Hi, this is my command: "pilon --genome dor1A_canu.contigs.fasta --bam sorted_cdbtrim_1A.bam --output cdbtrim1A --outdir "
I used this command to do the pilon many times successfully, but today when I do it use pilon , it gave me the following error, can someone help me out this situation? Thank you so much!
/rsrch5/home/hlth_prof/jwang52/dortrim_fastq23/canu_dor/pilon_canudbtrim
/home/jwang52/.lsbatch/1709748118.1540723.shell: line 13: pilon: command not found
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:281)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:866)
at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:1026)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:840)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:1079)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1069)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1033)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:574)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:553)
at scala.collection.convert.JavaCollectionWrappers$JIteratorWrapper.next(JavaCollectionWrappers.scala:38)
at scala.collection.Iterator$$anon$6.hasNext(Iterator.scala:471)
at scala.collection.immutable.List.prependedAll(List.scala:155)
at scala.collection.IterableOnceOps.toList(IterableOnce.scala:1251)
at scala.collection.IterableOnceOps.toList$(IterableOnce.scala:1251)
at scala.collection.AbstractIterator.toList(Iterator.scala:1279)
at org.broadinstitute.pilon.BamFile.readsInRegion(BamFile.scala:341)
at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:348)
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1(GapFiller.scala:367)
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1$adapted(GapFiller.scala:366)
at org.broadinstitute.pilon.GapFiller$$Lambda/0x00001554dc137b08.apply(Unknown Source)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GapFiller.recruitReadsFromBams(GapFiller.scala:366)
at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:375)
at org.broadinstitute.pilon.GapFiller.recruitUnpaired(GapFiller.scala:392)
at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:394)
at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:401)
at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:54)
at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:46)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6(GenomeRegion.scala:401)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6$adapted(GenomeRegion.scala:399)
Hi, this is my command: "pilon --genome dor1A_canu.contigs.fasta --bam sorted_cdbtrim_1A.bam --output cdbtrim1A --outdir " I used this command to do the pilon many times successfully, but today when I do it use pilon , it gave me the following error, can someone help me out this situation? Thank you so much!
/rsrch5/home/hlth_prof/jwang52/dortrim_fastq23/canu_dor/pilon_canudbtrim /home/jwang52/.lsbatch/1709748118.1540723.shell: line 13: pilon: command not found Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:281) at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:866) at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:1026) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:840) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:1079) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1069) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1033) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:574) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:553) at scala.collection.convert.JavaCollectionWrappers$JIteratorWrapper.next(JavaCollectionWrappers.scala:38) at scala.collection.Iterator$$anon$6.hasNext(Iterator.scala:471) at scala.collection.immutable.List.prependedAll(List.scala:155) at scala.collection.IterableOnceOps.toList(IterableOnce.scala:1251) at scala.collection.IterableOnceOps.toList$(IterableOnce.scala:1251) at scala.collection.AbstractIterator.toList(Iterator.scala:1279) at org.broadinstitute.pilon.BamFile.readsInRegion(BamFile.scala:341) at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:348) at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1(GapFiller.scala:367) at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1$adapted(GapFiller.scala:366) at org.broadinstitute.pilon.GapFiller$$Lambda/0x00001554dc137b08.apply(Unknown Source) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.GapFiller.recruitReadsFromBams(GapFiller.scala:366) at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:375) at org.broadinstitute.pilon.GapFiller.recruitUnpaired(GapFiller.scala:392) at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:394) at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:401) at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:54) at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:46) at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6(GenomeRegion.scala:401) at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6$adapted(GenomeRegion.scala:399)