Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

gkpStore without correction. #1233

Closed
migrau opened this issue Feb 7, 2019 · 4 comments
Closed

gkpStore without correction. #1233

migrau opened this issue Feb 7, 2019 · 4 comments

Comments

@migrau
Copy link

migrau commented Feb 7, 2019

If I run canu (v1.7 +114 changes (r8806 c875536) with the -nanopore-corrected parameter, I can't find the gkpStore 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 file correction/2-correction/results/0001.err:

Processing read 11 of length 2319 with 5 evidence reads.
ALIGN to 0-2319 length 2319
ALIGN to 0-2130 length 2319
ALIGN to 0-1398 length 2319
ALIGN to 0-2319 length 2319
read54221 #2 location 0 to template 39-1273 length 1234 diff 0.123177
mapped 54221     0- 1245 to template     39-  1274 trimmed by      0-     0 TGATACTTAT TGATACTTAT
ALIGN to 787-2103 length 2319
read42756 #4 location 0 to template 109-1209 length 1100 diff 0.158182
mapped 42756     0- 1087 to template    896-  1997 trimmed by      0-     0 CATCCCCTTC CATCCCCTTC
ALIGN to 913-2058 length 2319
read11 #0 location 0 to template 0-2318 length 2318 diff 0.000000
mapped    11     0- 2319 to template      0-  2319 trimmed by      0-     0 GTACCCTATA GTACCCTATA
read13216 #5 location 0 to template 93-1051 length 958 diff 0.191023
mapped 13216     0-  922 to template   1006-  1965 trimmed by      0-     0 TTCTTTAAAT TTCTTTAAAT
read42702 #1 location 0 to template 295-1908 length 1613 diff 0.202108
read42702 #1 location 1 to template 295-1909 length 1614 diff 0.201983
mapped 42702     0- 1653 to template    295-  1909 trimmed by      0-     1 TATTTCATTG CAT---ATTG
read55796 #3 location 0 to template 120-2230 length 2110 diff 0.127488
read55796 #3 location 1 to template 120-2231 length 2111 diff 0.127428
read55796 #3 location 2 to template 120-2232 length 2112 diff 0.127367
read55796 #3 location 3 to template 120-2233 length 2113 diff 0.127307
falconsense: overlapInCore/libedlib/edlib.C:347: void edlibAlignmentToStrings(const unsigned char*, int, int, int, int, int, const char*, const char*, char*, char*): Assertion `strlen(qry_aln_str) == alignmentLength && strlen(tgt_aln_str$

Failed with 'Aborted'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::97 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
(null)::0 in (null)()

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,

@skoren
Copy link
Member

skoren commented Feb 7, 2019

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).

@migrau
Copy link
Author

migrau commented Feb 8, 2019

Thanks skoren. Using the last canu version it generates the seqStore file but, ctgStore=<tigStore>?
I am running :
tgStoreDump -S nano.seqStore -T unitigging/nano.ctgStore 2 -coverage -o OUT -tig 1-10
but not output/error at all.

@skoren
Copy link
Member

skoren commented Feb 8, 2019

The output goes to the files named out* in your case. There should be a *.depth and a *.png file for each of the tigs you requested in the current folder.

@migrau
Copy link
Author

migrau commented Feb 9, 2019

Perfect, many thanks!

@migrau migrau closed this as completed Feb 9, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants