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Old 04-20-2016, 02:54 PM   #1
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: Failed with exit code 1.


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!
lguzmanz is offline   Reply With Quote

canu, errors, pacbio

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