Error running Picard tools (devteam)

Question: Error running Picard tools (devteam)

2.8 years ago by

Belgium

Hi all,

After debugging the install of picard, I'm testing it out.
When running the MarkDuplicates tool I get the following error:

Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m
Ignoring SAM validation error: ERROR: Record 1, Read name D74F8:06451:05495, RG ID on SAMRecord not found in header: D74F8.IonXpress_014-11D1BB55
Exception in thread "main" htsjdk.samtools.SAMException: Exception creating temporary directory.
	at htsjdk.samtools.util.IOUtil.createTempDir(IOUtil.java:718)
	at htsjdk.samtools.CoordinateSortedPairInfoMap.(CoordinateSortedPairInfoMap.java:59)
	at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.(DiskBasedReadEndsForMarkDuplicatesMap.java:57)
	at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:250)
	at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Caused by: java.io.IOException: Input/output error
	at java.io.UnixFileSystem.createFileExclusively(Native Method)
	at java.io.File.createTempFile(File.java:2024)
	at java.io.File.createTempFile(File.java:2070)
	at htsjdk.samtools.util.IOUtil.createTempDir(IOUtil.java:709)
	... 7 more

Any idea what's causing this? It seems there's an issue creating some kind of temporary directory, but I don't see why, since the working directory is definitely read/writeable by galaxy..

Thanks
Matthias

picard • 1.5k views

ADD COMMENT • link •

modified 2.8 years ago • written 2.8 years ago by matthias.desmet • 150

2.8 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

The answer given by Jennifer does help with the SAM validation error,
However, this error is ignorable. The main issue was there was something wrong with the tmp directory used by the java runtime.
Clearing the tmp directory cleared the issue.

ADD COMMENT • link written 2.8 years ago by matthias.desmet • 150

Glad this was sorted out and thanks for sending back in the solution that worked for you. Jen

ADD REPLY • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The input must be a complete SAM file with headers, or a BAM file. My guess is that the input does not have a complete header from the error or that sorting is the root issue.

SAM/BAM data must be coordinate sorted before using most Picard and Samtools (SortSam is one choice). Even if the output states that it is sorted in the dataset name (by Tophat, etc), resorting is necessary or odd errors can come out. Details: https://github.com/jennaj/support-known-issues/wiki/Sort-your-inputs

Hopefully this helps to resolve the problem, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »