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