Re: [wgs-assembler-users] Problem with PBcR when cleaning PacBio reads

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

Hi,

This error is caused by a missing component of BLASR (sawriter) not being available in your path. It looks like you’re using BLASR which is packaged with the SSPACE scaffolder so I’m not sure if they include the full BLASR package. I would suggest downloading/compiling BLASR directly from GitHub and adding it to your path to ensure the full package is available.

Sergey

> On Dec 8, 2014, at 3:22 PM, carlos vargas <cha...@gm...> wrote:
> 
> Hello,
> 
> I have been trying to clean some PacBio reads using Illumina reads with PBcR. However it has been failing during the overlapper. It builds several files using the Illumina reads, however when it fails it gives the following message: 
> 
> ----------------------------------------END CONCURRENT Mon Dec  8 20:52:43 2014 (3695 seconds)
> ERROR:  Overlap prep job Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part    1 FAILED.
> ERROR:  Overlap prep job Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part    2 FAILED.
> 
> 2 overlap partitioning jobs failed.
> 
> In 1-overlapper there is the following message in the 24.hash.err:
> 
> /usr/bin/time: cannot run /home/local_installs/software/SSPACE-LongRead/sawriter: No such file or directory
> Command exited with non-zero status 127
> 0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 2112maxresident)k
> 0inputs+8outputs (0major+83minor)pagefaults 0swaps
> 
> However it seems it is not a problem as it has it performs every step until reaching that step. Any idea as to what might be the problem?
> 
> Thanks in advance,
> Carlos 
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