Fix segfault

[edmundmiller]

nf-core/sarek#1358

.command.sh: line 8:    36 Segmentation fault      (core dumped) dragen-os -r narfmap --RGSM test_test --RGID "@RG\tID:null.test.test_L1\tPU:test_L1\tSM:test_test\tLB:test\tDS:[https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta\tPL:ILLUMINA](https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta/tPL:ILLUMINA)" --num-threads 2 -1 test_1.fastq.gz -2 test_2.fastq.gz 2> test-test_L1.sorted.narfmap.log
          37 Done                    | samtools sort --threads 2 -o test-test_L1.sorted.bam -

Wondering if I can reproduce this in nascent or if it's just how Sarek is passing in the file name(which looks like a markdownlink now?)

[edmundmiller]

And he was able to reproduce:

  .command.sh: line 8:    43 Segmentation fault      (core dumped) dragen-os -r narfmap --RGSM null --num-threads 2 -1 cd4_REP2.trimmed.fastp.fastq.gz 2> cd4_REP2.narfmap.log
          44 Done                    | samtools view --threads 2 -o cd4_REP2.bam -

[edmundmiller]

nf-core/modules#5946 (comment)

Hi @edmundmiller Sorry to disturb but is there any updates regarding dragmap?? Please let me know thanks :)

Responding here because that issue got lost in all of my GitHub issues 🫠

Hey @poddarharsh15 Sorry, the only update was that using the not statically linked libraries didn't work 😞 bioconda/bioconda-recipes#49189

I don't have a ubuntu machine handy, did the docker image I gave you in

[edmundmiller]

State of the issue

Basically I don't think there was a bug in 1.3.1 rather, I think bioconda removed the static libraries in boost and that broke the build, and it just happened that 1.3.1 was the first build to have that, and a coincidence that the team abandoned dragmap.

Things we've tried

• Fix NARFMAP static build bioconda/bioconda-recipes#49189
• Update NARFMAP to 1.4.2 bioconda/bioconda-recipes#48978
• https://github.com/gambalab/DRAGMAP/releases/tag/1.3.1 ? Static build in a docker image?
• Static linking on bioconda Static link NARFMAP bioconda/bioconda-recipes#49518

Other issues to link to this one:
nf-core/modules#5946
nf-core/sarek#1358

[YasirKusay]

Hi,

I am using this tool as an alternative to dragmap in Sarek (I noticed you had a pull request to incorporate this tool there). I edited the sarek/modules/nf-core/dragmap/align/environment.yml to use version 1.4.2 of this tool instead of dragmap but I got a segmentation fault error which was also present when I tried version 1.3.0 of dragmap. I originally thought that the issue was due to a lack of memory but even after increasing memory to 120GB, the command still failed with the same issue. I have uploaded the error from Sarek in narfmap_sarek.log. The reference I am using is the default one Sarek uses: GATK.GRCh38 (which includes the reference for Dragmap).
narfmap_sarek.log

To confirm that this was a issue with narfmap, I ran the below script in isolation and got the exact same issue:
narfmap_only.log

Could you recommend a few solutions that I can try?

[wcarre]

Hi,
I try the conda install of this version and also get the same issue as YasirKusay. Don't know if the issue is the conda aor the version 1.4.2 of narfmap.

Thanks