sarek
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nf-core
DragMap fails if --trim_fastq flag is enabled
Description of the bug
Good evening, I am experiencing problems with Sarek's pipeline. When I try to remove the adapters from my WES data, the dragmap tool runs into "Segmentation Fault". Do you have any idea what the problem might be?
Command line: nextflow run main.nf --input sample_sheet_3.csv --genome GATK.GRCh38 --aligner dragmap --save_output_as_bam --step mapping --outdir './results' --save_output_as_bam --wes false -resume -profile aws --trim_fastq
Command used and terminal output
No response
Relevant files
No response
System information
No response
What version are you running? Can you send the error message? there are several issues with dragmap that were never resolved: https://github.com/Illumina/DRAGMAP/issues/47
The error is:
line 8: 115 Segmentation fault (core dumped) dragen-os -r dragmap --num-threads 12 -1 0002.11718FA_1.fastp.fastq.gz -2 0002.11718FA_2.fastp.fastq.gz --output-directory output --output-file-prefix 11718FA 2> 11718FA.dragmap.log
and I am using dragmap version: root@f1bc5cc9b074:/# dragen-os --version 1.2.1
pulled from quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0
Yes I tried multiple times, and when i added --trim_fastq it failed.
Sarek by default put the arguments "--disable_adapter_trimming --split_by_lines 200000000 " in the process.
However, "--disable_adapter_trimming" to me is apparently in conflicts with "--detect_adapter_for_pe " which is written inside the module.
This issue persists as of version 3.4.3. Related: https://github.com/Illumina/DRAGMAP/issues/11
In my case, specifying any of --trim_fastq and/or --trim_nextseq 10 results in dragmap segfaulting. I also tried --three_prime_clip_r1 2 and --three_prime_clip_r2 2 and these don't seem to cause issues.
Since dragmap does not seem to be actively maintained at the moment, but there is an issue in place to replace it with a better maintained fork https://github.com/nf-core/sarek/pull/1358, I suggest putting a warning into the parameter docstrings of --aligner that fastp is currently buggy with dragmap.
