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bioinformaticsorphanage / NARFMAP

Fork of DRAGMAP, the first of it's name, merger of PRs, cutter of releases, takeoverer of worlds
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Fix segfault #10

Open edmundmiller opened 9 months ago

edmundmiller commented 9 months ago

https://github.com/nf-core/sarek/pull/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 commented 9 months ago

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 commented 3 months ago

https://github.com/nf-core/modules/pull/5946#issuecomment-2245426734

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 😞 https://github.com/bioconda/bioconda-recipes/pull/49189

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

edmundmiller commented 3 months ago

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

Other issues to link to this one: https://github.com/nf-core/modules/pull/5946 https://github.com/nf-core/sarek/pull/1358