	90.64
1	439899.6	801778.2	400889.1	91.13
30	1531728.0	3038512	1519256	99.19
13	270057.0	490192	245096	90.76
29	576755.0	1131418	565709	98.08
6	923503.0	1777400	888700	96.23
3	948308.4	1110182	934467.4	98.54
12	1090521.0	2170988	1085494	99.54
8	666912.0	1313512	656756	98.48
4	1091839.0	2148434	1074217	98.39
24	745651.0	1449940	724970	97.23
31	318638.0	619292	311093	97.63
5	782773.0	1535138	767569	98.06

Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	799694	799694	98.36
7	1078752.8	1045486.8	1045486.8	96.92
26	562548.0	520956	520956	92.61
2	231313.0	209667	209667	90.64
1	439899.6	400889.1	400889.1	91.13
30	1531728.0	1519256	1519256	99.19
13	270057.0	245096	245096	90.76
29	576755.0	565709	565709	98.08
6	923503.0	888700	888700	96.23
3	948308.4	934467.4	934467.4	98.54
12	1090521.0	1085494	1085494	99.54
8	666912.0	656756	656756	98.48
4	1091839.0	1074217	1074217	98.39
24	745651.0	724970	724970	97.23
31	318638.0	311093	311093	97.63
5	782773.0	767569	767569	98.06

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
tar file: /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/results.zip
The tar zip command completed.
Archive and zip of result files completed in 13 seconds.

End time: 2024-10-14 04:40:00

Total elapsed time: 36 seconds


Merging of /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/bionano.cmap with /tmp/tmp5oo0tnpd/job_working_directory/000/6/working/ngs.fasta is complete.

END of output

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
all_files	`false`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
configuration_options	`{"__current_case__": 0, "configuration": "vgp", "enzyme": "CTTAAG"}`
conflict_filter_genome	`"3"`
conflict_filter_sequence	`"3"`
conflict_resolution	`None`
dbkey	`"?"`
trim_cut_sites	`true`
zip_file	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5oo0tnpd/files/7/c/7/dataset_7c76e5ae-6d15-4c7d-980b-b28af013d093.dat' --agp-to-path /tmp/tmp5oo0tnpd/files/8/6/1/dataset_8617ccf2-7d80-40ef-a3eb-4ea340a7d9f3.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Error:

JOIN	ptg000009l_path+	ptg000026l_path+	13	gap66	Super-Scaffold_1	66
JOIN	ptg000032l_path+	ptg000015l_path+	13	gap71	Super-Scaffold_4	71
JOIN	ptg000028l_path+	ptg000011l_path+	13	gap77	Super-Scaffold_8	77
JOIN	ptg000007l_path+	ptg000024l_path+	13	gap80	Super-Scaffold_12	80
JOIN	ptg000006l_path+	ptg000023l_path+	13	gap83	Super-Scaffold_13	83
JOIN	ptg000008l_path+	ptg000025l_path+	13	gap87	Super-Scaffold_26	87
JOIN	ptg000005l_path+	ptg000022l_path+	13	gap90	Super-Scaffold_29	90
JOIN	ptg000004l_path+	ptg000021l_path+	13	gap93	Super-Scaffold_30	93
JOIN	ptg000002l_path+	ptg000019l_path+	13	gap97	Super-Scaffold_32	97

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 11, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5oo0tnpd/files/1/5/a/dataset_15a68f74-e91b-4142-82bd-095a44417d7d.dat'   -o dataset.fasta --line-length 60 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": "60", "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5oo0tnpd/files/1/5/a/dataset_15a68f74-e91b-4142-82bd-095a44417d7d.dat' 11748793 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp5oo0tnpd/job_working_directory/000/15/outputs/dataset_264cc922-e7f5-455d-970f-ef27f32ca133.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fef854bc89e511efb621000d3acfb034"`
chromInfo	`"/tmp/tmp5oo0tnpd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "11748793", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Other invocation details
- history_id
  - f5085075afe6960a
- history_state
  - ok
- invocation_id
  - f5085075afe6960a
- invocation_state
  - scheduled
- workflow_id
  - ee4d104513506fad

Contributor Author

gxydevbot commented Nov 11, 2024

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 branch from b342e74 to 25409f6 Compare

November 11, 2024 04:32

github-actions bot commented Nov 11, 2024

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Scaffolding-BioNano-VGP7.ga_0

Problems:

Output with path /tmp/tmpfd5ysftt/Bionano scaffolds reconciliated (GFA)__f4ec2bad-d056-44db-b65f-c55dac5e1c7e different than expected
Expected 67+-0 lines in the output found 66

Output with path /tmp/tmppjq85vqt/gfastats on data 12 stats__6e8a4780-c454-4933-a292-c494499a0fdc different than expected
Expected line '# scaffolds	24' in output ('Expected genome size	11,748,793
# scaffolds	23
Total scaffold length	22,664,609
Average scaffold length	985,417.78
Scaffold N50	1,153,303
Scaffold auN	1,499,118.36
Scaffold L50	6
Scaffold NG50	2,181,178
Scaffold auNG	2,891,950.81
Scaffold LG50	3
Largest scaffold	3,064,584
Smallest scaffold	85,850
# contigs	32
Total contig length	22,664,492
Average contig length	708,265.38
Contig N50	923,452
Contig auN	903,816.25
Contig L50	10
Contig NG50	1,090,521
Contig auNG	1,743,543.88
Contig LG50	5
Largest contig	1,532,843
Smallest contig	85,850
# gaps in scaffolds	9
Total gap length in scaffolds	117
Average gap length in scaffolds	13.00
Gap N50 in scaffolds	13
Gap auN in scaffolds	13.00
Gap L50 in scaffolds	5
Largest gap in scaffolds	13
Smallest gap in scaffolds	13
Base composition (A:C:G:T)	7,010,241:4,337,484:4,330,387:6,986,380
GC content %	38.24
# soft-masked bases	0
# segments	33
Total segment length	23,447,265
Average segment length	710,523.18
# gaps	9
# paths	23
Scaffold N10	3,064,584
Scaffold N20	2,181,538
Scaffold N30	2,181,178
Scaffold N40	1,334,105
Scaffold N50	1,153,303
Scaffold N60	1,077,964
Scaffold N70	923,452
Scaffold N80	876,026
Scaffold N90	744,844
Scaffold N100	85,850
Scaffold L10	1
Scaffold L20	2
Scaffold L30	3
Scaffold L40	5
Scaffold L50	6
Scaffold L60	8
Scaffold L70	11
Scaffold L80	13
Scaffold L90	16
Scaffold L100	23
Scaffold NG10	3,064,584
Scaffold NG20	3,064,584
Scaffold NG30	2,181,538
Scaffold NG40	2,181,538
Scaffold NG50	2,181,178
Scaffold NG60	2,181,178
Scaffold NG70	1,626,363
Scaffold NG80	1,334,105
Scaffold NG90	1,153,303
Scaffold NG100	1,122,470
Scaffold LG10	1
Scaffold LG20	1
Scaffold LG30	2
Scaffold LG40	2
Scaffold LG50	3
Scaffold LG60	3
Scaffold LG70	4
Scaffold LG80	5
Scaffold LG90	6
Scaffold LG100	7
Contig N10	1,531,728
Contig N20	1,091,004
Contig N30	1,089,326
Contig N40	1,076,779
Contig N50	923,452
Contig N60	813,039
Contig N70	744,844
Contig N80	576,755
Contig N90	436,172
Contig N100	85,850
Contig L10	2
Contig L20	4
Contig L30	6
Contig L40	8
Contig L50	10
Contig L60	13
Contig L70	16
Contig L80	19
Contig L90	24
Contig L100	32
Contig NG10	1,532,843
Contig NG20	1,531,728
Contig NG30	1,091,839
Contig NG40	1,091,004
Contig NG50	1,090,521
Contig NG60	1,089,326
Contig NG70	1,077,964
Contig NG80	1,076,779
Contig NG90	923,452
Contig NG100	922,430
Contig LG10	1
Contig LG20	2
Contig LG30	3
Contig LG40	4
Contig LG50	5
Contig LG60	6
Contig LG70	7
Contig LG80	8
Contig LG90	10
Contig LG100	11
Gap N10	13
Gap N20	13
Gap N30	13
Gap N40	13
Gap N50	13
Gap N60	13
Gap N70	13
Gap N80	13
Gap N90	13
Gap N100	13
Gap L10	1
Gap L20	2
Gap L30	3
Gap L40	4
Gap L50	5
Gap L60	6
Gap L70	7
Gap L80	8
Gap L90	9
Gap L100	9
')

