Thread: 454 assemly
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Old 01-22-2010, 12:06 PM   #17
sklages
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Location: Berlin, DE

Join Date: May 2008
Posts: 628
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Quote:
Originally Posted by kmcarr View Post
It could still be a problem with CAP3. All TIGCL knows is that CAP3 did not exit normally. There are error logs in each of the 'assemble_n' subdirectories. Look in those error logs to get a better idea of the actual error.
Well, you are probably right ... I have not remembered very well :-)

I had a problem with zmsort,

Quote:
[...]
WAITING for all children to finish before starting last child!
WAITING for all children to finish!
<<< --- clustering [Pimp454FLXcomplete_2008-04-07_2008-04-08.fasta]
finished at May 22 03:40:16 2008
Error getting file size for 'zdir_cluster_1_002.Z'
Error at command:
zmsort -f11 -n -r -o zdir_cluster_1 -s 700 cluster_1/*.Z

Process terminated with an error, at step 'clustering'!
[...]
cap3 has problems assembling very deep clusters, runs into memory problems. You are right, having a closer at the log is a good idea :-)

cheers,
Sven
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