I am a new Galaxy user and have some bam files that I need to run through RNA seq analyses. I have read that the first step is to convert my bam files to Fastq, using the NGS: Picard --> SamToFastq tool, but when I try this I am repeatedly getting fatal errors:
Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" picard.PicardException: Illegal mate state: HWI-D00569:30:C5UBTANXX:1:1201:15460:51543 at picard.sam.SamToFastq.assertPairedMates(SamToFastq.java:345) at picard.sam.SamToFastq.doWork(SamToFastq.java:168) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
Before attempting this, I ran the bam file through FastQC, which showed good results. Can anyone help me figure out how to get this to convert? I appreciate any assistance!