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GATB / bcalm

compacted de Bruijn graph construction in low memory
MIT License
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bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) #62

Closed ctb closed 4 years ago

ctb commented 4 years ago

hi folks, the bug we reported for Linux in #37 and #44 is baaaaaack! but this time for Mac OS X!

briefly, bcalm is producing a cDBG where there are links that are not bidirectional.

full details to reproduce are here, https://github.com/spacegraphcats/spacegraphcats/pull/281, summary:

git clone https://github.com/spacegraphcats/spacegraphcats/ -b mac_bcalm_problem
conda env create -f spacegraphcats/environment.yml -n sgc-broke2
conda activate sgc-broke2
cd spacegraphcats
make twofoo-test

and you can generate it w/o the make & snakemake infrastructure using the following commands (once the downloads etc above are done) --

bcalm -in twofoo/bcalm.twofoo.k31.inputlist.txt -out twofoo/bcalm.twofoo.k31 -kmer-size 31 -abundance-min 1
python -m spacegraphcats.cdbg.bcalm_to_gxt  -k 31 twofoo/bcalm.twofoo.k31.unitigs.fa twofoo_k31_r1/cdbg.gxt twofoo_k31_r1/contigs.fa.gz
ctb commented 4 years ago

(note, this all works fine on Linux.)

I'm running Mac OS X Catalina, 10.15.6. Note that when this was initially reported I don't think I could reproduce the bug on the previous version of Mac OS X, 10.14, which was what I was running - but since then I've upgraded, and now I can reproduce it (joy!) So it may be Catalina-specific.

please let me know if I can help in any way!

rchikhi commented 4 years ago

damn, this bug again heh? first off, thanks for reporting it. second, yes I'd appreciate your help please for a simple test as I don't have any macos'es conveniently close by. Does the latest version of bcalm, macosx binary, also trigger this bug? https://github.com/GATB/bcalm/releases/download/v2.2.3/bcalm-binaries-v2.2.3-Mac.tar.gz

ctb commented 4 years ago

that bcalm binary does work for me!

rchikhi commented 4 years ago

great!! thanks for testing it.

rchikhi commented 4 years ago

@natir can I please ask for your help once again with updating the bcalm bioconda package you created (and updated last year)? This time it is because the MacOS version seems to be problematic. We have a new version (v2.2.3) and a linux and Mac binaries here:

Linux: https://github.com/GATB/bcalm/releases/download/v2.2.3/bcalm-binaries-v2.2.3-Linux.tar.gz

Mac: https://github.com/GATB/bcalm/releases/download/v2.2.3/bcalm-binaries-v2.2.3-Mac.tar.gz

thanks in advance!

natir commented 4 years ago

Hi,

Bioconda build package from source, I can't use your binary. Actually bioconda linux version of bcalm is 2.2.3, but build on macOS failed I can try to solve this build issue.

rchikhi commented 4 years ago

oh yes, I had forgotten this. Hmm macOs build fails on this new 2.2.3 version but not before on 2.2.1? Feel free to put an issue and I can have a look too

natir commented 4 years ago

Pull request bioconda/bioconda-recipes/pull/23309 pass all test and will probably merge near in future.

ctb commented 4 years ago

you are wonderful!

natir commented 4 years ago

bcalm 2.2.3 is avaible for macOS is bioconda

rchikhi commented 4 years ago

great!! thanks very much Pierre

ctb commented 4 years ago

I just verified that it is all fixed -- thank you!!