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xiaochuanle / MECAT

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
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canu failed with 'didn't find 'unitigging/3-overlapErrorAdjustment/oea.files' to add to store, yet overlapper finished'. #55

Closed AGI-chandler closed 6 years ago

AGI-chandler commented 6 years ago

We got this error during 4th step with mecat2canu command,

mecat2canu -trim-assemble -p O_australiensis -d O_australiensis_mecat1st_40x genomeSize=960000000 ErrorRate=0.02 maxMemory=1000 maxThreads=40 useGrid=0 Overlapper=mecat2asmpw -pacbio-corrected corrected_40x_for_O_australiensis_mecat1st_40x.fasta

Don't panic, but a mostly harmless error occurred and canu failed.

canu failed with 'didn't find '/<snip>/unitigging/3-overlapErrorAdjustment/oea.files' to add to store, yet overlapper finished'.

the unitigging dir is on a local disk. This disk is also exported via NFS to our other servers. Yet, when we run the same mecat2canu command on another server (older and slower, and via NFS), it is running OK. The only difference on the other server is maxMemory=160 maxThreads=16

AGI-chandler commented 6 years ago

closing this so we can work on new issue https://github.com/xiaochuanle/MECAT/issues/59