[wgs-assembler-users] PBcR restart

[Seth M. <mu...@uw...>]

Hello Everyone,

I was running a PBcR through to assembly with nothing in my spec file excet
memory options since I share the server.  I got all the way to step 9
(terminator) when I got the following error:

----------------------------------------START Tue May 26 02:18:24 2015
/usr/bin/env perl /data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl
-euid
/lore/bill.crosby.storage/PI440795/PI440795_Self_Assembled/9-terminator/asm.asm
Can't locate Statistics/Descriptive.pm in @INC (@INC contains:
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at
/data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl line 18.
BEGIN failed--compilation aborted at
/data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl line 18.
----------------------------------------END Tue May 26 02:18:24 2015 (0
seconds)
ERROR: Failed with signal INT (2)
The Cleaner has arrived.  Doing 'none'.
----------------------------------------END Tue May 26 02:18:24 2015 (1490
seconds)

I google search tells me that I can try manually running asmOutputFasta to
try and make the missing output fasta (
http://sourceforge.net/p/wgs-assembler/mailman/message/33260123/).  When I
try it the fasta files are only ~3MB.  The same link warns that the asm may
be incomplete and I might have to repeat step 9 in runCA, this is where I
get stuck.

I've renamed the 9-terminator folder to 9-terminator-old, but what is the
command for runCA to pickup a PBcR run?  I tried specifying the directory,
prefix, and spec file and after changing to the hash memory options in my
spec file i get:

Failure message:

no fragment files specified, and stores not already created

While trying to rerun the PBcR command again gives:

Error: requested to output PI440795_Self_Assembled.frg but file already
exists. Will not overwrite.


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755