I am trying to correct PacBio data with a large HiSeq dataset using pacBioToCA.
Unfortunately pacBioToCA crashes during the overlapper stage. Here are the details:
exited with exit code 1
Failed to execute qsub
More useful info in the asm.layout file:
Picking cutoff as 7 mean would be 16.160603
Loaded 2399994 overlaps
ERROR: Could not find appropriate partition for 279415251 though it was either 2 or 3 (279293536-279335216) and (279418576-279460256) but it was neither
In the temp directory I can see all .olaps files are finished. The .rank files are all empty. Im running the latest stable release of Celera Assembler on our computer cluster using SGE. I patched CA to fix runCorrection.sh as described here:
Restarting the correction does not help.
I could not find any information about this error, so I hope you can help me figure this one out!
Thanks in advance,
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