[wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."

[Hornung, B. <bas...@wu...>]

Hi @all,

sorry if that's the wrong way, but I have a problem with the wgs assembler, and not really an idea if there's a bug or if I'm just dumb and doing something wrong (first time I use it).

I'm trying to run an assembly with PacBio short reads and illumina mate pair reads, and during the assembly runCA aborts, due to a failure in the overlapper.
I've converted my data to 2 .frg files, then I've run gatekeeper with both, which worked without errors (well...sort of, had to compile it myself, due to https://sourceforge.net/p/wgs-assembler/bugs/253/ ).
Then I run runCA, which then crashes because it can't deduplicate the reads.

Parts of the command line output:

----------------------------------------START Tue Aug 27 12:58:34 2013
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/deduplicate \
-gkp     /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/PacBio_and_mate_pair.gkpStore \
-ovs     /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.obtStore \
-ovs     /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.dupStore \
-report  /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.deduplicate.log \
-summary /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.deduplicate.summary \
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.deduplicate.err 2>&1
----------------------------------------END Tue Aug 27 12:58:34 2013 (0 seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at ./runCA line 1237
        main::caFailure('failed to deduplicate the reads', '/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkSto...') called at ./runCA line 3739
        main::overlapTrim() called at ./runCA line 5876

----------------------------------------
Last few lines of the relevant log file (/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.deduplicate.err):

AS_OVS_openBinaryOverlapFile()-- Failed to open '/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlaptrim/PacBio_and_mate_pair.dupStore/0001' for reading: No such file or directory

----------------------------------------
Failure message:

failed to deduplicate the reads


I have absolutely no clue what could be happening here.
If I run it with only the PacBio data, then it works, so the installation itself is okay.

Any advice?

Best regards,

Bastian