Output with path /tmp/tmpfhd35tsu/gfastats on data 12 edited sequences__780d4307-f03e-430b-ad8c-40566002ba2b different than expected
Expected 390825+-0 lines in the output found 4144605

Workflow invocation details

Invocation Messages

Steps

Step 1: Bionano Data:
- step_state: scheduled
Step 2: Estimated genome size - Parameter File:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5ir87sf_/files/f/4/e/dataset_f4ec2bad-d056-44db-b65f-c55dac5e1c7e.dat' --out-size s   --tabular > '/tmp/tmp5ir87sf_/job_working_directory/000/9/outputs/dataset_ae240a74-42b9-41ed-8ab7-7b8693509ed9.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp5ir87sf_/job_working_directory/000/16/outputs/dataset_df94f96c-6e42-44d7-baed-cd5139aa0393.dat' -g     '#' 'Number of' '/tmp/tmp5ir87sf_/files/6/e/8/dataset_6e8a4780-c454-4933-a292-c494499a0fdc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 13: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp5ir87sf_/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp5ir87sf_/files/a/e/2/dataset_ae240a74-42b9-41ed-8ab7-7b8693509ed9.dat' --output='/tmp/tmp5ir87sf_/job_working_directory/000/10/outputs/dataset_e267b322-e4a0-45e3-9087-e59cc1cb21f5.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp5ir87sf_/job_working_directory/000/11/configs/tmpnx4veupi' '/tmp/tmp5ir87sf_/files/e/2/6/dataset_e267b322-e4a0-45e3-9087-e59cc1cb21f5.dat' > '/tmp/tmp5ir87sf_/job_working_directory/000/11/outputs/dataset_800c962d-5506-4aff-bcf3-b806941514c9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp5ir87sf_/files/8/0/0/dataset_800c962d-5506-4aff-bcf3-b806941514c9.dat > '/tmp/tmp5ir87sf_/job_working_directory/000/12/outputs/dataset_b9c8be22-e5e7-4da7-8e55-d880590b7f9f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5ir87sf_/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp5ir87sf_/files/8/0/0/dataset_800c962d-5506-4aff-bcf3-b806941514c9.dat' '/tmp/tmp5ir87sf_/job_working_directory/000/13/outputs/dataset_5e7c1a23-2027-4bf9-a1a0-303bf4f35b6f.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "22664609", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp5ir87sf_/job_working_directory/000/18/configs/tmpu8b66xbi' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp5ir87sf_/files/5/e/7/dataset_5e7c1a23-2027-4bf9-a1a0-303bf4f35b6f.dat' '/tmp/tmp5ir87sf_/job_working_directory/000/18/outputs/dataset_415ad128-cd5d-4d11-b5fa-d3e82c97c29a.dat'

Exit Code:

```
0
```

Standard Output:

c3/22664609
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/22664609;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 23 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688f9fe611efb86791c30ddf0fa2"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/22664609"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 14: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5ir87sf_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5ir87sf_/files/4/1/5/dataset_415ad128-cd5d-4d11-b5fa-d3e82c97c29a.dat' 'c5,c6' T '/tmp/tmp5ir87sf_/job_working_directory/000/19/outputs/dataset_a23fc289-b2b4-4533-9125-bc2c5acda893.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 15: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp5ir87sf_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5ir87sf_/files/4/1/5/dataset_415ad128-cd5d-4d11-b5fa-d3e82c97c29a.dat' 'c4,c7' T '/tmp/tmp5ir87sf_/job_working_directory/000/20/outputs/dataset_4e6b8e1b-25a8-447e-be49-d5cd95839d4d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp5ir87sf_/job_working_directory/000/21/configs/tmpndl8jcub' && Rscript '/tmp/tmp5ir87sf_/job_working_directory/000/21/configs/tmpndl8jcub'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp5ir87sf_/files/a/2/3/dataset_a23fc289-b2b4-4533-9125-bc2c5acda893.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp5ir87sf_/job_working_directory/000/21/outputs/dataset_387408f5-518a-4167-af6e-346182d8bc0c.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp5ir87sf_/job_working_directory/000/22/configs/tmp41wha4jh' && Rscript '/tmp/tmp5ir87sf_/job_working_directory/000/22/configs/tmp41wha4jh'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp5ir87sf_/files/4/e/6/dataset_4e6b8e1b-25a8-447e-be49-d5cd95839d4d.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp5ir87sf_/job_working_directory/000/22/outputs/dataset_24674182-d804-4f2d-beee-b925708b7dbc.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 3: Input GFA:
- step_state: scheduled
Step 4: Conflict resolution files:
- step_state: scheduled

Step 5: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5ir87sf_/files/6/f/9/dataset_6f92025b-733f-41c6-9a1e-6640999d2f6b.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 33
Total scaffold length: 23447265
Average scaffold length: 710523.18
Scaffold N50: 922430
Scaffold auN: 899775.29
Scaffold L50: 11
Largest scaffold: 1532843
Smallest scaffold: 85850
# contigs: 33
Total contig length: 23447265
Average contig length: 710523.18
Contig N50: 922430
Contig auN: 899775.29
Contig L50: 11
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 7251315:4489171:4481349:7225430
GC content %: 38.26
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 0
# paths: 33

