missing bracer.conf #14
Comments
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Hi @ibseq , |
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HI there
I just had chance now to use bracer with my now results.
I tried to run the test as well but I’m stuck with the original issue, config file not found, called with -c of course
any advice?
thanks!
irene
… On 4 Sep 2018, at 12:24, idalind ***@***.***> wrote:
Hi @ibseq <https://github.com/ibseq> ,
I'm so sorry for the extremely late reply. If you are still interested in getting BraCeR to work, have you tried providing the path to your config file with the -c argument?
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Hi @ibseq , |
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HI
it says there is no config file in the path indicated.
what i have tried was to copy it from the website and created and saved it where is supposed to be but it didn’t work
irene
… On 31 Dec 2018, at 15:03, idalind ***@***.***> wrote:
Hi @ibseq <https://github.com/ibseq> ,
This seems strange. I'm not sure how much I can help you without more information, perhaps some screenshots? Where is your config file located? Are you specifying another config file location, but bracer looks for it at /home/ib/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracer.conf ?
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Hi again, could you please provide me some screenshots of the commands you are using and the resulting error? Without such information it is hard for me to give any advice. |
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Hi Ida, here it is: I’m running it very simple
bracer assemble 1R1.fastq.gz 1R2.fastq.gz
Config file not found at ~/.bracerrc. Using default bracer.conf in repo...
Please specify the path to where you originally installed BraCeR in the config file.
Traceback (most recent call last):
File "/home/ibassano/anaconda3/envs/BRACER/bin/bracer", line 11, in <module>
load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/launcher.py", line 43, in launch
Task().run()
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/tasks.py", line 290, in __init__
root=resource_dir)
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/tasks.py", line 177, in get_species_root
assert os.path.isdir(resources_root), "Species not found in resources"
AssertionError: Species not found in resources
BW
Irene
… On 13 Jan 2019, at 02:59, idalind ***@***.***> wrote:
Hi again, could you please provide me some screenshots of the commands you are using and the resulting error? Without such information it is hard for me to give any advice.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Af_hw5GlxBhiBTJMdwc_mEenW9OOLtb3ks5vCqEGgaJpZM4T98FQ>.
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and config file is where is supposed to be: just see top list
/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages$ ll
4096 May 14 2018 Bio
4096 May 14 2018 biopython-1.71-py3.6.egg-info
4096 May 14 2018 BioSQL
4096 May 14 2018 bracer-0.1-py3.6.egg-info
916 Dec 11 14:59 bracer.conf
4096 May 14 2018 bracerlib
4096 May 14 2018 certify
… On 13 Jan 2019, at 02:59, idalind ***@***.***> wrote:
Hi again, could you please provide me some screenshots of the commands you are using and the resulting error? Without such information it is hard for me to give any advice.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Af_hw5GlxBhiBTJMdwc_mEenW9OOLtb3ks5vCqEGgaJpZM4T98FQ>.
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latest error with same command. I adjusted the cons file to just indicate the path
Traceback (most recent call last):
File "/home/ibassano/anaconda3/envs/BRACER/bin/bracer", line 11, in <module>
load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/launcher.py", line 43, in launch
Task().run()
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/tasks.py", line 290, in __init__
root=resource_dir)
File "/home/ibassano/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracerlib/tasks.py", line 177, in get_species_root
assert os.path.isdir(resources_root), "Species not found in resources"
AssertionError: Species not found in resources
… On 13 Jan 2019, at 02:59, idalind ***@***.***> wrote:
Hi again, could you please provide me some screenshots of the commands you are using and the resulting error? Without such information it is hard for me to give any advice.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Af_hw5GlxBhiBTJMdwc_mEenW9OOLtb3ks5vCqEGgaJpZM4T98FQ>.
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Hi Ida,
I used the docker and run a test on my samples. See attached: it stopped after an error on kallisto
Any advice?
Thanks
Irene
On 13 Jan 2019, at 02:59, idalind ***@***.***> wrote:
Hi again, could you please provide me some screenshots of the commands you are using and the resulting error? Without such information it is hard for me to give any advice.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Af_hw5GlxBhiBTJMdwc_mEenW9OOLtb3ks5vCqEGgaJpZM4T98FQ>.
Last login: Fri Jan 25 14:37:19 on ttys004
wmnd-ibassano:~ ibassano$ docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer
usage: bracer <mode> [<args>]
Modes are :
- assemble: assemble BCR sequences from single-cell RNA-sequencing reads
- summarise: summarise BCR sequences from set of cells, build clonotype networks
- test : use a small dataset from three cells to test BraCeR installation
- build : build resource files from gene segment sequences
use bracer <mode> -h for specific help
bracer: error: the following arguments are required: <MODE>
wmnd-ibassano:~ ibassano$ pwd
/Users/ibassano
wmnd-ibassano:~ ibassano$ cd Desktop/raw_data/
wmnd-ibassano:raw_data ibassano$ ll
total 1722296
-rw-r--r-- 1 ibassano IC\Domain Users 114365444 17 Jan 10:17 1R1.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 42207290 17 Jan 10:17 1R1.fastq.gz
-rw------- 1 ibassano IC\Domain Users 57739284 17 Jan 10:17 1R1.part-1.fasta
-rw------- 1 ibassano IC\Domain Users 57739331 17 Jan 10:17 1R1.part-2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 113738820 17 Jan 10:18 1R2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 36810283 17 Jan 10:17 1R2.fastq.gz
-rw------- 1 ibassano IC\Domain Users 57423406 17 Jan 10:18 1R2.part-1.fasta
-rw------- 1 ibassano IC\Domain Users 57423567 17 Jan 10:17 1R2.part-2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 47374341 17 Jan 10:17 2R1.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 17409966 17 Jan 10:17 2R1.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 47104358 17 Jan 10:17 2R2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 15254105 17 Jan 10:18 2R2.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 26845893 17 Jan 10:17 3R1.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 11380891 17 Jan 10:18 3R1.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 27098853 17 Jan 10:18 3R2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 7506671 17 Jan 10:18 3R2.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 14633885 17 Jan 10:18 4R1.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 5014509 17 Jan 10:18 4R1.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 14589595 17 Jan 10:17 4R2.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 4009204 17 Jan 10:17 4R2.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 17132465 17 Jan 10:18 5R1.fasta
-rw-r--r-- 1 ibassano IC\Domain Users 29865749 17 Jan 10:18 5R1.fastq
-rw-r--r-- 1 ibassano IC\Domain Users 7439958 17 Jan 10:18 5R1.fastq.gz
-rw-r--r-- 1 ibassano IC\Domain Users 29648289 17 Jan 10:17 5R2.fastq
-rw-r--r-- 1 ibassano IC\Domain Users 5589581 17 Jan 10:18 5R2.fastq.gz
drwxr-xr-x 70 ibassano IC\Domain Users 2240 17 Jan 10:18 BWA
-rwxr-xr-x 1 ibassano IC\Domain Users 12398 17 Jan 10:18 fasta-splitter.pl
-rwxr-xr-- 1 ibassano IC\Domain Users 453 17 Jan 10:18 fastasplitter.pbs
-rw------- 1 ibassano IC\Domain Users 0 17 Jan 10:17 fastasplitter.pbs.e2273946
-rw------- 1 ibassano IC\Domain Users 0 17 Jan 10:18 fastasplitter.pbs.e2274023
-rw------- 1 ibassano IC\Domain Users 502 17 Jan 10:17 fastasplitter.pbs.o2273946
-rw------- 1 ibassano IC\Domain Users 493 17 Jan 10:17 fastasplitter.pbs.o2274023
drwxr-xr-x 13 ibassano IC\Domain Users 416 18 Jan 13:46 original_data
wmnd-ibassano:raw_data ibassano$ cd original_data/
wmnd-ibassano:original_data ibassano$ ll
total 404312
-rw-r--r-- 1 ibassano IC\Domain Users 4944821 17 Jan 10:17 IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 9688337 17 Jan 10:17 IB-031218-1_S1_L001_R2_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 5325799 17 Jan 10:17 IB-031218-2_S2_L001_R1_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 6113353 17 Jan 10:17 IB-031218-2_S2_L001_R2_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 9902859 17 Jan 10:17 IB-031218-3_S3_L001_R1_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 14349115 17 Jan 10:17 IB-031218-3_S3_L001_R2_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 23178066 17 Jan 10:17 IB-031218-4_S4_L001_R1_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 22541947 17 Jan 10:17 IB-031218-4_S4_L001_R2_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 56066202 17 Jan 10:17 IB-031218-5_S5_L001_R1_001.fastq.gz
