Closed drifty914 closed 7 years ago
w1bw
commented
8 years ago Very sorry for taking so long to respond to this. From the stack trace, I can tell what is happening but not why, and I haven't see this failure before.
If you still have the test case around, could you please run with adding the --changes argument and send along the .changes file for this scaffold? You can always run it for that scaffold only using the --targets option. Thanks, and sorry you ran into this issue with Pilon!
mmokrejs
commented
8 years ago Same here but on a contig. The output fasta was incomplete, entries since the problematic entry of were missing.
So I ran it to give you the detailed info, but no way.
... --unpaired contigs.bam --changes --vcf --fix bases --targets 14171 ...
Pilon version 1.16 Mon Dec 7 09:45:45 2015 -0500
Genome: reference.fasta
target file: 14171
Target: 14171:1-8966
Fixing bases
Input genome size: 88910963
Processing 14171:1-8966
unpaired 454Contigs.bam: coverage 112
Total Reads: 14020, Coverage: 112, minDepth: 11
Confirmed 8592 of 8966 bases (95,83%)
Corrected 0 snps; 0 ambiguous bases; 0 small insertions totaling 0 bases; 0 small deletions totaling 0 bases
14171:1-8966 log:
Finished processing 14171:1-8966
Writing 14171:1-8966 VCF to pilon3.vcf
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: java.lang.IllegalArgumentException: requirement failed: can't fetch base outside region
at scala.Predef$.require(Predef.scala:219)
at org.broadinstitute.pilon.GenomeRegion.refBase(GenomeRegion.scala:702)
at org.broadinstitute.pilon.Vcf.writeRecord(Vcf.scala:86)
at org.broadinstitute.pilon.GenomeRegion$$anonfun$writeVcf$1.apply$mcVI$sp(GenomeRegion.scala:559)
at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:166)
at org.broadinstitute.pilon.GenomeRegion.writeVcf(GenomeRegion.scala:544)
at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$6$$anonfun$apply$4.apply(GenomeFile.scala:148)
at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$6$$anonfun$apply$4.apply(GenomeFile.scala:145)
at scala.collection.immutable.List.foreach(List.scala:381)
at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$6.apply(GenomeFile.scala:145)
at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$6.apply(GenomeFile.scala:138)
at scala.collection.immutable.List.foreach(List.scala:381)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:138)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:90)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
... 6 more
Unfortunately, the .vcf, .changes and .fasta files are empty. I ran pilon with --targets 14171 so it should have acted on this one only.
I seem to be having an issue when saving VCF output using pilon-1.16 (same error with 1.15) after it finishes running on my genome. Doesn't seem to have any problems outputting a corrected FASTA file (as long as VCF output is not turned on) and it seems to be able to save the first 1499 scaffolds fine but I get the following error when it gets to the 1500th:
The scaffold (ErrorScaff.zip) joins two contigs with a run of ~5k N's in the middle but there doesn't seem to be any invalid characters or formatting etc. from what I can see.
I'm calling the program with the following:
java -Xmx220g -jar ~/pilon-1.16.jar --genome Genome.fasta --frags PairedFrags1 --frags PairedFrags2.bam --frags PairedFrags3.bam --frags PairedFrags4 --frags PairedFrags5.bam --jumps Mates.bam --unpaired Strays.bam --unpaired Corrected_PacBio.bam --variant --diploid --threads 32 --output MyGenomePilonFull debug output for scaffold: DebugOutput.zip