Celera Assembler runCA failed

Question

[Abdul Rafay Khan]

Determine Fastq Quality Encoding:

perl DetermineFastqQualityEncoding.pl datafastq/lg/human/humanUpaired.fastq

observed range: 35-73
format: Sanger or Illumina 1.9+ (offset by 33)

Converted by unpaired fastq file to frq file using fastqToCA:

fastqToCA -libraryname humanUpaired -technology illumina -type sanger -reads datafastq/lg/human/humanUpaired.fastq > datafastq/lg/human/humanUpaired.frg

Error while running the runCA

runCA -d /mnt/ext/results/lg/celera -p /mnt/ext/results/lg/celera datafastq/lg/human/humanUpaired.frg

----------------------------------------START Sat Dec  3 13:06:29 2016
/home/rafay/tools/wgs-8.3rc2/Linux-i686/bin/gatekeeper  -o /mnt/ext/results/lg/celera//mnt/ext/results/lg/celera.gkpStore.BUILDING  -T  -F  /mnt/ext/datafastq/lg/human/humanUpaired.frg > /mnt/ext/results/lg/celera//mnt/ext/results/lg/celera.gkpStore.err 2>&1
sh: 1: cannot create /mnt/ext/results/lg/celera//mnt/ext/results/lg/celera.gkpStore.err: Directory nonexistent
----------------------------------------END Sat Dec  3 13:06:29 2016 (0 seconds)
ERROR: Failed with signal INT (2)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /home/rafay/tools/wgs-8.3rc2/Linux-i686/bin/runCA line 1628.
        main::caFailure('gatekeeper failed', '/mnt/ext/results/lg/celera//mnt/ext/results/lg/celera.gkpStor...') called at /home/rafay/tools/wgs-8.3rc2/Linux-i686/bin/runCA line 1957
        main::preoverlap('/mnt/ext/datafastq/lg/human/humanUpaired.frg') called at /home/rafay/tools/wgs-8.3rc2/Linux-i686/bin/runCA line 6250

----------------------------------------
Failure message:

gatekeeper failed

[WouterDeCoster]

Could you try with something shorter for -p? The entire directory path as a prefix is likely to trip things up. Perhaps just -p test

[Abdul Rafay Khan]

Tried, same error

runCA -d test/ -p datafastq/ datafastq/lg/human/humanUpaired.frq

[WouterDeCoster]

I have no idea if this causes the problem, but again you used a directory rather than a prefix for -p. Try (as in the manual) to just use a string and not a path or directory.

[igor]

I am not sure if you are aware, but... "If you are assembling PacBio or Oxford Nanopore data, please use Canu instead. Celera Assembler is no longer being maintained." see: http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page

I remember having many issues with CA in the past, but Canu has been working great. It may be worth upgrading.