-rwxr-xr-x 1 ibassano IC\Domain Users 54872897 17 Jan 10:17 IB-031218-5_S5_L001_R2_001.fastq.gz
wmnd-ibassano:original_data ibassano$ docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer
usage: bracer <mode> [<args>]
Modes are :
- assemble: assemble BCR sequences from single-cell RNA-sequencing reads
- summarise: summarise BCR sequences from set of cells, build clonotype networks
- test : use a small dataset from three cells to test BraCeR installation
- build : build resource files from gene segment sequences
use bracer <mode> -h for specific help
bracer: error: the following arguments are required: <MODE>
wmnd-ibassano:original_data ibassano$ docker assemble run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer
unknown shorthand flag: 'i' in -it
See 'docker --help'.
Usage: docker [OPTIONS] COMMAND
A self-sufficient runtime for containers
Options:
--config string Location of client config files (default "/Users/ibassano/.docker")
-D, --debug Enable debug mode
-H, --host list Daemon socket(s) to connect to
-l, --log-level string Set the logging level ("debug"|"info"|"warn"|"error"|"fatal") (default "info")
--tls Use TLS; implied by --tlsverify
--tlscacert string Trust certs signed only by this CA (default "/Users/ibassano/.docker/ca.pem")
--tlscert string Path to TLS certificate file (default "/Users/ibassano/.docker/cert.pem")
--tlskey string Path to TLS key file (default "/Users/ibassano/.docker/key.pem")
--tlsverify Use TLS and verify the remote
-v, --version Print version information and quit
Management Commands:
builder Manage builds
checkpoint Manage checkpoints
config Manage Docker configs
container Manage containers
image Manage images
manifest Manage Docker image manifests and manifest lists
network Manage networks
node Manage Swarm nodes
plugin Manage plugins
secret Manage Docker secrets
service Manage services
stack Manage Docker stacks
swarm Manage Swarm
system Manage Docker
trust Manage trust on Docker images
volume Manage volumes
Commands:
attach Attach local standard input, output, and error streams to a running container
build Build an image from a Dockerfile
commit Create a new image from a container's changes
cp Copy files/folders between a container and the local filesystem
create Create a new container
deploy Deploy a new stack or update an existing stack
diff Inspect changes to files or directories on a container's filesystem
events Get real time events from the server
exec Run a command in a running container
export Export a container's filesystem as a tar archive
history Show the history of an image
images List images
import Import the contents from a tarball to create a filesystem image
info Display system-wide information
inspect Return low-level information on Docker objects
kill Kill one or more running containers
load Load an image from a tar archive or STDIN
login Log in to a Docker registry
logout Log out from a Docker registry
logs Fetch the logs of a container
pause Pause all processes within one or more containers
port List port mappings or a specific mapping for the container
ps List containers
pull Pull an image or a repository from a registry
push Push an image or a repository to a registry
rename Rename a container
restart Restart one or more containers
rm Remove one or more containers
rmi Remove one or more images
run Run a command in a new container
save Save one or more images to a tar archive (streamed to STDOUT by default)
search Search the Docker Hub for images
start Start one or more stopped containers
stats Display a live stream of container(s) resource usage statistics
stop Stop one or more running containers
tag Create a tag TARGET_IMAGE that refers to SOURCE_IMAGE
top Display the running processes of a container
unpause Unpause all processes within one or more containers
update Update configuration of one or more containers
version Show the Docker version information
wait Block until one or more containers stop, then print their exit codes
Run 'docker COMMAND --help' for more information on a command.
