Re: [wgs-assembler-users] PBcR question

[Serge K. <ser...@gm...>]

Hi,

On Jun 24, 2014, at 5:40 PM, Matthew Conte <co...@gm...> wrote:

> Hi all,
> 
> I'm trying out PBcR to make use of the new MHAP overlapper for self correcting a set of PacBio reads and I'm running into an issue.
> 
> I'm getting the following errors in the temp_dir/1-overlapper/1.err:
> Exception in thread "main" java.io.FileNotFoundException: /raid3/PBcR_CA_8.2_alpha/tempLibrary/1-overlapper/stream_1/correct_reads_part000002.dat (No such file or directory)
The dat file is a pre-computed index that is used to speed up the computation for smaller genomes. For larger genomes or if you are using local disk, it should not get created. Do you have the output of the pipeline up to this step along with the command-line you used to start the run? That will help diagnose why it is not properly recognizing that the index is not built. As a workaround, you can add "localStaging=</path to local disk>" to your PBcR command which will force the pipeline to never pre-compute the index.
> 
> There is no 'correct_reads_part000002.dat' file there, but there is a 'correct_reads_part000002.fasta' file where the 'stream_1/correct_reads_part000002.dat' points to. I'm not sure if it is just an extension naming issue or if the .dat files weren't created properly. 
> 
> Also, I've found another minor issue with the '-threads' option supplied to PBcR on the command line. It doesn't seem to use the number of threads supplied and simply uses the max number of cpus on the machine available. 
Thanks, I'll check this and update the code.
> 
> Thanks,
> Matt
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