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp5ir87sf_/files/0/f/d/dataset_0fd91a63-1a09-4cd3-abba-174ddd410a58.dat' ./ngs.fasta && cp '/tmp/tmp5ir87sf_/files/8/8/9/dataset_889f40a1-7147-4255-a9e7-61e53beeb73d.dat' ./bionano.cmap && export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && export SLOTS=$(( ${GALAXY_SLOTS:-2} > 2 ? ${GALAXY_SLOTS:-2} : 2 )) && cp '/tmp/tmp5ir87sf_/job_working_directory/000/6/configs/tmp11n2xiq6' ./config.xml && sed -i "s|__MEMORY__|$GALAXY_MEMORY_GB|" ./config.xml && sed -i "s|__CORES__|$SLOTS|" ./config.xml && cat ./config.xml && perl '/HybridScaffold/hybridScaffold.pl' -n ./ngs.fasta -b ./bionano.cmap -c ./config.xml -r /RefAligner/RefAligner -B 3 -N 3 -f -z results.zip -o ./ && export PATH=/opt/conda/bin/:$PATH && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' && touch hybrid_scaffolds/temp_cut.txt && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt

Exit Code:

```
0
```

Standard Error:

cannot remove path when cwd is /tmp/tmp5ir87sf_/job_working_directory/000/6/working for /tmp/tmp5ir87sf_/job_working_directory/000/6/working:  at /HybridScaffold/hybridScaffold.pl line 1952.

Standard Output:

                <hybridScaffold>
                    <version>
                        <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
                    </version>
                    <global>
                        <flag attr="maxmem" val0="8" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
                        <flag attr="maxthreads" val0="2" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
                        <flag attr="maxvirtmem" val0="8"/>
                        <flag attr="RAmem" val0="3" val1="1"/>
                    </global>
                    <fasta2cmap>
                        <flag attr="enzyme" val0="CTTAAG" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
                        <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
                        <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
                        <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
                    </fasta2cmap>
                    <align0>
                        <flag attr="M" val0="1" val1="3"/>
                        <flag attr="ScaleDelta" val0="0.02" val1="15"/>
                        <flag attr="ScaleDeltaBPP"/>
                        <flag attr="hashScaleDelta" val0="2"/>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align0>
                    <align1>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align1>
                    <assignAlignType>
                        <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
                        <flag attr="max_overhang" val0="5" display=""/>
                    </assignAlignType>
                    <cut_conflicts>
                        <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
                        <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
                        <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
                    </cut_conflicts>
                    <mergeNGS_BN>
                        <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
                        <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
                        <flag attr="max_merge_rounds" val0="40" display=""/>
                        <flag attr="endoutlier" val0="1e-4" display=""/>
                        <flag attr="outlier" val0="1e-4" display=""/>
                        <flag attr="biaswt" val0="0" display=""/>
                        <flag attr="sd" val0="0.1" display=""/>
                        <flag attr="res" val0="2.9" display=""/>
                        <flag attr="mres" val0="2.9" display=""/>
                        <flag attr="sf" val0="0.2" display=""/>
                        <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
                        <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
                        <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
                        <flag attr="maxmem" val0="8" display=""/>
                        <flag attr="pairmergeRepeat"/>
                        <flag attr="NoBpp"/>
                        <flag attr="first" val0="-1" display=""/>
                        <flag attr="f"/>
                    </mergeNGS_BN>
                    <align_final_1st_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_1st_pass>
                    <align_final_2nd_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="50"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_2nd_pass>
                    <align_final_BNG>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="6"/>
                        <flag attr="deltaY" val0="6"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="14"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="BestRef" val0="1"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align_final_BNG>
                    <refineFinal1>
                        
..


Beginning FASTA header conversion...
Running command: /usr/bin/perl scripts/fa_key_convert.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/ngs.fasta /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in no time.

New FASTA with CMAP Ids as headers: /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Beginning initial NGS CMAP to BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/bionano.cmap -o align0 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -M 1 3 -ScaleDelta 0.02 15 -ScaleDeltaBPP -hashScaleDelta 2 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial alignment complete in 17 seconds.

Rescaling BioNano CMAP...
Running command: /RefAligner/RefAligner -merge -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/bionano.cmap -o /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust -readparameters /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/align0.errbin -stdout -stderr
Rescaling complete in no time.

Beginning initial NGS CMAP to rescaled BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -o align1 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial rescaled alignment complete in 1 second.

32 alignments found between /tmp/tmp5ir87sf_/job_working_directory/000/6/working/ngs.fasta and /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Beginning AssignAlignType...
Running command: /usr/bin/perl ./scripts/AssignAlignType.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1.xmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1_r.cmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1_q.cmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType.xmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap 11 5 /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/conflicts.txt 30
AssignAlignType complete in no time.
0 BNG contigs have been flagged as conflicting
0 NGS contigs have been flagged as conflicting

Beginning cut_conflicts...
Running command: /usr/bin/perl ./scripts/cut_conflicts.pl -align1XmapFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1.xmap -align1GMFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1_q.cmap -align1SeqFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -oriSeqFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -conflictFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/conflicts.txt -outDir /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/cut_conflicts -outGMFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/cut_conflicts/bionano_bppAdjust_cut.cmap -outSeqFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/cut_conflicts/ngs_CTTAAG_0kb_0labels_cut.cmap -windowSize 10000 -qScoreThreshold 35 -covThreshold 10 -refAligner /RefAligner/RefAligner
cut_conflicts complete in no time.
16 BNG contigs are found after the cut-conflict step
33 NGS contigs are found after the cut-conflict step

Beginning MergeNGS_BN...
*Using non-conflicting-only BioNano and non-conflicting-only sequence CMAP*
Running command: /usr/bin/perl ./scripts/MergeNGS_BN.pl -outputDir /tmp/tmp5ir87sf_/job_working_directory/000/6/working/mergeNGS_BN -refaligner /RefAligner/RefAligner -logFile mergeNGS_BN_script.log -ngs_cmap_fn /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -bng_cmap_fn /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -id_shift 100000 -readparameters /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align1/align1.errbin -xmlFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/config.xml
MergeNGS_BN complete in no time.

Beginning extraction of used and not used NGS contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_ngs.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /RefAligner/RefAligner
Extraction of NGS contigs complete in no time.

Beginning alignment of NGS cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_seq_two_passes.pl -outDir /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/config.xml -seqFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -scaffoldFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 1 second.

Beginning extraction of used and not used BNG contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_bn.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /RefAligner/RefAligner
Extraction of BNG contigs complete in no time.

Beginning alignment of BNG cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_bng.pl -outDir /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/config.xml -bngFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -scaffoldFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 1 second.

Merging Hybrid CMAP with NGS not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_ngs.cmap -o HYBRID_SCAFFOLD_notUsedNGS_merged -merge -minsites 0 -stdout -stderr
Merging Hybrid CMAP with naive NGS CMAP complete in no time.

Merging Hybrid CMAP with BNG CMAP not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_bng.cmap -o HYBRID_SCAFFOLD_notUsedBNG_merged -merge -stdout -stderr
Merging Hybrid CMAP with naive BNG CMAP complete in no time.