wmnd-ibassano:original_data ibassano$ docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer assemble
usage: bracer [-h] [--ncores <CORES>] [--config_file <CONFIG_FILE>]
[--resource_dir <RESOURCE_DIR>] [--resume_with_existing_files]
[--assembled_file ASSEMBLED_FILE] [--species SPECIES]
[--loci LOCI [LOCI ...]] [--single_end]
[--fragment_length FRAGMENT_LENGTH] [--fragment_sd FRAGMENT_SD]
[--max_junc_len MAX_JUNC_LEN] [--no_trimming]
[--keep_trimmed_reads]
<CELL_NAME> <OUTPUT_DIR> [<FASTQ1>] [<FASTQ2>]
bracer: error: the following arguments are required: <CELL_NAME>, <OUTPUT_DIR>
wmnd-ibassano:original_data ibassano$ docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer assemble smartseq_test output IB-031218-5_S5_L001_R1_001.fastq.gz IB-031218-5_S5_L001_R2_001.fastq.gz
##Trimming raw reads##
Detecting installed version of Cutadapt:
1.14
Trimming completed
##Finding recombinant-derived reads##
Attempting new assembly for ['BCR_H', 'BCR_K', 'BCR_L']
Detected average R1 read length:
149.85601439856015
##BCR_H##
558258 reads; of these:
558258 (100.00%) were paired; of these:
554217 (99.28%) aligned concordantly 0 times
4041 (0.72%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
554217 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
554217 pairs aligned 0 times concordantly or discordantly; of these:
1108434 mates make up the pairs; of these:
1105938 (99.77%) aligned 0 times
2496 (0.23%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.95% overall alignment rate
##BCR_K##
558258 reads; of these:
558258 (100.00%) were paired; of these:
535086 (95.85%) aligned concordantly 0 times
23172 (4.15%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
535086 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
535086 pairs aligned 0 times concordantly or discordantly; of these:
1070172 mates make up the pairs; of these:
863136 (80.65%) aligned 0 times
207036 (19.35%) aligned exactly 1 time
0 (0.00%) aligned >1 times
22.69% overall alignment rate
##BCR_L##
558258 reads; of these:
558258 (100.00%) were paired; of these:
545340 (97.69%) aligned concordantly 0 times
12918 (2.31%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
545340 pairs aligned concordantly 0 times; of these:
2 (0.00%) aligned discordantly 1 time
----
545338 pairs aligned 0 times concordantly or discordantly; of these:
1090676 mates make up the pairs; of these:
919837 (84.34%) aligned 0 times
121431 (11.13%) aligned exactly 1 time
49408 (4.53%) aligned >1 times
17.62% overall alignment rate
##Assembling Trinity Contigs##
##BCR_H##
Left read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_H_1.fastq'
];
Right read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_H_2.fastq'
];
Trinity version: Trinity-v2.4.0
** NOTE: Latest version of Trinity is Trinity-v2.8.4, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases
Friday, January 25, 2019: 15:28:20 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 0
Friday, January 25, 2019: 15:28:20 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 1
Friday, January 25, 2019: 15:28:20 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H
Friday, January 25, 2019: 15:28:20 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis
…----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------
Converting input files. (in parallel)Friday, January 25, 2019: 15:28:20 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_H_1.fastq | seqtk-trinity seq -A - >> left.fa
Friday, January 25, 2019: 15:28:20 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_H_2.fastq | seqtk-trinity seq -A - >> right.fa
Friday, January 25, 2019: 15:28:20 CMD: touch right.fa.ok
Friday, January 25, 2019: 15:28:21 CMD: touch left.fa.ok
Friday, January 25, 2019: 15:28:21 CMD: touch left.fa.ok right.fa.ok
Friday, January 25, 2019: 15:28:21 CMD: cat left.fa right.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa
Friday, January 25, 2019: 15:28:21 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa.ok
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish count -t 1 -m 25 -s 100000000 --canonical /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish histo -t 1 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 1 --PARALLEL_IWORM > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa.tmp /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa
Friday, January 25, 2019: 15:28:24 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------
inchworm_target: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa
bowite_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa
chrysalis_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa 100 10 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: bowtie2-build -o 3 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
* Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 1 -f --score-min G,46,0 -x /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa | samtools view -@ 1 -F4 -Sb - | samtools sort -m 536870912 -@ 1 -no - - > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/iworm.bowtie.nameSorted.bam"
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/scaffold_iworm_contigs.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/iworm.bowtie.nameSorted.bam /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/iworm_scaffolds.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/GraphFromFasta -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa -r /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/iworm_cluster_welds_graph.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/BubbleUpClustering -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/inchworm.K25.L25.DS.fa -weld_graph /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/GraphFromIwormFasta.out
