DRAGMAP_Alignment_error

[poddarharsh15]

Description of the bug

my_param.json

error [nextflow.exception.ProcessFailedException]: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN (sample1-lane_1) terminated with an error exit status (1) Jun-10 12:48:18.909 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-10 12:48:18.909 [Task submitter] INFO nextflow.Session - [5d/c27009] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN (sample1-lane_1) Jun-10 12:48:18.917 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN (sample1-lane_1)'

Caused by: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN (sample1-lane_1) terminated with an error exit status (1)

Command executed:

dragen-os
-r dragmap
--RGSM patient1_sample1 --RGID "@RG\tID:H8VDAADXX.sample1.lane_1\tPU:lane_1\tSM:patient1_sample1\tLB:sample1\tDS:s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA"
--num-threads 12
-1 0002.sample1-lane_1_1.fastp.fastq.gz -2 0002.sample1-lane_1_2.fastp.fastq.gz
2> >(tee sample1-lane_1.0002.dragmap.log >&2)
| samtools sort -n --threads 12 -o sample1-lane_1.0002.bam -

cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN": dragmap: $(echo $(dragen-os --version 2>&1)) 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)

Command error: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information.

Command used and terminal output

nextflow run nf-core/sarek -r 3.4.2 \
-profile singularity \
-params-file my_param.json \
--outdir results_sarek_2 \
-resume

Relevant files

nextflow.log

System information

No response