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MuTect error
uthrabalaji
DALLASMember ✭
Hi,
I am running MuTect version 1.14 and I get the following error
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to create iterator for rod named cosmic
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:247)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:184)
at org.broadinstitute.sting.gatk.datasources.rmd.ResourcePool.iterator(ResourcePool.java:92)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:167)
at org.broadinstitute.sting.gatk.datasources.providers.ManagingReferenceOrderedView.(ManagingReferenceOrderedView.java:42)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:61)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:73)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)
Caused by: java.io.IOException: Invalid argument
at java.io.FileInputStream.readBytes(Native Method)
at java.io.FileInputStream.read(FileInputStream.java:239)
at org.broad.tribble.util.SeekableFileStream.read(SeekableFileStream.java:83)
at org.broad.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.read(TribbleIndexedFeatureReader.java:405)
at java.io.InputStream.read(InputStream.java:101)
at org.broad.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:141)
at org.broad.tribble.readers.PositionalBufferedStream.peek(PositionalBufferedStream.java:132)
at org.broad.tribble.readers.PositionalBufferedStream.isDone(PositionalBufferedStream.java:116)
at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:316)
at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.(TribbleIndexedFeatureReader.java:258)
at org.broad.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:128)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack.query(RMDTrack.java:117)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:240)
... 12 more
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
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 website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Unable to create iterator for rod named cosmic
ERROR ------------------------------------------------------------------------------------------
I read somewhere to try a different version of GATK for a similar error. I am not sure how I can change the versions of GATK. I have GATK-2.6 and GATK-3.3.0 both installed. I apologize if this is a very basic question. I would appreciate any input on how to get past this error.
Thanks in advance for all the help,
Uthra
Best Answer
-
Geraldine_VdAuwera
Cambridge, MA admin
@uthrabalaji Actually you can just download the latest version of MuTect (1.1.7) from our Downloads page.
Answers
@uthrabalaji
Hi Uthra,
You can either delete the old versions of GATK you have installed, or you can simply specify the correct GATK version to use in your path.
It looks like you are using version 2.2 which is quite outdated.
-Sheila
@uthrabalaji Actually you can just download the latest version of MuTect (1.1.7) from our Downloads page.
@Sheila and @Geraldine_VdAuwera : Thank you for the immediate respond. I really appreciate that.
@Geraldine_VdAuwera : I downloaded muTect (1.1.7) and it seems to work fine for now. And I also noticed that it used GATK - 3.1 version.
However muTect 1.1.7 does not let me use -nt to give the number of cores to use. Is there any other way to speed up the process using this version of muTect. The reason I am asking is I have about 30 files to run MuTect on and I am looking for an efficient way of doing this. Thank you again for all your input!
We prefer to use scatter-gather parallelism on a cluster rather than use multithreading. It is more reliable and can be very fast.