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/CreateIwormFastaBundle -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/GraphFromIwormFasta.out -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/bundled_iworm_contigs.fasta -min 200
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/ReadsToTranscripts -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/both.fa -f /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/bundled_iworm_contigs.fasta -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000
* Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/readsToComponents.out > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_H/chrysalis/readsToComponents.out.sort
Friday, January 25, 2019: 15:28:28 CMD: touch partitioned_reads.files.list.ok
Friday, January 25, 2019: 15:28:28 CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds
Error, reads file listing: partitioned_reads.files.list is empty. This tends to happen when there were too few reads to assemble. at /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/write_partitioned_trinity_cmds.pl line 51.
Error, cmd: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds died with ret 65280 at /trinityrnaseq-Trinity-v2.4.0/Trinity line 2462.
Trinity run failed. Must investigate error above.
Trinity failed for locus
##BCR_K##
Left read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_K_1.fastq'
];
Right read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_K_2.fastq'
];
Trinity version: Trinity-v2.4.0
** NOTE: Latest version of Trinity is Trinity-v2.8.4, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases
Friday, January 25, 2019: 15:28:29 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 0
Friday, January 25, 2019: 15:28:29 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 1
Friday, January 25, 2019: 15:28:30 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K
Friday, January 25, 2019: 15:28:30 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis
----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------
Converting input files. (in parallel)Friday, January 25, 2019: 15:28:30 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_K_1.fastq | seqtk-trinity seq -A - >> left.fa
Friday, January 25, 2019: 15:28:30 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_K_2.fastq | seqtk-trinity seq -A - >> right.fa
Friday, January 25, 2019: 15:28:30 CMD: touch right.fa.ok
Friday, January 25, 2019: 15:28:35 CMD: touch left.fa.ok
Friday, January 25, 2019: 15:28:35 CMD: touch left.fa.ok right.fa.ok
Friday, January 25, 2019: 15:28:35 CMD: cat left.fa right.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa
Friday, January 25, 2019: 15:28:36 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa.ok
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish count -t 1 -m 25 -s 100000000 --canonical /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish histo -t 1 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 1 --PARALLEL_IWORM > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa.tmp /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa
Friday, January 25, 2019: 15:28:45 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------
inchworm_target: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa
bowite_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa
chrysalis_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa 100 10 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: bowtie2-build -o 3 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
* Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 1 -f --score-min G,46,0 -x /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa | samtools view -@ 1 -F4 -Sb - | samtools sort -m 536870912 -@ 1 -no - - > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/iworm.bowtie.nameSorted.bam"
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/scaffold_iworm_contigs.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/iworm.bowtie.nameSorted.bam /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/iworm_scaffolds.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/GraphFromFasta -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa -r /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/iworm_cluster_welds_graph.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/BubbleUpClustering -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/inchworm.K25.L25.DS.fa -weld_graph /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/GraphFromIwormFasta.out
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/CreateIwormFastaBundle -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/GraphFromIwormFasta.out -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/bundled_iworm_contigs.fasta -min 200
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/ReadsToTranscripts -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/both.fa -f /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/bundled_iworm_contigs.fasta -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000
* Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/readsToComponents.out > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K/chrysalis/readsToComponents.out.sort
Friday, January 25, 2019: 15:29:55 CMD: mkdir -p read_partitions/Fb_0/CBin_0
Friday, January 25, 2019: 15:29:56 CMD: touch partitioned_reads.files.list.ok
Friday, January 25, 2019: 15:29:56 CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds
Friday, January 25, 2019: 15:29:56 CMD: touch recursive_trinity.cmds.ok
Friday, January 25, 2019: 15:29:56 CMD: touch recursive_trinity.cmds.ok
--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------
Friday, January 25, 2019: 15:29:56 CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v
Number of Commands: 5
succeeded(5) 100% completed.
