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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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How to resume #154

Open methylome opened 2 years ago

methylome commented 2 years ago

pilon was failed with the following log. Is there any way to resume the job?

Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400
Genome: /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/racon/assembly_racon.fa
Fixing snps, indels, gaps, local
Input genome size: 2359242266
Scanning BAMs
/ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam: 530334753 reads, 0 filtered, 529476652 mapped, 509061207 proper, 18527354 stray, FR 100% 496+/-121, max 1548
Processing contig_61897:1-52237
...
# fix break: contig_63515:26157-26251 0 -0 +0 NoSolution
# fix break: contig_63515:26636 0 -0 +0 NoSolution
Finished processing contig_63515:1-28000
Processing contig_18993:1-49004
WARNING: BAM index file /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai is older than BAM /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam
WARNING: BAM index file /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai is older than BAM /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam
WARNING: BAM index file /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai is older than BAM /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam
WARNING: BAM index file /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai is older than BAM /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam
WARNING: BAM index file /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai is older than BAM /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam
Exception in thread "main" java.lang.reflect.InvocationTargetException
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:498)
   at com.simontuffs.onejar.Boot.run(Boot.java:340)
   at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: htsjdk.samtools.util.RuntimeIOException: /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai (Cannot send after transport endpoint shutdown)
   at htsjdk.samtools.AbstractBAMFileIndex$MemoryMappedFileBuffer.<init>(AbstractBAMFileIndex.java:478)
   at htsjdk.samtools.AbstractBAMFileIndex.<init>(AbstractBAMFileIndex.java:79)
   at htsjdk.samtools.DiskBasedBAMFileIndex.<init>(DiskBasedBAMFileIndex.java:46)
   at htsjdk.samtools.BAMFileReader.getIndex(BAMFileReader.java:252)
   at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:726)
   at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:412)
   at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:498)
   at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
   at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:365)
   at org.broadinstitute.pilon.BamFile.readsInRegion(BamFile.scala:329)
   at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:336)
   at org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:367)
   at org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:366)
   at scala.collection.immutable.List.foreach(List.scala:381)
   at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:366)
   at org.broadinstitute.pilon.GapFiller.recruitFrags(GapFiller.scala:375)
   at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:389)
   at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:391)
   at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:51)
   at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:45)
   at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:383)
   at org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:381)
   at scala.collection.immutable.List.foreach(List.scala:381)
   at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:381)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:119)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:108)
   at scala.collection.Iterator$class.foreach(Iterator.scala:893)
   at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
   at scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972)
   at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
   at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
   at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
   at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
   at scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969)
   at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.internal(Tasks.scala:169)
   at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443)
   at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149)
   at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
   at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
   at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
   at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
   at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
   at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.io.FileNotFoundException: /ddn/datacenter/genomes/Polymesoda_erosa/assembly/flye/pilon/assembly_racon.bam.bai (Cannot send after transport endpoint shutdown)
   at java.io.FileInputStream.open0(Native Method)
   at java.io.FileInputStream.open(FileInputStream.java:195)
   at java.io.FileInputStream.<init>(FileInputStream.java:138)
   at htsjdk.samtools.AbstractBAMFileIndex$MemoryMappedFileBuffer.<init>(AbstractBAMFileIndex.java:471)
   ... 42 more