psg_prepare_reference failed

[Zhenhua Wu]

I tried to run psg_prepare_reference.py, but it failed:

...

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003nkq.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003pgf.3.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc021yva.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc010kkp.3.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003odo.1.psg 100

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Error: Command was terminated or failed:

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr5/uc021yer.1.psg 100

I found that "hg19.knownGene.063013/chr5/uc021yer.1.psg" file is empty. For chr5, there are many .psg files that are empty (with size 0). For other chromosomes like chr6, there is no empty .psg file. Why does this happen  to 'chr5'?

The .gtf file is downloaded from ucsc table, using ucsc gene, known gene.

Jeremy

[Zhenhua Wu]

The problem seems to be due to the number of core used. I reduced the number of core to 3, it works fine.

Jeremy