bioconda install of bcalm produces incorrect cDBG on linux? about bcalm HOT 10 CLOSED

you rock! thanks, @rchikhi!

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Oddly enough my shorter automated workflow https://github.com/ctb/2018-bcalm-debug doesn't detect any problems. Must not trigger the right problem.

Note that when I compile bcalm from scratch on my HPC the spacegraphcats-twofoo-example above runs just fine and passes the reciprocal edges test.

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Thanks for the detailed report! I confirm that I can reproduce the behavior of #37 (comment) on my own Linux, when using bioconda's bcalm. The problem doesn't occur when using the current master branch of bcalm. So something must be going on with bioconda's version, I'm on it.

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I think I see what's going on. Two bugs: 1) I thought BCALM outputted consecutive unitig IDs, but apparently with some compilers it had some rare inversions (e.g. 9,10,12,11,13,14,..). Likely a multi-threading bug. 2) The procedure used to link unitigs silently and wrongly assumed that unitigs needed to have consecutive IDs. I've commited a fix for both bugs and will release BCALM 2.2.1. @natir could you please update Conda when you have time, or show me how?

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ping! I'd suggest withdrawing bcalm from bioconda until someone has time to fix it.

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pinging @natir: bcalm 2.2.1 is released and needs to be updated in bioconda please :)

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@epruesse update bioconda bcalm to 2.2.1 in this pull request bioconda/bioconda-recipes#12811

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merci!

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