I am trying to correct a PacBio data with a HiSeq dataset using PacBioToCA.
I've come across another problem I hope you can help me with.
One out of 25 utg_asm jobs is failing. This results in runCA reporting:
"Failed to execute qsub .... ~/runPartition.sh"
For this particular job a standard .out file and a .excluded file is generated. The .fasta and .qual files are present but empty. The *.success file obviously is missing.
The .out file of the erroneous job seems fine but is missing the characteristic final line "Processed xxx layouts" that I can find in all other .out files. Instead I find this as final line:
"In contig 27976 forced alignment of 43 bases of string 179435008 subscript 1354 to 56 bases of consensus
with 23 errors (41.07% error)"
All the .lay, .olaps and *.rank files seem to be fine. I tried restarting the failed job by removing it together with runPartition.sh. The pipeline restarted fine but I ended up with the same error.
Hope you can help me once more.
Thanks in advance,