Beginnning construction of AGP and FASTA file of the scaffolded and unscaffolded sequences...
Running command: /usr/bin/perl scripts/ExportAGP.pl -i /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /tmp/tmp5ir87sf_/job_working_directory/000/6/working/agp_fasta -m /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt -s /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs.fasta -e CTTAAG 1
AGP and FASTA generation complete in no time.

Calculating statistics...

Original BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/bionano.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.030

Bpp-adjusted BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Original NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

Before merge: BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Before merge: NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

BNG Genome Map in hybrid scaffold statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

NGS sequences in hybrid scaffold (CMAP) statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 32
Min length (Mbp) = 0.185
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.730
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.361

Hybrid scaffold Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final/step2.hybrid.cmap

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 0.764
Mean length (Mbp) = 0.755
N50 length (Mbp) = 0.924
Max length (Mbp) = 1.532
Total length (Mbp) = 12.072

NGS FASTA sequence in hybrid scaffold statistics:
Running command: /usr/bin/perl scripts/calc_scaffolded_seq_fasta_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/ngs.fasta /tmp/tmp5ir87sf_/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 25
Min length (Mbp) = 0.231
Median length (Mbp) = 0.746
Mean length (Mbp) = 0.764
N50 length (Mbp) = 0.923
Max length (Mbp) = 1.533
Total length (Mbp) = 19.109

Hybrid scaffold FASTA statistics:
Running command: /usr/bin/perl scripts/calc_fasta_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 1.012
Mean length (Mbp) = 1.194
N50 length (Mbp) = 1.334
Max length (Mbp) = 3.065
Total length (Mbp) = 19.109

Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics:
Running command: /usr/bin/perl scripts/calc_hybrid_scaffold_not_scaffolded_seq_fasta_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /tmp/tmp5ir87sf_/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 24
Min length (Mbp) = 0.086
Median length (Mbp) = 0.899
Mean length (Mbp) = 0.977
N50 length (Mbp) = 1.122
Max length (Mbp) = 3.065
Total length (Mbp) = 23.447


Calculating CMAP statistics complete in 1 second.

Calculating XMAP statistics...
Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	1599388	799694	98.36
7	1078752.8	2090973.6	1045486.8	96.92
26	562548.0	1041912	520956	92.61
2	231313.0	419334	209667	90.64
1	439899.6	801778.2	400889.1	91.13
30	1531728.0	3038512	1519256	99.19
13	270057.0	490192	245096	90.76
29	576755.0	1131418	565709	98.08
6	923503.0	1777400	888700	96.23
3	948308.4	1110182	934467.4	98.54
12	1090521.0	2170988	1085494	99.54
8	666912.0	1313512	656756	98.48
4	1091839.0	2148434	1074217	98.39
24	745651.0	1449940	724970	97.23
31	318638.0	619292	311093	97.63
5	782773.0	1535138	767569	98.06

Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp5ir87sf_/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	799694	799694	98.36
7	1078752.8	1045486.8	1045486.8	96.92
26	562548.0	520956	520956	92.61
2	231313.0	209667	209667	90.64
1	439899.6	400889.1	400889.1	91.13
30	1531728.0	1519256	1519256	99.19
13	270057.0	245096	245096	90.76
29	576755.0	565709	565709	98.08
6	923503.0	888700	888700	96.23
3	948308.4	934467.4	934467.4	98.54
12	1090521.0	1085494	1085494	99.54
8	666912.0	656756	656756	98.48
4	1091839.0	1074217	1074217	98.39
24	745651.0	724970	724970	97.23
31	318638.0	311093	311093	97.63
5	782773.0	767569	767569	98.06

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
tar file: /tmp/tmp5ir87sf_/job_working_directory/000/6/working/results.zip
The tar zip command completed.
Archive and zip of result files completed in 13 seconds.

End time: 2024-11-11 04:42:59

Total elapsed time: 37 seconds


Merging of /tmp/tmp5ir87sf_/job_working_directory/000/6/working/bionano.cmap with /tmp/tmp5ir87sf_/job_working_directory/000/6/working/ngs.fasta is complete.

END of output

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
all_files	`false`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
configuration_options	`{"__current_case__": 0, "configuration": "vgp", "enzyme": "CTTAAG"}`
conflict_filter_genome	`"3"`
conflict_filter_sequence	`"3"`
conflict_resolution	`None`
dbkey	`"?"`
trim_cut_sites	`true`
zip_file	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5ir87sf_/files/6/f/9/dataset_6f92025b-733f-41c6-9a1e-6640999d2f6b.dat' --agp-to-path /tmp/tmp5ir87sf_/files/5/0/b/dataset_50b27957-a705-452f-9ff8-2c7eb0fab834.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Error:

JOIN	ptg000009l_path+	ptg000026l_path+	13	gap66	Super-Scaffold_1	66
JOIN	ptg000032l_path+	ptg000015l_path+	13	gap71	Super-Scaffold_4	71
JOIN	ptg000028l_path+	ptg000011l_path+	13	gap77	Super-Scaffold_8	77
JOIN	ptg000007l_path+	ptg000024l_path+	13	gap80	Super-Scaffold_12	80
JOIN	ptg000006l_path+	ptg000023l_path+	13	gap83	Super-Scaffold_13	83
JOIN	ptg000008l_path+	ptg000025l_path+	13	gap87	Super-Scaffold_26	87
JOIN	ptg000005l_path+	ptg000022l_path+	13	gap90	Super-Scaffold_29	90
JOIN	ptg000004l_path+	ptg000021l_path+	13	gap93	Super-Scaffold_30	93
JOIN	ptg000002l_path+	ptg000019l_path+	13	gap97	Super-Scaffold_32	97

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 11, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5ir87sf_/files/f/4/e/dataset_f4ec2bad-d056-44db-b65f-c55dac5e1c7e.dat'   -o dataset.fasta --line-length 60 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": "60", "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp5ir87sf_/files/f/4/e/dataset_f4ec2bad-d056-44db-b65f-c55dac5e1c7e.dat' 11748793 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp5ir87sf_/job_working_directory/000/15/outputs/dataset_6e8a4780-c454-4933-a292-c494499a0fdc.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e0d8688e9fe611efb86791c30ddf0fa2"`
chromInfo	`"/tmp/tmp5ir87sf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "11748793", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Other invocation details
- history_id
  - ae0417c68ca56fa4
- history_state
  - ok
- invocation_id
  - ae0417c68ca56fa4
- invocation_state
  - scheduled
- workflow_id
  - 15e3fbdc706e4eab


          Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1.…

22eb731

…4 to 0.1.5

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 branch from 25409f6 to 22eb731 Compare

December 16, 2024 04:51

Contributor Author

gxydevbot commented Dec 16, 2024

There are new updates, they have been integrated to the PR, check the file diff.

github-actions bot commented Dec 16, 2024

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Scaffolding-BioNano-VGP7.ga_0

Problems:

Output with path /tmp/tmpxrrh6n8j/Bionano scaffolds reconciliated (GFA)__cb755667-0762-49e0-b2ec-fbc7816084e3 different than expected
Expected 67+-0 lines in the output found 66

Output with path /tmp/tmp_aaaxa0c/gfastats on data 12 stats__abf0c3df-5748-48d3-ad5d-4d997e7654ca different than expected
Expected line '# scaffolds	24' in output ('Expected genome size	11,748,793
# scaffolds	23
Total scaffold length	22,664,609
Average scaffold length	985,417.78
Scaffold N50	1,153,303
Scaffold auN	1,499,118.36
Scaffold L50	6
Scaffold NG50	2,181,178
Scaffold auNG	2,891,950.81
Scaffold LG50	3
Largest scaffold	3,064,584
Smallest scaffold	85,850
# contigs	32
Total contig length	22,664,492
Average contig length	708,265.38
Contig N50	923,452
Contig auN	903,816.25
Contig L50	10
Contig NG50	1,090,521
Contig auNG	1,743,543.88
Contig LG50	5
Largest contig	1,532,843
Smallest contig	85,850
# gaps in scaffolds	9
Total gap length in scaffolds	117
Average gap length in scaffolds	13.00
Gap N50 in scaffolds	13
Gap auN in scaffolds	13.00
Gap L50 in scaffolds	5
Largest gap in scaffolds	13
Smallest gap in scaffolds	13
Base composition (A:C:G:T)	7,010,241:4,337,484:4,330,387:6,986,380
GC content %	38.24
# soft-masked bases	0
# segments	33
Total segment length	23,447,265
Average segment length	710,523.18
# gaps	9
# paths	23
Scaffold N10	3,064,584
Scaffold N20	2,181,538
Scaffold N30	2,181,178
Scaffold N40	1,334,105
Scaffold N50	1,153,303
Scaffold N60	1,077,964
Scaffold N70	923,452
Scaffold N80	876,026
Scaffold N90	744,844
Scaffold N100	85,850
Scaffold L10	1
Scaffold L20	2
Scaffold L30	3
Scaffold L40	5
Scaffold L50	6
Scaffold L60	8
Scaffold L70	11
Scaffold L80	13
Scaffold L90	16
Scaffold L100	23
Scaffold NG10	3,064,584
Scaffold NG20	3,064,584
Scaffold NG30	2,181,538
Scaffold NG40	2,181,538
Scaffold NG50	2,181,178
Scaffold NG60	2,181,178
Scaffold NG70	1,626,363
Scaffold NG80	1,334,105
Scaffold NG90	1,153,303
Scaffold NG100	1,122,470
Scaffold LG10	1
Scaffold LG20	1
Scaffold LG30	2
Scaffold LG40	2
Scaffold LG50	3
Scaffold LG60	3
Scaffold LG70	4
Scaffold LG80	5
Scaffold LG90	6
Scaffold LG100	7
Contig N10	1,531,728
Contig N20	1,091,004
Contig N30	1,089,326
Contig N40	1,076,779
Contig N50	923,452
Contig N60	813,039
Contig N70	744,844
Contig N80	576,755
Contig N90	436,172
Contig N100	85,850
Contig L10	2
Contig L20	4
Contig L30	6
Contig L40	8
Contig L50	10
Contig L60	13
Contig L70	16
Contig L80	19
Contig L90	24
Contig L100	32
Contig NG10	1,532,843
Contig NG20	1,531,728
Contig NG30	1,091,839
Contig NG40	1,091,004
Contig NG50	1,090,521
Contig NG60	1,089,326
Contig NG70	1,077,964
Contig NG80	1,076,779
Contig NG90	923,452
Contig NG100	922,430
Contig LG10	1
Contig LG20	2
Contig LG30	3
Contig LG40	4
Contig LG50	5
Contig LG60	6
Contig LG70	7
Contig LG80	8
Contig LG90	10
Contig LG100	11
Gap N10	13
Gap N20	13
Gap N30	13
Gap N40	13
Gap N50	13
Gap N60	13
Gap N70	13
Gap N80	13
Gap N90	13
Gap N100	13
Gap L10	1
Gap L20	2
Gap L30	3
Gap L40	4
Gap L50	5
Gap L60	6
Gap L70	7
Gap L80	8
Gap L90	9
Gap L100	9
')

Output with path /tmp/tmp7ezxm5yu/gfastats on data 12 edited sequences__e50ffeb1-3a31-4bf9-aa51-ec82a8f30051 different than expected
Expected 390825+-0 lines in the output found 4144605

Workflow invocation details

Invocation Messages

Steps

Step 1: Bionano Data:
- step_state: scheduled
Step 2: Estimated genome size - Parameter File:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7squ168i/files/c/b/7/dataset_cb755667-0762-49e0-b2ec-fbc7816084e3.dat' --out-size s   --tabular > '/tmp/tmp7squ168i/job_working_directory/000/9/outputs/dataset_8e432919-d401-4ddb-ba59-4363a2c94a95.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp7squ168i/job_working_directory/000/16/outputs/dataset_faa94bb4-3204-4518-8425-227fc370e2de.dat' -g     '#' 'Number of' '/tmp/tmp7squ168i/files/a/b/f/dataset_abf0c3df-5748-48d3-ad5d-4d997e7654ca.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 13: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp7squ168i/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp7squ168i/files/8/e/4/dataset_8e432919-d401-4ddb-ba59-4363a2c94a95.dat' --output='/tmp/tmp7squ168i/job_working_directory/000/10/outputs/dataset_bd6f27fd-0c54-4c34-af9f-f257aa9ffd00.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp7squ168i/job_working_directory/000/11/configs/tmpnun19aqo' '/tmp/tmp7squ168i/files/b/d/6/dataset_bd6f27fd-0c54-4c34-af9f-f257aa9ffd00.dat' > '/tmp/tmp7squ168i/job_working_directory/000/11/outputs/dataset_0d1477fe-43f8-4984-930d-3361692111dd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp7squ168i/files/0/d/1/dataset_0d1477fe-43f8-4984-930d-3361692111dd.dat > '/tmp/tmp7squ168i/job_working_directory/000/12/outputs/dataset_a41d8846-e394-4b41-92ab-9f4b38aeff73.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7squ168i/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp7squ168i/files/0/d/1/dataset_0d1477fe-43f8-4984-930d-3361692111dd.dat' '/tmp/tmp7squ168i/job_working_directory/000/13/outputs/dataset_4eea4829-5d90-4c8c-819e-370aa4a692c2.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "22664609", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp7squ168i/job_working_directory/000/18/configs/tmpcd_2pvo0' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp7squ168i/files/4/e/e/dataset_4eea4829-5d90-4c8c-819e-370aa4a692c2.dat' '/tmp/tmp7squ168i/job_working_directory/000/18/outputs/dataset_338554d7-54a5-40d4-99b3-d324e28ec6e4.dat'

