Re: [wgs-assembler-users] PBcR restart

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

Hi Serge,

I double checked BLASR/PBDAGCON, kept the old stage 9 folder changed,
upgraded to wgs8.3rc2 and tried to rerun it but still got the same "Will
not overwrite" error.  At this point the command line output is gone so I
can't grep it.  Would it be safed to a log file somewhere?

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 Thu, May 28, 2015 at 10:39 AM, Serge Koren <ser...@gm...> wrote:

> Yes, the 25X coverage is for after correction. However, 12X should be
> sufficient for a reasonable assembly, certainly not a tiny fraction of your
> genome like you’re seeing. If you run
> gatekeeper -dumpinfo PI440795_Self_Assembled/asm.gkpStore
>
> That should give more info on what reads made it into the assembly.
>
>
> On May 28, 2015, at 10:37 AM, Seth Munholland <mu...@uw...> wrote:
>
> 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
>>>
>>> ------------------------------------------------------------------------------
>>> One dashboard for servers and applications across Physical-Virtual-Cloud
>>> Widest out-of-the-box monitoring support with 50+ applications
>>> Performance metrics, stats and reports that give you Actionable Insights
>>> Deep dive visibility with transaction tracing using APM Insight.
>>>
>>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________________________________________
>>> wgs-assembler-users mailing list
>>> wgs...@li...
>>> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>>>
>>>
>>>
>>
>>
>
>