Re: [wgs-assembler-users] PBcR restart

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Hi,

Sorry for the delay in replying. If you are trying to re-run with the sensitive low-coverage options, you need to start from scratch by either removing the existing results or using a new library name.

Serge

> On Jun 12, 2015, at 5:08 PM, Seth Munholland <mu...@uw...> wrote:
> 
> 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... <mailto: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... <mailto: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... <mailto: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 <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... <mailto: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... <mailto: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... <mailto: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 <http://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 <http://caqc.pl/> line 18.
>>>> BEGIN failed--compilation aborted at /data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl <http://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/ <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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>>> 
>>> 
>> 
>> 
> 
> 