Exit Code:

```
0
```

Standard Output:

c3/22664609
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/22664609;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 23 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e5bb6a11ef899e7c1e522baf55"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/22664609"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 14: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7squ168i/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp7squ168i/files/3/3/8/dataset_338554d7-54a5-40d4-99b3-d324e28ec6e4.dat' 'c5,c6' T '/tmp/tmp7squ168i/job_working_directory/000/19/outputs/dataset_d4a10980-c721-4bad-b9ad-6e548aa3636e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 15: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7squ168i/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp7squ168i/files/3/3/8/dataset_338554d7-54a5-40d4-99b3-d324e28ec6e4.dat' 'c4,c7' T '/tmp/tmp7squ168i/job_working_directory/000/20/outputs/dataset_ed93b001-5d95-4114-8d68-f3205d43d363.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp7squ168i/job_working_directory/000/21/configs/tmp8nb_mul1' && Rscript '/tmp/tmp7squ168i/job_working_directory/000/21/configs/tmp8nb_mul1'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp7squ168i/files/d/4/a/dataset_d4a10980-c721-4bad-b9ad-6e548aa3636e.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp7squ168i/job_working_directory/000/21/outputs/dataset_28ef816a-673b-4723-8658-9785c172e2cd.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp7squ168i/job_working_directory/000/22/configs/tmp7_r83c6z' && Rscript '/tmp/tmp7squ168i/job_working_directory/000/22/configs/tmp7_r83c6z'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp7squ168i/files/e/d/9/dataset_ed93b001-5d95-4114-8d68-f3205d43d363.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('7.0')
        gg_height <- as.double('7.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp7squ168i/job_working_directory/000/22/outputs/dataset_fe1bdc17-8455-4c82-b1c7-ffa8a301e0a6.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 3: Input GFA:
- step_state: scheduled
Step 4: Conflict resolution files:
- step_state: scheduled

Step 5: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7squ168i/files/0/e/6/dataset_0e62d62a-7563-444c-a945-bd2f6adc9a70.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 33
Total scaffold length: 23447265
Average scaffold length: 710523.18
Scaffold N50: 922430
Scaffold auN: 899775.29
Scaffold L50: 11
Largest scaffold: 1532843
Smallest scaffold: 85850
# contigs: 33
Total contig length: 23447265
Average contig length: 710523.18
Contig N50: 922430
Contig auN: 899775.29
Contig L50: 11
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 7251315:4489171:4481349:7225430
GC content %: 38.26
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 0
# paths: 33

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp7squ168i/files/9/e/4/dataset_9e422d33-6b96-4623-a282-4cd642ca2f27.dat' ./ngs.fasta && cp '/tmp/tmp7squ168i/files/6/e/d/dataset_6edbb293-419c-4b18-b896-8f55d36f90fc.dat' ./bionano.cmap && export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && export SLOTS=$(( ${GALAXY_SLOTS:-2} > 2 ? ${GALAXY_SLOTS:-2} : 2 )) && cp '/tmp/tmp7squ168i/job_working_directory/000/6/configs/tmplom4gq3i' ./config.xml && sed -i "s|__MEMORY__|$GALAXY_MEMORY_GB|" ./config.xml && sed -i "s|__CORES__|$SLOTS|" ./config.xml && cat ./config.xml && perl '/HybridScaffold/hybridScaffold.pl' -n ./ngs.fasta -b ./bionano.cmap -c ./config.xml -r /RefAligner/RefAligner -B 3 -N 3 -f -z results.zip -o ./ && export PATH=/opt/conda/bin/:$PATH && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/3371c5bdc17a/bionano_scaffold/remove_fake_cut_sites.py' hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' && touch hybrid_scaffolds/temp_cut.txt && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt

Exit Code:

```
0
```

Standard Error:

cannot remove path when cwd is /tmp/tmp7squ168i/job_working_directory/000/6/working for /tmp/tmp7squ168i/job_working_directory/000/6/working:  at /HybridScaffold/hybridScaffold.pl line 1952.

Standard Output:

                <hybridScaffold>
                    <version>
                        <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
                    </version>
                    <global>
                        <flag attr="maxmem" val0="8" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
                        <flag attr="maxthreads" val0="2" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
                        <flag attr="maxvirtmem" val0="8"/>
                        <flag attr="RAmem" val0="3" val1="1"/>
                    </global>
                    <fasta2cmap>
                        <flag attr="enzyme" val0="CTTAAG" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
                        <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
                        <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
                        <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
                    </fasta2cmap>
                    <align0>
                        <flag attr="M" val0="1" val1="3"/>
                        <flag attr="ScaleDelta" val0="0.02" val1="15"/>
                        <flag attr="ScaleDeltaBPP"/>
                        <flag attr="hashScaleDelta" val0="2"/>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align0>
                    <align1>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align1>
                    <assignAlignType>
                        <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
                        <flag attr="max_overhang" val0="5" display=""/>
                    </assignAlignType>
                    <cut_conflicts>
                        <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
                        <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
                        <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
                    </cut_conflicts>
                    <mergeNGS_BN>
                        <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
                        <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
                        <flag attr="max_merge_rounds" val0="40" display=""/>
                        <flag attr="endoutlier" val0="1e-4" display=""/>
                        <flag attr="outlier" val0="1e-4" display=""/>
                        <flag attr="biaswt" val0="0" display=""/>
                        <flag attr="sd" val0="0.1" display=""/>
                        <flag attr="res" val0="2.9" display=""/>
                        <flag attr="mres" val0="2.9" display=""/>
                        <flag attr="sf" val0="0.2" display=""/>
                        <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
                        <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
                        <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
                        <flag attr="maxmem" val0="8" display=""/>
                        <flag attr="pairmergeRepeat"/>
                        <flag attr="NoBpp"/>
                        <flag attr="first" val0="-1" display=""/>
                        <flag attr="f"/>
                    </mergeNGS_BN>
                    <align_final_1st_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_1st_pass>
                    <align_final_2nd_pass>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="12"/>
                        <flag attr="deltaY" val0="12"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="50"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="12"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="12" val1="24"/>
                        <flag attr="Kmax" val0="12"/>
                        <flag attr="resEstimate"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                        <flag attr="MultiMatches" val0="5"/>
                    </align_final_2nd_pass>
                    <align_final_BNG>
                        <flag attr="res" val0="2.9"/>
                        <flag attr="FP" val0="0.6"/>
                        <flag attr="FN" val0="0.06"/>
                        <flag attr="sf" val0="0.20"/>
                        <flag attr="sd" val0="0.0"/>
                        <flag attr="sr" val0="0.01"/>
                        <flag attr="extend" val0="1"/>
                        <flag attr="outlier" val0="0.0001"/>
                        <flag attr="endoutlier" val0="0.001"/>
                        <flag attr="PVendoutlier"/>
                        <flag attr="deltaX" val0="6"/>
                        <flag attr="deltaY" val0="6"/>
                        <flag attr="xmapchim" val0="12"/>
                        <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
                        <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
                        <flag attr="hashMultiMatch" val0="30" val1="10"/>
                        <flag attr="insertThreads" val0="2"/>
                        <flag attr="nosplit" val0="2"/>
                        <flag attr="biaswt" val0="0"/>
                        <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
                        <flag attr="S" val0="-1000"/>
                        <flag attr="indel"/>
                        <flag attr="PVres" val0="2"/>
                        <flag attr="rres" val0="0.9"/>
                        <flag attr="MaxSE" val0="0.5"/>
                        <flag attr="HSDrange" val0="1.0"/>
                        <flag attr="outlierBC"/>
                        <flag attr="xmapUnique" val0="14"/>
                        <flag attr="AlignRes" val0="2."/>
                        <flag attr="outlierExtend" val0="6" val1="24"/>
                        <flag attr="Kmax" val0="6"/>
                        <flag attr="resEstimate"/>
                        <flag attr="BestRef" val0="1"/>
                        <flag attr="f"/>
                        <flag attr="mres" val0="0.9"/>
                    </align_final_BNG>
                    <refineFinal1>
                        
..

