biocorecrg / allele_specific_RNAseq

Allele Specific RNAseq
9 stars 2 forks source link

Mapping error #36

Closed mercedes-barrero closed 2 years ago

mercedes-barrero commented 2 years ago

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/96/64248a8b984465abda0413c3fb2bf7

Source 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}/

        samtools index ${pair_id}/*.out.bam
      """

Work dir: /nfs/users/bpayer/mbarrero/allele_specific_RNAseq/work/96/64248a8b984465abda0413c3fb2bf7

lucacozzuto commented 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...

mercedes-barrero commented 2 years ago

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

id: read_counts

plot_type: 'bargraph'

section_name: 'Read counts on alleles'

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

lucacozzuto commented 2 years ago

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.