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dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
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Segmentation fault for velveth on short paired separate reads #46

Closed spencel closed 3 years ago

spencel commented 5 years ago

Ran the command below on Bridges. Made sure I had the velvet module loaded. Its version is 1.2.10-maxk63-categ14-big.

$ velveth velvet 63 -shortPaired -fastq.gz -separate SRR8547393_1.fastq.gz SRR8547393_2.fastq.gz

The error below is returned follow by the command.

velvet.sh: line 5: 25824 Segmentation fault

Tried finding a solution and playing with file formats and kmer length but nothing worked. There's no mention of segmentation fault in the manual.

Update: I tried cloning velvet from the git repo and making it. Ran into the same error above.

dzerbino commented 5 years ago

Hello @spencel,

Could you please provide some context on the environment. In particular, what is Bridges, what velvet module are you referring to, and what is that velvet.sh script?

Thank you,

Daniel

dzerbino commented 3 years ago

This thread has gone silent for a year, now closing.