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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Canu stops before aligning contigs #508

Closed annaallueg closed 7 years ago

annaallueg commented 7 years ago

Hi,

I used Canu in the past and worked great! We recently did a migration to a new server (SGE) and I have been trying to run a job there, but it keeps stopping before the last step, failing to align the contigs. The log file says that it is mostly a harmless error, but I cannot find out what is wrong. Here is the command I used:

canu gridEngineThreadsOption="-pe orte THREADS" gridEngineMemoryOption="-l mem_free=MEMORY" useGrid=false -d A1552WT_shamu -p A1552WT genomeSize=4m -nanopore-raw /home-new/ltj621/cbi-data/Minion_VC_A1552_051817/poretools_WT/poretools_fastq_A1552_WT-21291.fastq

I am attaching the log file, where you can see the the error at the end ('failed with signal .'). Any help would be really appreciated. Thanks a lot!

Anna Allue (University of Texas at San Antonio)

canu_WT-21342.txt

brianwalenz commented 7 years ago

That's a very new feature, and was recently fixed. Update to the latest code - you're about a month and a half out of date.

The 'orte' environment might not be the correct one for Canu. Are there others available (qconf -spl)? See if any of those have allocation_rule = $pe_slots (use qconf -sp <pe_name>).

annaallueg commented 7 years ago

Thanks a lot for the rapid response! I'll update the code and see if I can change the orte environment. Much appreciated!

brianwalenz commented 7 years ago

Reopen if needed.