Question: Error running Picard tools (devteam)
0
gravatar for matthias.desmet
2.8 years ago by
Belgium
matthias.desmet150 wrote:

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 COMMENTlink modified 2.8 years ago • written 2.8 years ago by matthias.desmet150
1
gravatar for matthias.desmet
2.8 years ago by
Belgium
matthias.desmet150 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 COMMENTlink written 2.8 years ago by matthias.desmet150

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

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k
1
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k
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