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Old 04-20-2016, 02:54 PM   #1
lguzmanz
Junior Member
 
Location: Pacifica, CA

Join Date: Mar 2016
Posts: 4
Default Canu error: 'failed to create the overlap store'

Trying to run the following command:

$ canu -trim -p PacBio10_trimmed -d PacBio10_trimmed genomeSize=200000 -pacbio-corrected /work/03868/lguzmanz/liz_trials/PacBio_correctedreads/corrected_Canu_pacbio10.correctedReads.fasta.gz "useGrid=false"

Got the following error message:


ERROR:
ERROR: Failed with exit code 1.

ERROR:

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

Disk space available: 17025761.9 GB

Last 50 lines of the relevant log file (/work/03868/lguzmanz/liz_trials/april_20/PacBio10_trimmed/trimming/PacBio10_trimmed.ovlStore.err):

Summing overlap counts for 1 reads from '/work/03868/lguzmanz/liz_trials/april_20/PacBio10_trimmed/trimming/1-overlapper/001/000001.counts'.
Found no overlaps to sort.

canu failed with 'failed to create the overlap store'.


I had to manually correct 18 PacBio reads because the correct/trim/assemble default canu code ran into issues, now that I look back on it, it was probably the same error with the "failed to create overlap store" when trimming.

Any help would be greatly appreciated!
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