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MBoemo / DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
https://www.boemogroup.org/
GNU General Public License v3.0
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forkSense Segmentation fault #72

Closed rstraver closed 1 week ago

rstraver commented 1 month ago

Hi again, I'm trying to run forkSense on the bam output (using DNAscent commit 5bc3279) but it seems to crash the moment it needs to write the output file:

Processed 20 reads...
./test_scent_fork.sh: line 5: 2016257 Segmentation fault      (core dumped) DNAscent forkSense -d ./test_scent_gpu/few.bam -o ./test_scent_gpu/few.forkSense --order EdU,BrdU

Seems the actual reads don't matter (much), I extracted the first < 50 for this test, I get the same issue for a bigger file (>19800 reads): It appears to process all reads, then crash. The output file location is writable, and I tested both with and without a pre-existing (empty) output file.

Any suggestions on what this could be?

MBoemo commented 1 month ago

Is few.bam small enough that you can send it to me? If so happy to take a look.

rstraver commented 4 weeks ago

Here's the tiny bam file, it's about 33 reads: few.bam.zip

rstraver commented 1 week ago

Hi @MBoemo, I haven't heard from you for a while. I responded to your e-mail, twice, did you perhaps not receive anything? I'm still waiting for a solution, not sure if this is a difficult to solve issue or something went wrong. Let me know if I need to try sending you the data through other means.

MBoemo commented 1 week ago

Should now be fixed in 1432cf75f1e57920856f1ca465ad3bc5650ebbe9 (and singularity image has been updated with the fix).