Fatal error with SamToFastq using BAM files

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)

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The source BAM dataset likely has non-unique names for pairs. This must be corrected first. It is was a merged dataset, try executing this conversation tool before merging BAMs. If you received it merged and read groups were assigned, Samtools Split could resolve the problem.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thank you for the quick reply. I split the bam file and then tried converting it to fastq, but I am still getting an error:

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(

I am little confused with the split function, I was expecting to get two outputs for that, but only got one. I was wondering if after splitting I should re-merge with the NGS: Bam Tools, but I couldn't do that since I only had one output file from the split. Again, I appreciate the help!

-Joe

ADD REPLY • link written 3.1 years ago by jrmeirin • 0

It sounds as if there was only one read group or possibly no read groups assigned to split on.

Duplicates are the main reported reason for this tool error, but you could confirm this in an issue with your data by using the Group then Sort tools ("count distinct" on the identifier, then reverse sort the count to see which/how many are duplicated).

The problem is not with Galaxy, but with the original file content and how some Picard functions work. Galaxy can only repair upstream inputs that do not meet tool input criteria in certain cases. If this was my data, I would probably run another Picard tool like FixMateInformation to see if that errored, too, for the same reason, as a test.

There are several line-command/utility fixes reported online. I cannot endorse any in particular, but you could definitely test those that seem reasonable to see if it clears up the duplicates (if that is in fact the problem). Just do a google with "Picard" and "Illegal mate state" to see public reports/descriptions/fixes for the error.

Sorry I could not help fully resolve this. But others may also still post a reply.

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Ok I'll keep working at it and dig around more for other similar reported issues. Thanks!

ADD REPLY • link written 3.1 years ago by jrmeirin • 0

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