Comments (6)
Hi, thanks for the detailed report.
- 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, - 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
from bcalm.
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
from bcalm.
hello,
i have the same problem, is the fix still on the work to do?
from bcalm.
Same problem here :(
from bcalm.
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
from bcalm.
Great, thanks!
from bcalm.
Related Issues (20)
- 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
- Set the minimum value of -kmer-size HOT 1
- Counting kmers error HOT 2
- Fails to build from source on ARM MacOS HOT 1
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