hang at cd trimming/1-overlapper ./overlap.sh 1 > ./overlap.000001.out 2>&1

marbl / canu

A single molecule sequence assembler for genomes large and small.

http://canu.readthedocs.io/

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hang at cd trimming/1-overlapper ./overlap.sh 1 > ./overlap.000001.out 2>&1 #484

Closed bluessherpa closed 7 years ago

bluessherpa commented 7 years ago

Hi,

I've been trying to run on my Mac (64 GB RAM 1.4 TB free on drive) Quad core Xeon) 10.12.4. I first tried to run with a small data set (200MB total) and it did ok. Then tried to run over the weekend with nano corrected seq and it hung up on the above command. So I retried with a smaller data set and it hung up on the same spot.

Any ideas? Thanks

skoren commented 7 years ago

As long as the job is getting CPU (e.g. in top) then it is OK. This would be the slowest part of the assembly, especially with nanopore data, so you can let it keep running. You can also try the experimental overlapper=mhap utgReAlign=true option if you are using Canu 1.5 (see https://github.com/marbl/canu/releases/tag/v1.5 for details)