Error: Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (WT_HA_IP_REP1_T1)` terminated with an error exit status (1)

[Sungryong-Oh]

Description of the bug

Hi,
I grep ChIPSeq/2.0.0 pipeline to run, but I met the issue in alignment step as like:

ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (WT_HA_IP_REP1_T
1)'

Caused by:
Process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (WT_HA_IP_REP1_T1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"
[ -z "$INDEX" ] && INDEX=find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"
[ -z "$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1

bowtie2
-x $INDEX
-1 1-HA_R1_trimmed.fq.gz -2 1-HA_R2_trimmed.fq.gz
--threads 20


2> WT_HA_IP_REP1_T1.Lb.bowtie2.log
| samtools view --threads 20 -o WT_HA_IP_REP1_T1.Lb.bam -

if [ -f WT_HA_IP_REP1_T1.Lb.unmapped.fastq.1.gz ]; then
mv WT_HA_IP_REP1_T1.Lb.unmapped.fastq.1.gz WT_HA_IP_REP1_T1.Lb.unmapped_1.fastq.gz
fi

if [ -f WT_HA_IP_REP1_T1.Lb.unmapped.fastq.2.gz ]; then
mv WT_HA_IP_REP1_T1.Lb.unmapped.fastq.2.gz WT_HA_IP_REP1_T1.Lb.unmapped_2.fastq.gz
fi

cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN":
bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.bowtie2-align-s version //; s/ .$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS

Command exit status:
1

Command output:
(empty)

I tested to run the pipeline with other alignment BWA, but met the same issue. Could you help me how to resolve this issue? Thanks.

Command used and terminal output

nextflow run /home/ohs5/TOOLS/Nextflow/chipseq/ -profile singularity \
--input ${INPUT} \
--read_length 50 \
--outdir ${OUTPUT} \
--genome ${species} \
--aligner bowtie2 \
--bowtie2_index ${INDEX_BOWTIE2} \
--narrow_peak \
--skip_trimming \
--blacklist ${BLACKLIST} \
--max_cpus 20 --max_memory 200.GB --max_time 240.h

Relevant files

No response

System information

Nextflow Version: 24.04.4 build 5917
System: Linux 5.14.0-162.6.1.el9_1.x86_64
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.11-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Hardware/Executor : HPC/slurm
container engine : singularity
Version of nf-core/chipseq : 2.0.0 pulldown by nf-core download

[Sungryong-Oh]

Hi, I realized that this error only occurs with --skip-trimming option. I started without this option and finished successfully. I close my issue.