Question: running of Unified Genotyper encounters error
0
gravatar for pes1217
4.0 years ago by
pes121740
China
pes121740 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 • 1.3k views
ADD COMMENTlink modified 3.9 years ago by gou.gou121730 • written 4.0 years ago by pes121740
1
gravatar for liyingcai2014
3.9 years ago by
China
liyingcai201410 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,

Yi

ADD COMMENTlink written 3.9 years ago by liyingcai201410

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 REPLYlink written 3.9 years ago by Jennifer Hillman Jackson25k
1
gravatar for gou.gou1217
3.9 years ago by
gou.gou121730
China
gou.gou121730 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 COMMENTlink written 3.9 years ago by gou.gou121730
1

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 REPLYlink written 3.9 years ago by gou.gou121730

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,

Yi

ADD REPLYlink written 3.9 years ago by liyingcai201410
1

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 REPLYlink written 3.9 years ago by gou.gou121730
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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