Re: [svtoolkit-help] Having trouble with SVPreprocess
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Re: [svtoolkit-help] Having trouble with SVPreprocess
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From: Homann, O. <oh...@am...> - 2015-02-25 21:23:57
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Hello Bob, Thanks for the response. Queue wrote a *.fail file for the step. I will attempt a rerun with --disableJobReport and report back tomorrow. Any advice you can have on getting queue to work with LSF 9.1 + Drmaa would be much appreciated. I installed the library at https://github.com/PlatformLSF/lsf-drmaa, and while that took me beyond the 'missing libdrmaa.so' error I eventually got stuck on an exception complaining that I haven't set up SGE_ROOT (which struck me as odd, since I was trying to use LSF, not SGE). Regards, Oliver From: Bob Handsaker [mailto:han...@br...] Sent: Wednesday, February 25, 2015 12:56 PM To: svt...@li... Subject: Re: [svtoolkit-help] Having trouble with SVPreprocess Hi, Oliver, First of all, the "mysample/mysample/null" is OK. That is actually sample/library/readgroup (and in this case you are grouping by library, which is the default and usual thing to do). Second, there is a known bug, which we are in the process of fixing, where some of the preprocessing steps do not catch and report I/O errors (they use java PrintWriter but do not check for errors). But since you are checking the output file, that is probably not the issue here. But just fyi. Third, we have seen occasional problem with this happening with LSF (but it is random and occasional and goes away when you rerun). I don't know if shell mode has the same problem, since I never use that. One thing to try is --disableJobReport, if you are not already doing that. Also check to see if Queue wrote a .*.done file for this step. If those things are going wrong, it is a queue problem. Also, we successfully run LSF 9.1 here with Drmaa. We had to have our IT staff install the LSF Drmaa library. But it did take a while to get it working. I think they had to try different versions of the drmaa library. Seva Kashin worked on that and may be able to help if that would be useful. -Bob On 2/25/15, 12:02 PM, Homann, Oliver wrote: Hello, I'm running into difficulties trying to run SVPreprocess, and was hoping you might have some ideas about what has gone wrong. After a while the run fails with a (seemingly uninformative) ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run that exact same command at the command line (just changing the output name), and it works without reporting any errors. In both cases an output file of the same size is created, which makes me wonder if this is even the step that is truly failing. A few other observations/comments: * I note that the log appends 'null' to the name of the sample it is processing... is this a clue to something being amiss? * I've had to build my own genome bundle because my alignments include the hs37d5 decoy "chromosome". Perhaps I did something odd there that is contributing to the problem? * I am doing this test using the Shell mode since I can't seem to get Queue to work with LSF 9 and drmaa. Any suggestions would be greatly appreciated. Regards, Oliver Homann ================================================================== Error from Shell SVPreprocess run ================================================================== ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/mypath/output/isd/mysample.hist.bin' '-O' '/mypath/output/isd/mysample.dist.bin' ERROR 17:34:50,830 FunctionEdge - Contents of /mypath/output/logs/SVPreprocess-6.out: INFO 16:35:09,560 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,562 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:35:09,566 HelpFormatter - Program Args: -I /mypath/output/isd/mysample.hist.bin -O /mypath/output/isd/mysample.dist.bin INFO 16:35:09,569 HelpFormatter - Executing as me...@my...<mailto:me...@my...> on Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- Processing mysample/mysample/null ... INFO 16:35:20,573 CommandLineProgram - Program completed. ================================================================== ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. 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