Comments (4)
I tried again and it's working now... weird!
from bcalm.
hi JF!
The error seems to be :
c++: internal compiler error: Killed (program cc1plus)
which, if I could hasard a guess, could be a memory error? How many threads did you compile with?
Rayan
from bcalm.
Hi Rayan,
I did not specify the number of threads, so I guess that it used all the threads available on the node at that time (i.e. up to 40). But then I tried again a while later and it worked... Perhaps there was something going wrong on the cluster at that time?
from bcalm.
If you did make -j
then yeah, it uses all threads and could possibly run out of memory.
from bcalm.
Related Issues (20)
- 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
- When multiple inputs specified, BCALM silently loses data
- No version printed when installed with Bioconda and executed with the `-version` flag
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