running of Unified Genotyper encounters error

Question: running of Unified Genotyper encounters error

4.2 years ago by

China

pes1217 • 40 wrote:

Hi,

I am doing mapping using galaxy. Just now the process of Unified Genotyper encounters error and stops. I believe the parameter setting is all ok. Have anyone had the same question? please help me, thanks.

the error is:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp
[Tue Sep 23 06:22:00 CDT 2014] net.sf.picard.sam.CreateSequenceDictionary
REFERENCE=/tmp/tmp-gatk-mIU3_R/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-mIU3_R/dict8586168236248156676.tmp
TRUNCATE_NAMES_AT_WHITESPA

snp • 1.5k views

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modified 4.1 years ago by gou.gou1217 • 30 • written 4.2 years ago by pes1217 • 40

4.1 years ago by

liyingcai2014 • 10

China

liyingcai2014 • 10 wrote:

Hi,

I got the same problem. It says

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to write data to BAM schedule file.
	at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.write(BAMSchedule.java:311)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.<init>(BAMSchedule.java:150)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:263)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:170)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.populateFilteredIntervalList(BAMScheduler.java:99)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.createOverMappedReads(BAMScheduler.java:62)
	at org.broadinstitute.sting.gatk.datasources.reads.IntervalSharder.shardOverMappedReads(IntervalSharder.java:54)
	at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.createShardIteratorOverMappedReads(SAMDataSource.java:1180)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:450)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:230)
	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
Caused by: java.io.IOException: No space left on device
	at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.write(Unknown Source)
	at sun.nio.ch.IOUtil.writeFromNativeBuffer(Unknown Source)
	at sun.nio.ch.IOUtil.write(Unknown Source)
	at sun.nio.ch.FileChannelImpl.write(Unknown Source)
	at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.write(BAMSchedule.java:306)
	... 13 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version exported):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Unable to write data to BAM schedule file.
##### ERROR ------------------------------------------------------------------------------------------

Any suggestions?

Thanks a lot,

ADD COMMENT • link written 4.1 years ago by liyingcai2014 • 10

Great way to post a problem, thanks!

For others that may post GATK tool errors in the future - note the most important bits at the end. The section with lines like:

##### ERROR

And especially this one:

##### ERROR MESSAGE:

Are most often the first clue to what is going on. A google or search at the GATK website will tell you about the problem and potential causes. These are generally parameter/input issues, not true Galaxy errors. A different error output is written that is not in GATK format (in nearly all cases) if there is the rare cluster issue or such.

Thanks! Jen, Galaxy team

ADD REPLY • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

4.1 years ago by

gou.gou1217 • 30

China

gou.gou1217 • 30 wrote:

Did you set mapping quality >=10 when you did variant calling? I found it works when i don't set this while there is this error when i do. As i do need to control mapping quality when i do variant calling, i downloaded the last bam file(after mark duplicates), converted it into sam file, filtered reads with mapping quality samller than 10 and then coverted the sam file back to bam file. Then i uploaded the file to Galaxy and redo the variant calling. It worked. Hope it will be useful to you.

Shaohuan

ADD COMMENT • link written 4.1 years ago by gou.gou1217 • 30

Normally mapping quality lower threshold is 10. you can set a higher value in order to control lower false positive rates, but it
will also filter some false negatives.

ADD REPLY • link written 4.1 years ago by gou.gou1217 • 30

Thanks a lot. I actually found when I increased the value of mapping quality control, it got through. Is it alright to make the value bigger? I suspect my seq data is to big.

Best,

ADD REPLY • link written 4.1 years ago by liyingcai2014 • 10

Normally mapping quality lower threshold is 10. you can set a higher value in order to control lower false positive rates, but it
will also filter some false negatives.

ADD REPLY • link written 4.1 years ago by gou.gou1217 • 30

4.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There is most likely a problem with the format of the inputs. Check lower in the error report - GATK tools generally provide an explanation of the exact format error to correct. Click on the bug icon to see the full error report and/or on the "i" info button then examine the stderr/stdout. You can review the contents of a bug report without submitting it. Often more feedback isn't needed, and bug reporting is not supported on all Galaxy instances (the administrator that runs the instance determines this).

Best, Jen, Galaxy team

ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

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