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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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Predef.scala:224 #45

Closed diaparim closed 7 years ago

diaparim commented 7 years ago

Hi,

I used pilon with the following command: java -Xmx256g -jar ~/bin/software/pilon/pilon-1.22.jar --genome ./Phco/output/contigs.fa --jumps sorted.bam --output pilon1 --fix all --mindepth 0.5 --changes --verbose --vcf It worked well before.

Then I run for the second, but i only saw this messages, and the run stop. any help?

0003815, tig00002995, tig00004231, tig00014389, tig00001872, tig00003722, tig00002515, tig00001202, tig00005432, tig00002706, tig00009748, tig00001066, tig00013488, tig00006621, tig00010413, tig00003413, tig00001249, tig00011538, tig00004747, tig00002265, tig00003244, tig00010517, tig00004960, tig00005041, tig00001175, tig00005472, tig00010377, tig00004546, tig00003204 at scala.Predef$.require(Predef.scala:224) at org.broadinstitute.pilon.BamFile.validateSeqs(BamFile.scala:67) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$2.apply(GenomeFile.scala:87) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$2.apply(GenomeFile.scala:87) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:87) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:101) at org.broadinstitute.pilon.Pilon.main(Pilon.scala) ... 6 more

Thanks, Marwan

diaparim commented 7 years ago

turned out the genome was not the correct one.

Thanks