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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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DRAGMAP_Alignment_error #1555

Open poddarharsh15 opened 3 months ago

poddarharsh15 commented 3 months ago

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

FriederikeHanssen commented 3 months ago

This looks like it might be direct error with dragmap. Did you check with their developers if there is anything particular about your data and the way it is used?

poddarharsh15 commented 3 months ago

This looks like it might be direct error with dragmap. Did you check with their developers if there is anything particular about your data and the way it is used?

Yes, the problem is with dragmap, but they haven't fixed it yet. However, we are working on it with the help of @edmundmiller here and you can also follow the progress on GitHub here. hopefully it will be solved soon.

edmundmiller commented 3 months ago

1.4.2 should be on bioconda!

https://quay.io/repository/biocontainers/narfmap?tab=tags

edmundmiller commented 2 months ago

@poddarharsh15 https://github.com/nf-core/modules/pull/4895 bumped the images here if you want to add your test case!

poddarharsh15 commented 2 months ago

@poddarharsh15 nf-core/modules#4895 bumped the images here if you want to add your test case!

Hi @edmundmiller sorry for this question but I didn't understand exactly what do mean by bumping the image, the image from this link [https://quay.io/repository/biocontainers/narfmap?tab=tags] or the one I used earlier for running test??

edmundmiller commented 2 months ago

The one from the link. It has the static compilation fix in 1.4.1 and then 1.4.2 which fixed the bioconda compile error.

poddarharsh15 commented 2 months ago

The one from the link. It has the static compilation fix in 1.4.1 and then 1.4.2 which fixed the bioconda compile error.

I understand what you're suggesting, but can't I use the same module that you're updating? In the end, I will need dragmap working with the nf-core/sarek pipeline for patient data inspection. Please let me know if it's possible?

edmundmiller commented 2 months ago

In theory, you can, eventually the repos will diverge. Should work for your purposes, though!

poddarharsh15 commented 2 months ago

In theory, you can, eventually the repos will diverge. Should work for your purposes, though!

Are you going to diverge these repos in dragmap modules? Or introducing a new module under your repos?

edmundmiller commented 3 weeks ago

Late response, planning on introducing a new module under the narfmap repo to denote that it's not the same project to avoid confusing anyone.