Snakemake wrapper issue
0
0
Entering edit mode
3 months ago
snakemake --cores all EPA23-SSPQ_1_fastqc.html EPA23-SSPQ_1_fastqc.zip

command produces this error:

Assuming unrestricted shared filesystem usage for local execution.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job       count
------  -------
fastqc        1
total         1

Select jobs to execute...
Execute 1 jobs...

[Mon Mar 11 19:20:30 2024]
localrule fastqc:
    input: EPA23-SSPQ_1.fastq.gz
    output: EPA23-SSPQ_1_fastqc.html, EPA23-SSPQ_1_fastqc.zip
    log: logs/fastqc/EPA23-SSPQ_1.log
    jobid: 0
    reason: Missing output files: EPA23-SSPQ_1_fastqc.zip
    wildcards: sample=EPA23-SSPQ_1
    resources: tmpdir=/tmp, mem_mb=14000, mem_mib=13352

Skipped removing non-empty directory EPA23-SSPQ_1_fastqc.html
Traceback (most recent call last):
  File "/home/matviimykhailichenko/.snakemake/scripts/tmpvsb_85lf.wrapper.py", line 49, in <module>
    shell(
  File "/home/matviimykhailichenko/miniconda3/envs/fastqc/lib/python3.12/site-packages/snakemake/shell.py", line 297, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  fastqc --threads 1 --memory 14000 --quiet --outdir /tmp/tmp_6xfqni0 EPA23-SSPQ_1.fastq.gz  > logs/fastqc/EPA23-SSPQ_1.log 2>&1' returned non-zero exit status 2.
RuleException:
CalledProcessError in file /home/matviimykhailichenko/snakefile, line 15:
Command 'set -euo pipefail;  /home/matviimykhailichenko/miniconda3/envs/fastqc/bin/python3.12 /home/matviimykhailichenko/.snakemake/scripts/tmpvsb_85lf.wrapper.py' returned non-zero exit status 1.
[Mon Mar 11 19:20:31 2024]
Error in rule fastqc:
    jobid: 0
    input: EPA23-SSPQ_1.fastq.gz
    output: EPA23-SSPQ_1_fastqc.html, EPA23-SSPQ_1_fastqc.zip
    log: logs/fastqc/EPA23-SSPQ_1.log (check log file(s) for error details)
    conda-env: /home/matviimykhailichenko/.snakemake/conda/2d3396791fcc89db1f086f1e5ae1b3a0_

Removing output files of failed job fastqc since they might be corrupted:
EPA23-SSPQ_1_fastqc.html
Skipped removing non-empty directory EPA23-SSPQ_1_fastqc.html
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-03-11T192030.633107.snakemake.log
WorkflowError:
At least one job did not complete successfully.

the snake file is like that:

rule fastqc:
input:
    "{sample}.fastq.gz"
output:
    html="{sample}_fastqc.html",
    zip="{sample}_fastqc.zip"
params:
    extra = "--quiet"
log:
    "logs/fastqc/{sample}.log"
threads: 1
resources:
    mem_mb = 14000
wrapper:
    "v3.4.1/bio/fastqc"

I have dependencies for this wrapper (fastqc=0.12.1, snakemake-wrapper-utils=0.6.2). Naturally, the problem seems to be connected directly to wrapper, but I can't understand what it is specifically. If you could give me clues it would be good

fastqc snakemake • 420 views
ADD COMMENT
0
Entering edit mode

What is the content of logs/fastqc/EPA23-SSPQ_1.log?

ADD REPLY
0
Entering edit mode

Hi, did you solve your problem ?

I also encounter same issue but it's wrapper:"v3.9.0/bio/picard/mergevcfs".

In my log file, it said:

/usr/bin/bash: line 1: picard: command not found

But I have already exported picard.jar to .bashrc

export PICARD_JAR=/home/fanny/Documents/picard-3.1.1/picard.jaralias picard='java -jar $PICARD_JAR'
alias picard='java -jar $PICARD_JAR'

Can you or anyone give me some advice ?

Thanks a lot !

ADD REPLY
0
Entering edit mode

Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you could try it with conda?

ADD REPLY

Login before adding your answer.

Traffic: 1502 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6