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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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Asking for indexed bam file #158

Open saras224 opened 1 year ago

saras224 commented 1 year ago

Hi @bwlang I encountered an error saying that it needs an indexed bam file when I have already provided it an indexed bam file. How to resolved this error? Log of the terminal output:

Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 Exception in thread "main" java.lang.IllegalArgumentException: requirement failed: /lustre/saraswati/WASTEWATER3/WW_NOVA_SORTED.bam.bai must be indexed BAM at scala.Predef$.require(Predef.scala:338) at org.broadinstitute.pilon.BamFile.(BamFile.scala:58) at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:165) at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:172) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:84) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

Thanks in Advance!

bwlang commented 1 year ago

i'm not really connected with this project... but that error message reads to me like you might have specified the index (.bai) instead of the bam ??