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Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
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From: Walenz, B. <bw...@jc...> - 2013-08-27 15:58:08
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Hi- It is complaining that there are no overlaps in the 'dupStore'. This could mean store creation failed, but it probably just means there are no duplicate reads. Can you upgrade to the latest 'unstable' version in subversion and rerun? If it still fails, I should be able to fix easily. I think it might be fixed already. Alternatively, you can disable all trimming (doOBT=0) or just dedupe (doDeDuplication=0). Odd that it worked with just the pacbio! b ________________________________________ From: Hornung, Bastian [bas...@wu...] Sent: Tuesday, August 27, 2013 7:16 AM To: wgs...@li... Subject: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..." 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 ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ wgs-assembler-users mailing list wgs...@li... https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users |
