DRAGMAP
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Segmentation fault version 1.3.0
Hi,
I am running dragmap 1.3.0 on some small test data and continue to get a failure with
0 Segmentation fault dragen-os -r dragmap --num-threads 2 -1 test_1.fastq.gz -2 test_2.fastq.gz 2> test.sorted.dragmap.log
31 Done | samtools sort --threads 2 -o test.sorted.bam -
as soon as I downgrade back to 1.2.1, it works on the same data/setup.
Command run:
dragen-os \
-r dragmap \
\
--num-threads 2 \
-1 test_1.fastq.gz -2 test_2.fastq.gz \
2> test.sorted.dragmap.log \
| samtools sort --threads 2 -o test.sorted.bam -
Hi, I am also experiencing the same issue with segmentationfault with version 1.3.0. Any progress?
My commands
reference indexing
dragen-os \
--build-hash-table true \
--ht-reference input.fasta \
--output-directory reference_folder/
mapping
dragen-os \
-r reference_folder/ \
-1 forward_pair.fastq.gz \
-2 reverse_pair.fastq.gz \
--num-thread 22| \
samtools view -b - | samtools sort -o output.bam
same here :)
Has anybody managed to run v1.3.0
without getting a segmentation fault? If so, could you please share your conda environment using e.g. conda env export
? I wonder if the problem is caused by one of the dependencies.
Same problem here
same for me (installed from conda)
Anyone figured how to get over this issue?
Looks like https://github.com/Illumina/DRAGMAP/commit/c4cb6c94baaf6821db3fa696c53cdd809fb92304 might fix this, but the release was never cut on GitHub at least, so it hasn't triggered the conda builds and what not.
I created a new env named dragmap and only installed conda dragmap in this environment, it worked for me.
I created a new env named dragmap and only installed conda dragmap in this environment, it worked for me.
So maybe it's samtools? It also worked for @nvnieuwk 🤔
BTW forked the repo because of various open PRs that didn't get the love they deserved, and merged them. Working on Rust FFI integration and going to start a rewrite if anyone's interested
https://github.com/edmundmiller/NARFMAP
Hi everyone. I still get the segmentation fault (core dumped) error message when using dragmap V1.3. It is installed with conda and also not working when installing it to a separate individual conda environment. Anyone has any advice what to do about it?
Hi everyone. I still get the segmentation fault (core dumped) error message when using dragmap V1.3. It is installed with conda and also not working when installing it to a separate individual conda environment. Anyone has any advice what to do about it?
It is working when I am using V1.2.1, so my input files should be fine.
Yeah that's what we've found at nf-core 😞
You can try out https://github.com/edmundmiller/NARFMAP and I merged all of the open PRs #55 might have fixed it, but it didn't seem to.