Beginning FASTA header conversion...
Running command: /usr/bin/perl scripts/fa_key_convert.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/ngs.fasta /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in no time.

New FASTA with CMAP Ids as headers: /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Beginning initial NGS CMAP to BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp7squ168i/job_working_directory/000/6/working/bionano.cmap -o align0 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -M 1 3 -ScaleDelta 0.02 15 -ScaleDeltaBPP -hashScaleDelta 2 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial alignment complete in 17 seconds.

Rescaling BioNano CMAP...
Running command: /RefAligner/RefAligner -merge -i /tmp/tmp7squ168i/job_working_directory/000/6/working/bionano.cmap -o /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust -readparameters /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/align0.errbin -stdout -stderr
Rescaling complete in no time.

Beginning initial NGS CMAP to rescaled BioNano CMAP alignment...
Running command: /RefAligner/RefAligner -ref /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -i /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -o align1 -stdout -stderr -maxmem 8 -maxthreads 2 -maxvirtmem 8 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 2 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -resEstimate -f -mres 0.9
Initial rescaled alignment complete in 1 second.

32 alignments found between /tmp/tmp7squ168i/job_working_directory/000/6/working/ngs.fasta and /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Beginning AssignAlignType...
Running command: /usr/bin/perl ./scripts/AssignAlignType.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1.xmap /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1_r.cmap /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1_q.cmap /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType.xmap /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap 11 5 /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/conflicts.txt 30
AssignAlignType complete in no time.
0 BNG contigs have been flagged as conflicting
0 NGS contigs have been flagged as conflicting

Beginning cut_conflicts...
Running command: /usr/bin/perl ./scripts/cut_conflicts.pl -align1XmapFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1.xmap -align1GMFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1_q.cmap -align1SeqFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap -oriSeqFile /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap -conflictFile /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/conflicts.txt -outDir /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/cut_conflicts -outGMFile /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/cut_conflicts/bionano_bppAdjust_cut.cmap -outSeqFile /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/cut_conflicts/ngs_CTTAAG_0kb_0labels_cut.cmap -windowSize 10000 -qScoreThreshold 35 -covThreshold 10 -refAligner /RefAligner/RefAligner
cut_conflicts complete in 1 second.
16 BNG contigs are found after the cut-conflict step
33 NGS contigs are found after the cut-conflict step

Beginning MergeNGS_BN...
*Using non-conflicting-only BioNano and non-conflicting-only sequence CMAP*
Running command: /usr/bin/perl ./scripts/MergeNGS_BN.pl -outputDir /tmp/tmp7squ168i/job_working_directory/000/6/working/mergeNGS_BN -refaligner /RefAligner/RefAligner -logFile mergeNGS_BN_script.log -ngs_cmap_fn /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -bng_cmap_fn /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -id_shift 100000 -readparameters /tmp/tmp7squ168i/job_working_directory/000/6/working/align1/align1.errbin -xmlFile /tmp/tmp7squ168i/job_working_directory/000/6/working/config.xml
MergeNGS_BN complete in no time.

Beginning extraction of used and not used NGS contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_ngs.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap /RefAligner/RefAligner
Extraction of NGS contigs complete in no time.

Beginning alignment of NGS cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_seq_two_passes.pl -outDir /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp7squ168i/job_working_directory/000/6/working/config.xml -seqFile /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap -scaffoldFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 2 seconds.

Beginning extraction of used and not used BNG contigs in hybrid scaffold pairmerge step...
Running command: /usr/bin/perl scripts/find_used_not_used_bn.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/mergeNGS_BN 100000 /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap /RefAligner/RefAligner
Extraction of BNG contigs complete in no time.

Beginning alignment of BNG cmap to Hybrid CMAP...
Running command: /usr/bin/perl ./scripts/align_final_bng.pl -outDir /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final -outFilePrefix bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /RefAligner/RefAligner -xmlFile /tmp/tmp7squ168i/job_working_directory/000/6/working/config.xml -bngFile /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap -scaffoldFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -logFile /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in no time.

Merging Hybrid CMAP with NGS not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp7squ168i/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_ngs.cmap -o HYBRID_SCAFFOLD_notUsedNGS_merged -merge -minsites 0 -stdout -stderr
Merging Hybrid CMAP with naive NGS CMAP complete in no time.

Merging Hybrid CMAP with BNG CMAP not participated in the hybrid scaffold...
Running command: /RefAligner/RefAligner -f -i /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/step2.hybrid.cmap -i /tmp/tmp7squ168i/job_working_directory/000/6/working/mergeNGS_BN/all_not_used_bng.cmap -o HYBRID_SCAFFOLD_notUsedBNG_merged -merge -stdout -stderr
Merging Hybrid CMAP with naive BNG CMAP complete in no time.

Beginnning construction of AGP and FASTA file of the scaffolded and unscaffolded sequences...
Running command: /usr/bin/perl scripts/ExportAGP.pl -i /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /tmp/tmp7squ168i/job_working_directory/000/6/working/agp_fasta -m /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels_key.txt -s /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs.fasta -e CTTAAG 1
AGP and FASTA generation complete in no time.

Calculating statistics...

Original BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/bionano.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.030

Bpp-adjusted BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align0/bionano_bppAdjust.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Original NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/fa2cmap/ngs_CTTAAG_0kb_0labels.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

Before merge: BioNano Genome Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

Before merge: NGS sequences statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/assignAlignType/assignAlignType_r.cmap

Count  = 33
Min length (Mbp) = 0.086
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.711
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.447

BNG Genome Map in hybrid scaffold statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 16
Min length (Mbp) = 0.227
Median length (Mbp) = 0.763
Mean length (Mbp) = 0.752
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.530
Total length (Mbp) = 12.029

NGS sequences in hybrid scaffold (CMAP) statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 32
Min length (Mbp) = 0.185
Median length (Mbp) = 0.745
Mean length (Mbp) = 0.730
N50 length (Mbp) = 0.922
Max length (Mbp) = 1.533
Total length (Mbp) = 23.361

Hybrid scaffold Map statistics:
Running command: /usr/bin/perl ./scripts/calc_cmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final/step2.hybrid.cmap

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 0.764
Mean length (Mbp) = 0.755
N50 length (Mbp) = 0.924
Max length (Mbp) = 1.532
Total length (Mbp) = 12.072

NGS FASTA sequence in hybrid scaffold statistics:
Running command: /usr/bin/perl scripts/calc_scaffolded_seq_fasta_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/ngs.fasta /tmp/tmp7squ168i/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 25
Min length (Mbp) = 0.231
Median length (Mbp) = 0.746
Mean length (Mbp) = 0.764
N50 length (Mbp) = 0.923
Max length (Mbp) = 1.533
Total length (Mbp) = 19.109

Hybrid scaffold FASTA statistics:
Running command: /usr/bin/perl scripts/calc_fasta_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 16
Min length (Mbp) = 0.231
Median length (Mbp) = 1.012
Mean length (Mbp) = 1.194
N50 length (Mbp) = 1.334
Max length (Mbp) = 3.065
Total length (Mbp) = 19.109

Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics:
Running command: /usr/bin/perl scripts/calc_hybrid_scaffold_not_scaffolded_seq_fasta_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /tmp/tmp7squ168i/job_working_directory/000/6/working/agp_fasta/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 24
Min length (Mbp) = 0.086
Median length (Mbp) = 0.899
Mean length (Mbp) = 0.977
N50 length (Mbp) = 1.122
Max length (Mbp) = 3.065
Total length (Mbp) = 23.447


Calculating CMAP statistics complete in 1 second.

Calculating XMAP statistics...
Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	1599388	799694	98.36
7	1078752.8	2090973.6	1045486.8	96.92
26	562548.0	1041912	520956	92.61
2	231313.0	419334	209667	90.64
1	439899.6	801778.2	400889.1	91.13
30	1531728.0	3038512	1519256	99.19
13	270057.0	490192	245096	90.76
29	576755.0	1131418	565709	98.08
6	923503.0	1777400	888700	96.23
3	948308.4	1110182	934467.4	98.54
12	1090521.0	2170988	1085494	99.54
8	666912.0	1313512	656756	98.48
4	1091839.0	2148434	1074217	98.39
24	745651.0	1449940	724970	97.23
31	318638.0	619292	311093	97.63
5	782773.0	1535138	767569	98.06

Running command: /usr/bin/perl scripts/calc_xmap_stats.pl /tmp/tmp7squ168i/job_working_directory/000/6/working/align_final bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
32	813039.0	799694	799694	98.36
7	1078752.8	1045486.8	1045486.8	96.92
26	562548.0	520956	520956	92.61
2	231313.0	209667	209667	90.64
1	439899.6	400889.1	400889.1	91.13
30	1531728.0	1519256	1519256	99.19
13	270057.0	245096	245096	90.76
29	576755.0	565709	565709	98.08
6	923503.0	888700	888700	96.23
3	948308.4	934467.4	934467.4	98.54
12	1090521.0	1085494	1085494	99.54
8	666912.0	656756	656756	98.48
4	1091839.0	1074217	1074217	98.39
24	745651.0	724970	724970	97.23
31	318638.0	311093	311093	97.63
5	782773.0	767569	767569	98.06

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
tar file: /tmp/tmp7squ168i/job_working_directory/000/6/working/results.zip
The tar zip command completed.
Archive and zip of result files completed in 13 seconds.

End time: 2024-12-16 05:05:22

Total elapsed time: 37 seconds


Merging of /tmp/tmp7squ168i/job_working_directory/000/6/working/bionano.cmap with /tmp/tmp7squ168i/job_working_directory/000/6/working/ngs.fasta is complete.

END of output

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
all_files	`false`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
configuration_options	`{"__current_case__": 0, "configuration": "vgp", "enzyme": "CTTAAG"}`
conflict_filter_genome	`"3"`
conflict_filter_sequence	`"3"`
conflict_resolution	`None`
dbkey	`"?"`
trim_cut_sites	`true`
zip_file	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7squ168i/files/0/e/6/dataset_0e62d62a-7563-444c-a945-bd2f6adc9a70.dat' --agp-to-path /tmp/tmp7squ168i/files/a/b/5/dataset_ab59e1af-801c-486b-aca4-105c9e237642.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Error:

JOIN	ptg000009l_path+	ptg000026l_path+	13	gap66	Super-Scaffold_1	66
JOIN	ptg000032l_path+	ptg000015l_path+	13	gap71	Super-Scaffold_4	71
JOIN	ptg000028l_path+	ptg000011l_path+	13	gap77	Super-Scaffold_8	77
JOIN	ptg000007l_path+	ptg000024l_path+	13	gap80	Super-Scaffold_12	80
JOIN	ptg000006l_path+	ptg000023l_path+	13	gap83	Super-Scaffold_13	83
JOIN	ptg000008l_path+	ptg000025l_path+	13	gap87	Super-Scaffold_26	87
JOIN	ptg000005l_path+	ptg000022l_path+	13	gap90	Super-Scaffold_29	90
JOIN	ptg000004l_path+	ptg000021l_path+	13	gap93	Super-Scaffold_30	93
JOIN	ptg000002l_path+	ptg000019l_path+	13	gap97	Super-Scaffold_32	97

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 11, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7squ168i/files/c/b/7/dataset_cb755667-0762-49e0-b2ec-fbc7816084e3.dat'   -o dataset.fasta --line-length 60 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 23
Total scaffold length: 22664609
Average scaffold length: 985417.78
Scaffold N50: 1153303
Scaffold auN: 1499118.36
Scaffold L50: 6
Largest scaffold: 3064584
Smallest scaffold: 85850
# contigs: 32
Total contig length: 22664492
Average contig length: 708265.38
Contig N50: 923452
Contig auN: 903816.25
Contig L50: 10
Largest contig: 1532843
Smallest contig: 85850
# gaps in scaffolds: 9
Total gap length in scaffolds: 117
Average gap length in scaffolds: 13.00
Gap N50 in scaffolds: 13
Gap auN in scaffolds: 13.00
Gap L50 in scaffolds: 5
Largest gap in scaffolds: 13
Smallest gap in scaffolds: 13
Base composition (A:C:G:T): 7010241:4337484:4330387:6986380
GC content %: 38.24
# soft-masked bases: 0
# segments: 33
Total segment length: 23447265
Average segment length: 710523.18
# gaps: 9
# paths: 23

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": "60", "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7squ168i/files/c/b/7/dataset_cb755667-0762-49e0-b2ec-fbc7816084e3.dat' 11748793 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp7squ168i/job_working_directory/000/15/outputs/dataset_abf0c3df-5748-48d3-ad5d-4d997e7654ca.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fa0577e4bb6a11ef899e7c1e522baf55"`
chromInfo	`"/tmp/tmp7squ168i/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "11748793", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Other invocation details
- history_id
  - db3b9008cdda4d5d
- history_state
  - ok
- invocation_id
  - db3b9008cdda4d5d
- invocation_state
  - scheduled
- workflow_id
  - bd7916153f67c53e

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