Closed mercedes-barrero closed 2 years ago
Hi, I think the problem is in the definition of the reads...
reads : /users/bpayer/mbarrero/allele_specific_RNAseq/test/{NPC1_14191AAC_CGA TGT_R1_001,NPC1_14191AAC_CGATGT_R2_001}.fastq.g
it should be something like
reads : /users/bpayer/mbarrero/allele_specific_RNAseq/test/*.fastq.gz
since the program uses the part indicated by the asterisk as ID. Maybe this should be explained better in the README...
Thanks a lot. Actually I changed it but now the problem is in the multiQC report step.
The exit status of the task that caused the workflow execution to fail was: 2
Error executing process > 'multiQC_report'
Caused by:
Process multiQC_report
terminated with an error exit status (2)
Command executed:
export LC_ALL=en_US.utf8
export LANG=en_US.utf8
make_conf_multiqc.sh 'Allele specific RNAseq project PAYER_09' 'PAYER_09_npc1' 'Payer' 'Mercedes Barrero' 'mercedes.barrero@crg.eu' 'mm10' pre_config.yaml
cat > counts_mqc.txt << EOL
Sample Genotype A Genotype B Reference Ambiguous
EOL
grep -h -v "#" .stats >> counts_mqc.txt
multiqc -c config.yaml .
Command exit status:
2
Command output:
(empty)
Command error:
grep: .stats: No such file or directory
Work dir:
/nfs/users/bpayer/mbarrero/allele_specific_RNAseq/work/2a/892cb50981a976677862449d6586a0
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
wait, sorry I did not see that is paired end... So for paired end you need another syntax for specifying the pairs:
/users/bpayer/mbarrero/allele_specific_RNAseq/test/*_R{1,2}_001.fastq.gz
I'll add this to the README too.
Hi Luca,
The pipeline was working until it got to the mapping step. Then I got this error:
Error executing process > 'mapping ()'
Caused by: File
/ReadsPerGene.out.tab
is out of the scope of process working dir: /nfs/users/bpayer/mbarrero/allele_specific_RNAseq/work/96/64248a8b984465abda0413c3fb2bf7Source block: def output = "${pair_id}" def variants = unzipBash("${variants_file}") """ if [
echo "${reads}"| cut -f 1 -d " " | grep ".gz"
]; then gzipped=" --readFilesCommand zcat "; else gzipped=""; fi STAR --genomeDir ${STARgenome} \ --readFilesIn ${reads} \ \$gzipped \ --waspOutputMode SAMtag \ --outSAMunmapped Within \ --outSAMtype BAM SortedByCoordinate \ --runThreadN ${task.cpus} \ --outFileNamePrefix ${pair_id} \ --quantMode GeneCounts \ --outSAMattributes NH HI AS nM NM MD jM jI XS MC ch vA vW vG \ --varVCFfile ${variants}; mkdir ${output} mv .out.tab ${output}/ mv Aligned ${output}/ mv Log* ${output}/Work dir: /nfs/users/bpayer/mbarrero/allele_specific_RNAseq/work/96/64248a8b984465abda0413c3fb2bf7