Question: Celera Assembler runCA failed
1
gravatar for Abdul Rafay Khan
3.2 years ago by
Karachi, PK
Abdul Rafay Khan1.1k wrote:

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
ngs assembly celera assembler • 1.4k views
ADD COMMENTlink written 3.2 years ago by Abdul Rafay Khan1.1k

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

ADD REPLYlink written 3.2 years ago by WouterDeCoster43k
1

Tried, same error

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

ADD REPLYlink written 3.2 years ago by Abdul Rafay Khan1.1k

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.

ADD REPLYlink written 3.2 years ago by WouterDeCoster43k

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by igor9.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1779 users visited in the last hour