Comments (4)
Hi,
The error actually seems to happen during the HG-CoLoR / correction step.
It happened to me a few times too, usually because the size of the stack was too small.
Did the ulimit -s 65536
command included in the main script work?
Otherwhise, can you try to run it yourself, maybe with a higher max stack value, and rerun the program?
Also if your data is public, I could take a look as to where / why this segfault happens, if you want.
Cheers,
Pierre
from hg-color.
Thanks for the quick answer !
The ulimit
command appear to work (ulimit -s
return 65536 when executed in script) but i try to double it (to 131072) and the same error happen.
Should i try with higher value ?
from hg-color.
Hi,
Very late answer this time, sorry.
Well, if the command does work, the problem probably doesn't come from that.
Can you please provide me the command line you used to run HG-CoLoR?
Cheers,
Pierre
from hg-color.
Hello,,
I have the same problem.
It is my command:../HG-CoLoR --longreads ~/data/P_deltoides_nano.fasta --shortreads ~/worka/deltoides_PE/SRR3204673_merge_filtered.fastq --out corr -K 100 --nproc 40 --kmcmem 6
How to solve it?
Thanks in advance.
from hg-color.
Related Issues (17)
- Error messages HOT 12
- runtime estimation HOT 3
- Error HOT 2
- What is the proper output file HOT 2
- Error While Running QuorUM HOT 5
- compile error: fatal error: test/testdata.h: No such file or directory HOT 1
- tmp files deleted before job is finished HOT 2
- Running time? HOT 4
- Run fails and only prints 'Correcting the short reads' HOT 2
- Serious safety problem, --tmpdir parameter is deleted with no checking HOT 2
- Fail due to erroneous string in alignment file? HOT 1
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- Error HOT 1
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