Re: [wgs-assembler-users] PBcR restart

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

After correction I ended up with about 12x coverage.  I presume the ~25x
coverage suggested on the PBcR page is for after correction?  I'll try the
low-coverage parameters and double check BLASR/PBDAGCON next, thanks.

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

On Wed, May 27, 2015 at 6:56 PM, Serge Koren <ser...@gm...> wrote:

> That most likely means you ended up with too little coverage for assembly
> after correction. You can check the coverage in the
> PI440795_Self_Assembled*.fastq files. If you’re not already, I’d suggest
> using the low-coverage parameters on the wiki page:
>
> http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR#Low_Coverage_Assembly
>
> I’d also double-check that you have BLASR/PBDAGCON available in your path
> and that it is being used for assembly (in your
> tempPI440795_Self_Assembled/runPartition.sh file look for the word
> pbdagcon).
>
> On May 26, 2015, at 12:03 PM, Seth Munholland <mu...@uw...> wrote:
>
> Hi Serge,
>
> I looked into the 9-terminator folder and found the asm.utg.fasta file,
> but it's only 4.5MB (~0.007x coverage) when I started wth ~33x coverage.
> Any suggestions for where to look for the data loss?
>
> 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
>
> On Tue, May 26, 2015 at 11:18 AM, Serge Koren <ser...@gm...>
> wrote:
>
>> Hi,
>>
>> This was a bug fixed in CA 8.3rc2 (when the assembly of the corrected
>> data failed, the restart did not work properly). If you grep for runCA in
>> your command line output from your run and re-run the last command (it
>> should have the library name as the -d option). That will re-create the
>> 9-terminator directory and corresponding files. Unless you install the
>> missing perl package, the qc generation will still fail, but it only
>> contains statistics on the assembly, the asm.utg.fasta file should be your
>> complete assembly.
>>
>> Serge
>>
>>
>> On May 26, 2015, at 10:49 AM, Seth Munholland <mu...@uw...>
>> wrote:
>>
>> 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
>>
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>
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