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

[carlos v. <cha...@gm...>]

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