Re: [wgs-assembler-users] Missing output fasta files and information from qc file, .

[Walenz, B. <wa...@nb...>]

You can generate the fasta and posmap outputs with:

asmOutputFasta -p a6 < a6.asm
buildPosMap -o a6 -g a6.gkpStore < a6.asm

I'm worried that the asm file is incomplete.  It's possible that an incomplete asm has no data that these two programs would report, resulting in no output files.  If the asm file is incomplete, move 9-terminator someplace safe (like 9-terminator-old) and restart runCA.  It will recreate outputs.  Check disk space!

The caqc script died because it relies on perl module Statistics/Descriptive.  Caqc computes the stats that are in the *.qc file.

b


________________________________
From: Miguel Grau [mi...@uj...]
Sent: Friday, January 23, 2015 3:03 AM
To: wgs...@li...
Subject: [wgs-assembler-users] Missing output fasta files and information from qc file, .

Dear all,

I have finished my assembly using wgs 8.2 assembler but in my ouput folder, I only have the .asm and the .qc file, without fasta files.

I didn't have any error during all the process apart of this one in the last step:
....
----------------------------------------START Fri Jan 23 10:25:04 2015
/usr/bin/env perl /miquel/wgs-8.2/Linux-amd64/bin/caqc.pl -euid /reads/a6/9-terminator/a6.asm
Can't locate Statistics/Descriptive.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /miquel/wgs-8.2/Linux-amd64/bin/caqc.pl line 18.
BEGIN failed--compilation aborted at  /miquel/wgs-8.2/Linux-amd64/bin/caqc.pl line 18.
----------------------------------------END Fri Jan 23 10:25:04 2015 (0 seconds)
ERROR: Failed with signal INT (2)
The Cleaner has arrived.  Doing 'none'.

And the first lines from my qc file:

[Unitig Consensus]
NumColumnsInUnitigs=5385950647
NumGapsInUnitigs=378938
NumRunsOfGapsInUnitigReads=13067488

[Contig Consensus]
NumColumnsInUnitigs=312297292
NumGapsInUnitigs=398693
NumRunsOfGapsInUnitigReads=10707275
NumColumnsInContigs=312248428
NumGapsInContigs=347998
NumRunsOfGapsInContigReads=9673938
NumAAMismatches=171477362
NumVARStringsWithFlankingGaps=80202

[Read Depth Histogram]
d    < 3Kbp    < 10Kbp   < 1Mbp    < inf
0    162862     601904     619465     0
1    136303     189622     163968     0
...
...

Thank you,



Miquel