All commands completed successfully. :-)
** Harvesting all assembled transcripts into a single multi-fasta file...
Friday, January 25, 2019: 15:31:15 CMD: find read_partitions/ -name '*inity.fasta' | /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp
###################################################################
Butterfly assemblies are written to /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_K.Trinity.fasta
###################################################################
##BCR_L##
Left read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_L_1.fastq'
];
Right read files: $VAR1 = [
'/scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_L_2.fastq'
];
Trinity version: Trinity-v2.4.0
** NOTE: Latest version of Trinity is Trinity-v2.8.4, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases
Friday, January 25, 2019: 15:31:16 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 0
Friday, January 25, 2019: 15:31:17 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 1
Friday, January 25, 2019: 15:31:17 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L
Friday, January 25, 2019: 15:31:17 CMD: mkdir -p /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis
----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------
Converting input files. (in parallel)Friday, January 25, 2019: 15:31:17 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_L_1.fastq | seqtk-trinity seq -A - >> left.fa
Friday, January 25, 2019: 15:31:17 CMD: cat /scratch/output/smartseq_test/aligned_reads/smartseq_test_BCR_L_2.fastq | seqtk-trinity seq -A - >> right.fa
Friday, January 25, 2019: 15:31:17 CMD: touch right.fa.ok
Friday, January 25, 2019: 15:31:19 CMD: touch left.fa.ok
Friday, January 25, 2019: 15:31:19 CMD: touch left.fa.ok right.fa.ok
Friday, January 25, 2019: 15:31:19 CMD: cat left.fa right.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa
Friday, January 25, 2019: 15:31:19 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa.ok
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish count -t 1 -m 25 -s 100000000 --canonical /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish/bin/jellyfish histo -t 1 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 1 --PARALLEL_IWORM > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa.tmp /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa
Friday, January 25, 2019: 15:31:23 CMD: touch /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------
inchworm_target: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa
bowite_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa
chrysalis_reads_fa: /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa 100 10 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: bowtie2-build -o 3 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
* Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 1 -f --score-min G,46,0 -x /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa | samtools view -@ 1 -F4 -Sb - | samtools sort -m 536870912 -@ 1 -no - - > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/iworm.bowtie.nameSorted.bam"
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/scaffold_iworm_contigs.pl /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/iworm.bowtie.nameSorted.bam /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/iworm_scaffolds.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/GraphFromFasta -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa -r /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/iworm_cluster_welds_graph.txt
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/BubbleUpClustering -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/inchworm.K25.L25.DS.fa -weld_graph /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200 > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/GraphFromIwormFasta.out
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/CreateIwormFastaBundle -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/GraphFromIwormFasta.out -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/bundled_iworm_contigs.fasta -min 200
* Running CMD: /trinityrnaseq-Trinity-v2.4.0/Chrysalis/ReadsToTranscripts -i /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/both.fa -f /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/bundled_iworm_contigs.fasta -o /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000
* Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/readsToComponents.out > /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L/chrysalis/readsToComponents.out.sort
Friday, January 25, 2019: 15:32:08 CMD: mkdir -p read_partitions/Fb_0/CBin_0
Friday, January 25, 2019: 15:32:09 CMD: touch partitioned_reads.files.list.ok
Friday, January 25, 2019: 15:32:09 CMD: /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds
Friday, January 25, 2019: 15:32:09 CMD: touch recursive_trinity.cmds.ok
Friday, January 25, 2019: 15:32:09 CMD: touch recursive_trinity.cmds.ok
--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------
Friday, January 25, 2019: 15:32:09 CMD: /trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v
Number of Commands: 3
succeeded(3) 100% completed.
