I am trying to convert bam files from TCGA to fastq. Picard gives the following error:
picard.sam.SamToFastq done. Elapsed time: 0.78 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" picard.PicardException: Illegal mate state: H090WADXX130325:1:1106:10520:95300 at picard.sam.SamToFastq.assertPairedMates(SamToFastq.java:342) at picard.sam.SamToFastq.doWork(SamToFastq.java:164) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185) at picard.sam.SamToFastq.main(SamToFastq.java:137)
The error is due to more than one pair of reads having the same query name.
it has been suggested to use bedtools bamtofastq. This produce the fastq files, however there are duplicated read names that makes my pipeline to crash in downstream steps…
I also tested “resolvepair” script but it does not produce anything…
I would like to either remove these duplicate read names or rename them. Do you have a solution to solve this issue?