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gkpStore without correction. #1233
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You're in between two version, the gkpStore got renamed to seqStore between Canu 1.7 and 1.8 so you may have a seqStore instead. I'd suggest switching to 1.8 or tip instead for your work. As for the crash, that was caused by non-ACGT sequences in your reads and was also fixed in 1.8 (see #1061). |
Thanks skoren. Using the last canu version it generates the seqStore file but, ctgStore= |
The output goes to the files named out* in your case. There should be a |
Perfect, many thanks! |
If I run canu (v1.7 +114 changes (r8806 c875536) with the
-nanopore-corrected
parameter, I can't find thegkpStore
in the output folder. Is it generated only with-nanopore-raw
?Actually I am not interested in the canu correction, the reads are already corrected, but I want to check the coverage per contig using:
tgStoreDump -G sample.gkpStore -T sample.ctgStore 2 -o OUT -coverage -tig 1-10
If I run canu using
-nanopore-raw
, I got an error. This is the output of filecorrection/2-correction/results/0001.err
:I tried the solution from here (#881) but deleting the read from .readsToCorrect didn't work. The fasta file contain ~125k reads, with an averae of 5kbp length, but there are reads very long, ~32kbp. Can it be a problem?
Many thanks,
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