Comments (2)
rchikhi
commented on May 31, 2024
hi Marco!
Thanks for the very detailed bug report. What a strange bug! Am in the process of recoding some aspects of bcalm, so will see if I can reproduce this issue. If you have any small input where you can reproduce the problem, yes please do share it with me (email is fine).
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rchikhi
commented on May 31, 2024
Several months after.. I finally found and fixed that nasty multithreading bug (for the story: took me several days of inefficient investigation with breaks due to frustration). Commit: GATB/gatb-core@46d6cf9
Thanks much for taking the time to provide the small test datasets! these were invaluable.
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Related Issues (20)
- new release soon? HOT 2
- Running bcalm raises error: `cannot create a union-find data structure, too many elements.` HOT 6
- error: 'predecessors' following the 'template' keyword does not refer to a template HOT 8
- Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string HOT 5
- Compiling bcalm causes trouble when no .git repository is found HOT 1
- Output of bcalm2 similar to minia 3.2.1 unitigs? HOT 2
- Memory error with many reference genomes as input HOT 16
- High frequency of nodes with degree of two with length = 2k-1 HOT 2
- .fa files contain lowercase `km` instead of the documented uppercase `KM` HOT 3
- bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) HOT 12
- Add better input parsing HOT 1
- Improve error message for bad fasta input HOT 1
- Apparently bcalm crashes with very large k's (4096) HOT 1
- bcalm -version return code 1 to shell
- Glue is too strong, because glue files are not deleted.
- insert unitig disregarding the reverse complement HOT 1
- Option `-out-dir` is not used ? HOT 1
- bug report on a metagenomics dataset HOT 3
- Add header description with `-all-abundance-counts` HOT 2
- Is the output file reproducible? HOT 2
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