The exit status of the task that caused the workflow execution to fail was: 2.
The full error message was:
Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY'
Caused by:
Process `NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY` terminated with an error exit status (2)
Command executed:
bismark2summary POR-73-TP2.POR-73-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam POR-245-TP2.POR-245-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam POR-236-TP1.POR-236-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-69-TP1.POR-69-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-69-TP2.POR-69-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam POR-236-TP2.POR-236-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam POR-83-TP3.POR-83-TP3_R1_001.fastp-trim_bismark_bt2_pe.bam POR-72-TP3.POR-72-TP3_R1_001.fastp-trim_bismark_bt2_pe.bam POR-245-TP1.POR-245-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-74-TP3.POR-74-TP3_R1_001.fastp-trim_bismark_bt2_pe.bam POR-72-TP4.POR-72-TP4_R1_001.fastp-trim_bismark_bt2_pe.bam POR-74-TP1.POR-74-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-260-TP3.POR-260-TP3_R1_001.fastp-trim_bismark_bt2_pe.bam POR-74-TP4.POR-74-TP4_R1_001.fastp-trim_bismark_bt2_pe.bam POR-216-TP1.POR-216-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-262-TP1.POR-262-TP1_R1_001.fastp-trim_bismark_bt2_pe.bam POR-74-TP2.POR-74-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam POR-216-TP2.POR-216-TP2_R1_001.fastp-trim_bismark_bt2_pe.bam
cat <<-END_VERSIONS > versions.yml
"NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY":
bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
Generating Bismark summary report from 18 Bismark BAM file(s)...
>> Reading from Bismark report: POR-73-TP2.POR-73-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt
>> Reading from Bismark report: POR-245-TP2.POR-245-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-236-TP1.POR-236-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-69-TP1.POR-69-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-69-TP2.POR-69-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-236-TP2.POR-236-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-83-TP3.POR-83-TP3_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-72-TP3.POR-72-TP3_R1_001.fastp-trim_bismark_bt2_PE_report.txt
>> Reading from Bismark report: POR-245-TP1.POR-245-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-74-TP3.POR-74-TP3_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-72-TP4.POR-72-TP4_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-74-TP1.POR-74-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-260-TP3.POR-260-TP3_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-74-TP4.POR-74-TP4_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-216-TP1.POR-216-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
>> Reading from Bismark report: POR-262-TP1.POR-262-TP1_R1_001.fastp-trim_bismark_bt2_PE_report.txt
>> Reading from Bismark report: POR-74-TP2.POR-74-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt
No methylation extractor report present, skipping...
Could not find Bismark report (POR-216-TP2.POR-216-TP2_R1_001.fastp-trim_bismark_bt2_PE_report.txt) to open
Work dir:
/mmfs1/gscratch/scrubbed/strigg/analyses/20250529_methylseq/work/70/3addc3694d6e87d028aa1e33b5048b
Container:
/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-bismark-0.24.2--hdfd78af_0.img
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`
nextflow run nf-core/methylseq -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config --input /gscratch/scrubbed/strigg/analyses/20250529_methylseq/samplesheet.csv --outdir /gscratch/scrubbed/strigg/analyses/20250529_methylseq --fasta /gscratch/srlab/strigg/GENOMES/Porites_evermanni_v1.fa --em_seq -resume -with-report nf_report.html -with-trace -with-timeline nf_timeline.html --skip_trimming --nomeseq5d80ec838a261829b26e2dd196e415b48140bc57-86ea-4608-a792-fcb293d05190https://github.com/nf-core/methylseq, revision master (commit hash 4415e90a60faba40ccefd4c847666d28688a86ee)These plots give an overview of the distribution of resource usage for each process.
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