Open halexand opened 4 years ago
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
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
hello, i have the same problem, is the fix still on the work to do?
Same problem here :(
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
Great, thanks!
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:
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!