#328 mertrimApply failed to find a list file that actually exist

[Byoungnam Min]

Hi,

I'm using 1 illumina library to assemble using CA.
When I ran runCA, I got this error during merTrimApply.

I'm sure that list file exist in proper location.
mbnmbn00@eevee:/eevee/analysis3/Choanephora_cucurbitarum$ ls /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.list -alt
-rw-rw-r-- 1 mbnmbn00 mbnmbn00 1919 Oct 21 11:06 /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.list

I tried recent versions wgs-8.1 and wgs-8.3rc, but not worked.

It's Ubuntu 14.04 and I downloaded pre-compiled files.
I'll give anything you need to figure out the proplem.

All the Best,
Byoungnam

==

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_PAPER = "en_US.UTF-8",
LC_ADDRESS = "en_US.UTF-8",
LC_MONETARY = "en_US.UTF-8",
LC_NUMERIC = "en_US.UTF-8",
LC_TELEPHONE = "en_US.UTF-8",
LC_IDENTIFICATION = "en_US.UTF-8",
LC_MEASUREMENT = "en_US.UTF-8",
LC_CTYPE = "UTF-8",
LC_TIME = "en_US.UTF-8",
LC_NAME = "en_US.UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
----------------------------------------START Wed Oct 21 11:06:34 2015
find -L /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim -name *.merTrim -print | sort > /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.list
----------------------------------------END Wed Oct 21 11:06:34 2015 (0 seconds)
----------------------------------------START Wed Oct 21 11:06:34 2015
/csbl/tool/ngs/wgs-8.0/Linux-amd64/bin/merTrimApply \ -g /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/Choanephora_cucurbitarum.gkpStore \ -L /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.list \ -l /eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.log \

/eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrimApply.err 2>&1
----------------------------------------END Wed Oct 21 11:06:34 2015 (0 seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

---

Stack trace:

at /csbl/tool/ngs/wgs-8.0/Linux-amd64/bin/runCA line 1501.
main::caFailure('merTrimApply failed', '/eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertri...') called at /csbl/tool/ngs/wgs-8.0/Linux-amd64/bin/runCA line 3072
main::merTrim() called at /csbl/tool/ngs/wgs-8.0/Linux-amd64/bin/runCA line 6307

---

Last few lines of the relevant log file (/eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrimApply.err):

Failed to open -L '/eevee/analysis3/Choanephora_cucurbitarum/asm_celera/0-mertrim/Choanephora_cucurbitarum.merTrim.list' for reading: No such file or directory

---

Failure message:

merTrimApply failed