Testing Problem #68
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Hi Eddi, Are you running the latest version of MIDAS? Have you tried testing with python 2.7? I just downloaded and tested the latest version on my system running 2.7 and the test completed without errors. If you can confirm the error is related to python 2.6 I can fix the code. Best, |
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Yes, I am using the latest version of MIDAS. This error message appeared in
Python2.7 environment. I don't think the error is related to python2.6.
What more information you need for this?
Thanks,
…On Mon, Aug 21, 2017 at 10:58 AM, Stephen Nayfach ***@***.***> wrote:
Hi Eddi,
Are you running the latest version of MIDAS? Have you tried testing with
python 2.7? I just downloaded and tested the latest version on my system
running 2.7 and the test completed without errors. If you can confirm the
error is related to python 2.6 I can fix the code.
Best,
Stephen
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Hmmm, I'm not sure what's wrong. Could you please try executing the commands listed in the tutorial? After running the Thanks, |
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Hi I have the error message here Thanks you! Similar error occured when running |
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There should be a log file present in: midas_output/sample_1/genes/log.txt
Could you send that to me?
…On Tue, Aug 22, 2017 at 11:15 AM, yingeddi2008 ***@***.***> wrote:
Hi I have the error message here
(ve) ***@***.*** midas]$ run_midas.py genes midas_output/sample_1 -1 example/sample_1.fq.gz &
[1] 61136
(ve) ***@***.*** midas]$
MIDAS: Metagenomic Intra-species Diversity Analysis System
version 1.3.0; github.com/snayfach/MIDAS
Copyright (C) 2015-2016 Stephen Nayfach
Freely distributed under the GNU General Public License (GPLv3)
===========Parameters===========
Command: /home/hulin/data/tools/midas/MIDAS/scripts/run_midas.py genes midas_output/sample_1 -1 example/sample_1.fq.gz
Script: run_midas.py genes
Database: /home/hulin/data/tools/midas/midas_db_v1.2
Output directory: midas_output/sample_1
Remove temporary files: False
Pipeline options:
build bowtie2 database of pangenomes
align reads to bowtie2 pangenome database
quantify coverage of pangenomes genes
Database options:
include all species with >=3.0X genome coverage
Read alignment options:
input reads (unpaired): example/sample_1.fq.gz
alignment speed/sensitivity: very-sensitive
number of reads to use from input: use all
number of threads for database search: 1
Gene coverage options:
minimum alignment percent identity: 94.0
minimum alignment coverage of reads: 0.75
minimum read quality score: 20
minimum mapping quality score: 0
trim 0 base-pairs from 3'/right end of read
================================
Reading reference data
0.04 minutes
0.07 Gb maximum memory
Building pangenome database
total species: 1
total genes: 22080
total base-pairs: 19868510
(ve) ***@***.*** midas]$ 0.52 minutes
0.18 Gb maximum memory
Aligning reads to pangenomes
finished aligning
checking bamfile integrity
0.0 minutes
0.18 Gb maximum memory
Computing coverage of pangenomes
Traceback (most recent call last):
File "/home/hulin/data/tools/midas/MIDAS/scripts/run_midas.py", line 742, in <module>
run_program(program, args)
File "/home/hulin/data/tools/midas/MIDAS/scripts/run_midas.py", line 79, in run_program
genes.run_pipeline(args)
File "/home/hulin/data/tools/midas/MIDAS/midas/run/genes.py", line 285, in run_pipeline
pangenome_coverage(args, species, genes)
File "/home/hulin/data/tools/midas/MIDAS/midas/run/genes.py", line 148, in pangenome_coverage
count_mapped_bp(args, species, genes)
File "/home/hulin/data/tools/midas/MIDAS/midas/run/genes.py", line 174, in count_mapped_bp
bamfile = pysam.AlignmentFile(bam_path, "rb")
File "pysam/libcalignmentfile.pyx", line 401, in pysam.libcalignmentfile.AlignmentFile.__cinit__ (pysam/libcalignmentfile.c:5835)
File "pysam/libcalignmentfile.pyx", line 611, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:8072)
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
[1]+ Exit 1 run_midas.py genes midas_output/sample_1 -1 example/sample_1.fq.gz
Thanks you!
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Sure, there is. MIDAS: Metagenomic Intra-species Diversity Analysis System ===========Parameters=========== Building pangenome database Aligning reads to pangenomes Computing coverage of pangenomes |
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Could you send me the output when you run:
`/home/hulin/data/tools/midas/MIDAS/bin/Linux/bowtie2 --no-unal -x
midas_output/sample_1/genes/temp/pangenomes --very-sensitive-local
--threads 1 -q -U example/sample_1.fq.gz |
/home/hulin/data/tools/midas/MIDAS/bin/Linux/samtools
view --threads 1 -b - > midas_output/sample_1/genes/temp/pangenomes.bam`
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Now I know, that's the problem with bowtie2, so no bam file is generated. |
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I had this problem with release 1.3.0. It is not a problem with MIDAS itself though, it is a problem with the samtools/bowtie binaries being compiled with a newer version of a couple of libraries. If you try to run the included binary samtools at You need to install the newest zlib and maybe bzlib. Sur |
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I fixed the samtools problem. I will see what I can do.
```
(ve) [hulin@HSDMongo1 MIDAS]$ bin/Linux/samtools --help
Program: samtools (Tools for alignments in the SAM format)
Version: 1.4 (using htslib 1.4)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
index index alignment
…-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
rmdup remove PCR duplicates
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
-- Statistics
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
```
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Thanks for alerting me to this error.
I will work on a fix in the next couple of days that will allow MIDAS to
use bowtie2 and samtools binaries present in the PATH if the ones included
with MIDAS fail. Stay tuned.
Stephen
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I've fixed this issue in the latest release. If the problem persists please reopen this issue |
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Hello, I have installed MIDAS using conda command in an empty virtual environment. I also installed samtools under the same conda environment. The installation is a success. But when I execute the run_midas.py command, I get the samtool error like the following. I double-check the $PATH and samtools is included in the $PATH. Samtools can be also run separately under the conda environment, but it looks like MIDAS couldn't find it. This is an example of my error:
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Dear Midas programmers,
In order to set up MIDAS, I created a python virtual environment on our server, since our server has to use python2.6 for its core programs. I set up the python environmental variables as instructed and running the testing script. However, I encounter the following error message, and do not have any clue to solve it. Could you please help me with this?
Thank you very much.
Eddi
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