Question: Error with snakemake
0
gravatar for Biologist
18 months ago by
Biologist190
Biologist190 wrote:

Hi,

This was the first time I'm using snakemake to build a pipeline. I got an error while using it.

I'm using scripts found in GitHub but still I have the following error. salmon_snakemake

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   collate_salmon
    3   salmon_quant
    5

rule salmon_quant:
    input: myfastqs/sample1/sample1_R2.fastq.gz, myfastqs/sample1/sample1_R1.fastq.gz, /documents/annot_AND_refFASTA/salmon/Homo_sapiens.GRCh38.92.cdna.ncrn
    output: out/sample1/quant.sf, out/sample1/lib_format_counts.json
    log: logs/sample1_salmons_quant.log
    jobid: 2
    wildcards: sample=sample1

/usr/bin/bash: -c: line 1: unexpected EOF while looking for matching `''
    Error in rule salmon_quant:
        jobid: 2
        output: out/sample1/quant.sf, out/sample1/lib_format_counts.json
        log: logs/sample1_salmons_quant.log

RuleException:
CalledProcessError in line 51 of /documents/RNA-seq-analysis/RNA-seq-snakemake-pipeline/Snakefile:
Command ' set -euo pipefail;  
        salmon quant -p 4 -i /documents/annot_AND_refFASTA/salmon/Homo_sapiens.GRCh38.92.cdna.ncrn -l ISR -1 <(gunzip -c myfastqs/sample1/sample1_R1.fastq.gz) -2 <(gunzip -c myfastqs/sample1/sample1_R2.fastq.gz) -o OUT_DIR/sample1 &> logs/sample1_salmons_quant.log' ' returned non-zero exit status 2
  File "/documents/RNA-seq-analysis/RNA-seq-snakemake-pipeline/Snakefile", line 51, in __rule_salmon_quant
  File "/soft/apps/Python/3.5.2-goolf-1.7.20/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /documents/RNA-seq-analysis/RNA-seq-snakemake-pipeline/.snakemake/log/2018-06-15T163736.693150.snakemake.log
salmon snakemake pipeline python • 1.4k views
ADD COMMENTlink modified 18 months ago by WouterDeCoster42k • written 18 months ago by Biologist190

As far as I know the developers of snakemake prefer stackoverflow for questions.

ADD REPLYlink written 18 months ago by WouterDeCoster42k
0
gravatar for WouterDeCoster
18 months ago by
Belgium
WouterDeCoster42k wrote:

If the link you posted is the snakefile you are using: there is a single quote sign at the end of the salmon_quant shell command.

ADD COMMENTlink written 18 months ago by WouterDeCoster42k

Yes, but after removing that, it gave this gzip: myfastqs/sample3/sample3_R1.fastq.gz: unexpected end of file along with the error in the question.

ADD REPLYlink written 18 months ago by Biologist190

Most likely your gz file is then corrupt (truncated?)

ADD REPLYlink written 18 months ago by lieven.sterck6.4k

I think liven is correct. Files from CHT are corrupted and SK files seem to be okay. I was able to unzip the files from SK github.. Look at the file sizes in pics below. CHT (github) copied/reused raw files from SK (github).

@OP: Try using sequence files from SK github.

From CHT:

cht

From SK:

sk

ADD REPLYlink modified 18 months ago • written 18 months ago by cpad011212k

Those *.gz files in the repo are not properly compressed.

[/scratch/tmp]$ pigz -d sample1_R1.fastq.gz 
pigz: skipping: sample1_R1.fastq.gz is not compressed
pigz: abort: read error on sample1_R1.fastq.gz (Bad file descriptor)
[/scratch/tmp]$ mv sample1_R1.fastq.gz sample1_R1.fastq    
[/scratch/tmp]$ pigz sample1_R1.fastq 
[/scratch/tmp]$ pigz -d sample1_R1.fastq.gz 
[/scratch/tmp]$
ADD REPLYlink written 18 months ago by Eric Lim1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1359 users visited in the last hour