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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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core dump at final step #71

Open rwhetten opened 2 years ago

rwhetten commented 2 years ago

I'm encountering an error using Quickmerge installed from Bioconda in September of this year, in the stderr output: 

# COMPLETETIME
# SPACE
4: FINISHING DATA
Abort (core dumped)

The anchor_summary, param_summary, and aln_summary files are all produced and contain data, but the merged.fasta output file is empty. The stdout file contains the line 

Exited with exit code 134

The job was not limited by allocated RAM or run time, so it seems to be an internal problem. Any suggestions on how to solve this?

benyoung93 commented 1 year ago

also running into this problem so interested to see fixes.

mahulchak commented 1 year ago

does it happen if you change the -l or -ml parametera?

benyoung93 commented 1 year ago

so mine was fixed changing the -l and -ml parameters yes. I also gave the supercomputer an ungodly amount of memory to run the quickmerge which I know isnt the best fix but sometimes it works.

Happy to provide more information if needed.