Comments (3)
glennhickey
commented on May 29, 2024
To further clarify: this is a crash in segalign_repeat_masker that happens on a 5.7Gb mollusk genome. run_segalign does seem to work on this genome, at least when aligning to human. It does not seem to be exceeding either system or video memory limits from my tests. We can share the genome on request.
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gsneha26
commented on May 29, 2024
Can you share the genome files? I need to investigate the error outside of the container run logs.
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glennhickey
commented on May 29, 2024
I emailed a link to you.
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Related Issues (20)
- run_segalign_repeat_masker can fail without error code HOT 1
- Error in LASTZ process! HOT 1
- segalign_repeat_masker runs out of memory on kangaroo rat HOT 2
- couldn't find boost HOT 7
- Running on multi-fasta HOT 2
- "grep: *.err" and "m: cannot remove '*.segments'" errors HOT 2
- FAILURE: extra segments in file HOT 4
- SegAlign/progressivecactus errors on LSF HOT 1
- run_segalign_repeat_masker file HOT 2
- cudaErrorIllegalAddress: an illegal memory access was encountered HOT 1
- stdbuf: failed to run command ‘segalign’: No such file or directory HOT 2
- error during cmake HOT 1
- segalign_repeat_masker crashes HOT 3
- segaling_repeat_masker still crashes HOT 7
- segalign crashes while aligning final against final reference block HOT 1
- run_segalign crashes on human-chimp (and exits 0!) HOT 2
- thrust::system::system_error | CUDA free failed: cudaErrorCudartUnloading
- Error: cudaMalloc of 256 bytes for sub_mat failed with error " the provided PTX was compiled with an unsupported toolchain. " HOT 1
- /usr/local/bin/run_segalign: line 60: segalign: command not found HOT 1
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