[wgs-assembler-users] PBcR question

[Matthew C. <co...@gm...>]

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)*

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,
Matt