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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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crass-assembly #78

Closed lianzhh closed 8 years ago

lianzhh commented 8 years ago

To perform the assembly of metagenomic data

crass-assembler --velvet -g 217643 -x crisper_reads/crass.crispr -i crisper_reads/ -s 1

[0.000000] Velvet can't handle k-mers as long as 44! We'll stick to 31 if you don't mind.
[0.022289] Reading FastA file crisper_reads//crass_tmp.fa;
[0.022407] 2 sequences found
[0.022414] Done
[0.022801] Reading read set file ./Sequences;
[0.022849] 2 sequences found
[0.022918] Done
[0.022923] 2 sequences in total.
[0.023857] Writing into roadmap file ./Roadmaps...
[0.023883] Inputting sequences...
[0.023887] Inputting sequence 0 / 2
[0.059337]  === Sequences loaded in 0.035455 s
[0.059550] Done inputting sequences
[0.059557] Destroying splay table
[0.059826] Splay table destroyed
velveth: Word length 33 greater than max allowed value (31).
Recompile Velvet to deal with this word length.: Success
crass [ERROR]: velveth did not exit normally
velveth . 44 crisper_reads//crass_tmp.fa

what was likely cause of the error?

ctSkennerton commented 8 years ago

The error message tells you what you need to do:

velveth: Word length 33 greater than max allowed value (31).
Recompile Velvet to deal with this word length.

You need to change your velvet installation to allow kmers greater than 31 - I would suggest a value like 64. See the velvet installation instructions for how to do this.