Running bcalm raises error: cannot create a union-find data structure, too many elements.

[halexand]

Hello,

I am running bcalm as part of the spacegraph cats pipeline in collaboration with @taylorreiter. The command I am running is: bcalm -in INFILES -out OUTFILE -kmer-size 31 -abundance-min 1

I got an interesting error today that ended with:

UF MPHF constructed (4803 MB)                   01:52:39     memory [current, maxRSS]: [19184, 88111] MB 
cannot create a union-find data structure, too many elements. This should in fact not even happen. Please contact a BCALM developer

So, I am contacting you.

You can see the full error here: bcalm.MS-all-SRF-5-20.00.k31.unitigs.fa.log.txt

Any insight into what this error might indicate?

Thank you!

[rchikhi]

Hi, thanks for the detailed report.

1. Try using -min-abundance 2 to make that instance a bit smaller, unless you really have a good reason to care about kmers seen only once, or,
2. Wait for a short while. I've seen that bug on my end too. It happened on a huge instance with more than 70 billion distinct kmers. I'll work on fixing it.

Best,
Rayan

[halexand]

Thanks so much! We are trying to deal with some pretty complex samples... so I think that is likely the issue.

We are trying a new run with the -min-abundance 2 for now to make the instance smaller-- but would be curious to try out any fix you might have in the future.

Best,

Harriet

[PandorasRed]

hello,
i have the same problem, is the fix still on the work to do?

[sebschmi]

Same problem here :(

[rchikhi]

hi, no fix in the works, seems to be a fundamental limitation of BCALM2 so far. I'd recommend you try the excellent Cuttlefish2 software: https://github.com/COMBINE-lab/cuttlefish

[sebschmi]

Great, thanks!