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Old 03-25-2014, 04:08 AM   #17
Thias
Member
 
Location: Münster, Germany

Join Date: Mar 2013
Posts: 42
Default Has anybody experience with running bbmap on clusters?

Hello everybody,

I would like to know, if anyone has (good) experience with running bbmap alignments on clusters, which require to submit jobs via a scheduler?

Because I can successfully start/finish an alignment on the university's cluster when started directly from the terminal (which is prohibited, but who cares on Sundays at 3am?), but the exactly same command written to Portable Batch System (PBS) job script and submitted via qsub to Torque/Maui scheduler fails:

Code:
Exception in thread "Thread-5" java.lang.NullPointerException
     at align2.Block.<init>(Block.java:33)
     at align2.Block.read(Block.java:156)
     at align2.IndexMaker4$BlockMaker.makeArrays(IndexMaker4.java:139)
     at align2.IndexMaker4$BlockMaker.run(IndexMaker4.java:127)
Generated Index:    3.816 seconds.
Exception in thread "main" java.lang.NullPointerException
     at align2.BBIndex.analyzeIndex(BBIndex.java:116)
     at align2.BBMap.loadIndex(BBMap.java:389)
     at align2.BBMap.main(BBMap.java:30)
I guess bbmap recognizes that there are more cores available on the system, than I am allowing for the job via the job script and tries to use them nevertheless?

Since I would like to extent my alignment times beyond weekend nights , I would be happy for suggestions.
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