Closed
Description
8000
Description of the bug
Running the pipeline with multiple contrasts in the contrast sheet results in multiple errors as mentioned in the filename. The pipeline runs fine with only one contrast at a time. As such, it's possible that this issue might be related to a separate report, which was focused on SUPPA: #71
Relevant input files, as well as the full log, are attached below.
Command used and terminal output
nextflow run nf-core/rnasplice -r dev -latest -c custom.config -params-file params.yml --igenomes_ignore --genome null \
--input /data/share/santina-cutrupi/sample-sheet-rnasplice.csv \
--outdir test-rnasplice -profile docker --source genome_bam \
--fasta /data/share/santina-cutrupi/genome/gencode_v44_spike-ins.fasta \
--gtf /data/share/santina-cutrupi/genome/gencode_v44_spike-ins.gtf \
--star_index /data/share/santina-cutrupi/genome/index/star \
--salmon_index /data/share/santina-cutrupi/genome/index/salmon \
--rmats --rmats_read_len 100 --rmats_paired_stats \
--contrasts /data/share/santina-cutrupi/contrasts-rnasplice.csv \
--aligner star --dexseq_exon false --miso_genes "ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18"
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (HepG2_TARDBP_TRT-HepG2_TARDBP_CTL)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (HepG2_TARDBP_TRT-HepG2_TARDBP_CTL)` terminated with an error exit status (1)
Command executed:
mkdir -p HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post
rmats.py \
--gtf gencode_v44_spike-ins.gtf \
--b1 HepG2_TARDBP_TRT_bamlist.txt \
--b2 HepG2_TARDBP_CTL_bamlist.txt \
--od HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post \
--tmp HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_temp \
-t paired \
--libType fr-unstranded \
--readLength 100 \
--variable-read-length \
--nthread 12 \
--tstat 12 \
--cstat 0.0001 \
--task post \
--paired-stats \
\
\
\
--allow-clipping \
1> HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST":
rmats: $(echo $(rmats.py --version) | sed -e "s/v//g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
HepG2_TARDBP_TRT_REP2_sorted.bam not found in .rmats files
HepG2_TARDBP_TRT_REP1_sorted.bam not found in .rmats files
HepG2_TARDBP_CTL_REP1_sorted.bam not found in .rmats files
HepG2_TARDBP_CTL_REP2_sorted.bam not found in .rmats files
Work dir:
/data/share/santina-cutrupi/work/44/1986fadc43abab0d325223ec214ee9
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for detailsRelevant files
custom.config.txt
params.yml.txt
contrasts-rnasplice.csv.txt
sample-sheet-rnasplice.csv.txt
nextflow.log.txt
System information
Nextflow 23.04.2
Latest Dev version of the rnasplice pipeline