pilon error: Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig_1

[saras224]

Hi @bwlang
I ran the following command : pilon --genome assembly.fasta --bam C8_sorted.bam --threads 40

its giving this error:
Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig_1
at htsjdk.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:80)
at htsjdk.samtools.SAMSequenceDictionary.(SAMSequenceDictionary.java:53)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:123)
at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:704)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:298)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:176)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:396)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:208)
at org.broadinstitute.pilon.BamFile.reader(BamFile.scala:51)
at org.broadinstitute.pilon.BamFile.(BamFile.scala:57)
at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:131)
at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:172)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:84)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

Please help me resolve this error.
Thanks!!

[bwlang]

If I read this error message correclty, it seems that you have 2 contigs in your fasta file named "contig_1". That's not allowed. It might indicate dupliate data. Probably you should investigate how that happened.

You can confirm the problem by looking at at your assembly.fasta (maybe run samtools faidx assembly.fasta to produce an assembly.fasta.fai file that may be easier to read).