All commands completed successfully. :-)
** Harvesting all assembled transcripts into a single multi-fasta file...
Friday, January 25, 2019: 15:32:45 CMD: find read_partitions/ -name '*inity.fasta' | /trinityrnaseq-Trinity-v2.4.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp
###################################################################
Butterfly assemblies are written to /scratch/output/smartseq_test/Trinity_output/Trinity_smartseq_test_BCR_L.Trinity.fasta
###################################################################
##Running BLAST##
Performing Blast on ['BCR_H', 'BCR_K', 'BCR_L']
##BCR_H##
##BCR_K##
##BCR_L##
##Running IgBLAST##
Ig_seqtype: Ig
Performing IgBlast on ['BCR_H', 'BCR_K', 'BCR_L']
##BCR_H##
##BCR_K##
##BCR_L##
START> MakeDB
ALIGNER> IgBlast
ALIGNER_OUTPUT> smartseq_test_BCR_K.fmt7
SEQ_FILE> smartseq_test_BCR_K.Trinity.fasta
NO_PARSE> False
PARTIAL> False
SCORES> True
REGIONS> True
PROGRESS> 15:32:56 [Done ] 0.0 min
PROGRESS> 15:32:56 [####################] 100% (1) 0.0 min
OUTPUT> /scratch/output/smartseq_test/IgBLAST_output/smartseq_test_BCR_K_db-pass.tab
PASS> 1
FAIL> 0
END> MakeDb
START> MakeDB
ALIGNER> IgBlast
ALIGNER_OUTPUT> smartseq_test_BCR_L.fmt7
SEQ_FILE> smartseq_test_BCR_L.Trinity.fasta
NO_PARSE> False
PARTIAL> False
SCORES> True
REGIONS> True
PROGRESS> 15:32:56 [Done ] 0.0 min
PROGRESS> 15:32:56 [####################] 100% (3) 0.0 min
OUTPUT> /scratch/output/smartseq_test/IgBLAST_output/smartseq_test_BCR_L_db-pass.tab
PASS> 0
FAIL> 3
END> MakeDb
##Running Kallisto##
##Making Kallisto indices##
[build] loading fasta file /scratch/output/smartseq_test/expression_quantification/kallisto_index/smartseq_test_transcriptome.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 1549 target sequences
[build] warning: replaced 4 non-ACGUT characters in the input sequence
with pseudorandom nucleotides
[build] counting k-mers ... Traceback (most recent call last):
File "/usr/local/bin/bracer", line 11, in <module>
load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/launcher.py", line 43, in launch
Task().run()
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 369, in run
self.quantify(cell)
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 605, in quantify
self.trimmed_fastq2, self.keep_trimmed_reads)
File "/usr/local/lib/python3.5/dist-packages/bracer-0.1-py3.5.egg/bracerlib/bracer_func.py", line 2110, in quantify_with_kallisto
subprocess.check_call(index_command)
File "/usr/lib/python3.5/subprocess.py", line 271, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/kallisto_linux-v0.43.1/kallisto', 'index', '-i', '/scratch/output/smartseq_test/expression_quantification/kallisto_index/smartseq_test_transcriptome.idx', '/scratch/output/smartseq_test/expression_quantification/kallisto_index/smartseq_test_transcriptome.fa']' returned non-zero exit status -9
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I had the same problem that “AssertionError: Species not found in resources”，while reading the detailed documentation:https://github.com/Teichlab/bracer/,i found that i set "bracer_path" parameter wrong,"bracer_path" should be the dirpath of bracer executable file ,another reason maybe kallisto_transcriptomes must be fa file. |
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Hello,
i have created a conda env and istalled bracer, but when i ran the test run i get:
"Couldn't find config file: /home/ib/anaconda3/envs/BRACER/lib/python3.6/site-packages/bracer.conf"
which effectively is not in that directory
any advice?
thanks
ib
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