Tagged with #nullpointerexception
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Created 2016-03-28 19:09:47 | Updated 2016-03-28 19:10:59 | Tags: picard nullpointerexception samtofastq

Comments (7)

Hello,

When running Picard's SamToFastq with OUTPUT_PER_RG=T on a bam file without read group information, you get the following error:

Exception in thread "main" java.lang.NullPointerException
        at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:148)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:119)

Obviously the command shouldn't work if there is no read group information, but it would be nice if there was a more informative error provided, as the NullPointerException makes it seem like an issue with memory allocation.


Created 2016-03-23 09:33:06 | Updated | Tags: depthofcoverage nullpointerexception runtime-error

Comments (7)

Hi, I'm getting a nullpointerexception when trying to run the depthofcoverage tool. The stack trace is as follows:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.NullPointerException
        at java.util.TreeMap.compare(TreeMap.java:1290)
        at java.util.TreeMap.put(TreeMap.java:538)
        at java.util.TreeSet.add(TreeSet.java:255)
        at org.broadinstitute.gatk.utils.sam.ReadUtils.getSAMFileSamples(ReadUtils.java:70)
        at org.broadinstitute.gatk.engine.samples.SampleDBBuilder.addSamplesFromSAMHeader(SampleDBBuilder.java:66)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeSampleDB(GenomeAnalysisEngine.java:846)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:296)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version nightly-2016-03-23-g4d8dc3c):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, 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: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

and the command is called as follows:

java -jar $HOME/software/gatk/nightly_build/GenomeAnalysisTK.jar \
-T DepthOfCoverage \
-R $ref \
-I $bam \
-o $SUBMITDIR/output/seqdepth_s1t

Where $bam is a path pointing to an accepted_hits.sorted.bam aligned using HISAT2. It's directory also contains the bam index (note that I do get a warning stating that my index is older than my bam file). $ref is an ensembl sequence .fasta file

I've tried running the latest stable release and the latest nightly build, both give errors. For what it's worth, GATK should have read/write permissions to the specified output path and the path of the bam-file, but not in the directory holding the reference, could that cause a problem or is it something else? Also, it's run on a cluster using slurm, if that's of any relevance.

Thanks in advance. -Jonas


Created 2015-03-26 16:03:02 | Updated | Tags: bam picard nullpointerexception fixmateinformation

Comments (3)

Hello,

I was asked to re-post this question here. It was originally posted in the Picard forum at GitHub at https://github.com/broadinstitute/picard/issues/161.

Regards,

Bernt


ORIGINAL POST (edited)

There seems to be a problems with FixMateInformation crashing with

Exception in thread "main" java.lang.``````NullPointerException``````
at htsjdk.samtools.SamPairUtil.setMateInformationOnSupplementalAlignment(SamPairUtil.java:300)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.advance(SamPairUtil.java:442)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:454)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:360)
at picard.sam.FixMateInformation.doWork(FixMateInformation.java:194)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:125)
at picard.sam.FixMateInformation.main(FixMateInformation.java:93)

The problem first appeared in version 1.121. It is present in version 1.128. Versions prior to 1.120 worked and continue to work fine. I am currently using Java 1.7.0_75, but I observed the same problem with earlier version of Java. The problem occurs under several different version of Fedora.

The command lines I am using are:

java -jar picard-1.128/picard.jar FixMateInformation INPUT=test.bam OUTPUT=fixed.bam (fails)

java -jar picard-1.121/FixMateInformation.jar INPUT=test.bam OUTPUT=fixed.bam (fails)

java -jar picard-1.120/FixMateInformation.jar INPUT=test.bam OUTPUT=fixed.bam (succeeds)

I have observed the problem with various BAM files. This one is (a small subset of) the output of an indel realignment with GATK.


Later in the same thread:

ValidateSam produces: java -jar /opt/ghpc/picard-1.121/ValidateSamFile.jar INPUT=test.bam OUTPUT=out.bam [Wed Feb 18 08:48:40 CET 2015] picard.sam.ValidateSamFile INPUT=test.bam OUTPUT=out.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Feb 18 08:48:40 CET 2015] Executing as bernt@interactive.ghpc.dk on Linux 2.6.35.14-106.fc14.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.121(da291b4d265f877808b216dce96eaeffd2f30bd3_1411396652) IntelDeflater [Wed Feb 18 08:48:41 CET 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=505937920 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp


And later:

The problem also exists in the new version, 1.129.


New

Re-posted in GATK forum

Picard (1.129)'s ValidateSamFile complains about Mate not found - which was the reason for running FixMateInformation in the first place.

The output is:

java -jar /opt/ghpc/picard-current/picard.jar ValidateSamFile I=test.bam

[Thu Mar 26 16:44:49 CET 2015] picard.sam.ValidateSamFile INPUT=test.bam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Mar 26 16:44:49 CET 2015] Executing as bernt@interactive.ghpc.dk on Linux 2.6.35.14-106.fc14.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.129(b508b2885562a4e932d3a3a60b8ea283b7ec78e2_1424706677) IntelDeflater
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2215:5439:78978, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1216:7853:25411, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2301:9078:52020, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:18417:29553, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2310:18752:24451, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2310:6551:24766, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1105:9672:78339, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2112:20003:44801, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2213:8473:74864, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2306:11852:94726, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1110:11106:17369, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2215:12401:47072, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:13964:14859, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1312:3886:41184, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:12827:34659, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1107:18908:98983, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1313:7640:45146, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1306:1595:15034, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2209:2036:47281, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1201:6826:100382, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2213:4861:63517, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:10202:63100, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1207:7125:93640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1101:9691:36089, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2211:1839:100174, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:7331:16518, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2303:13396:44533, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1103:15274:86897, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2110:1541:39614, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:10320:20874, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:12084:25830, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2115:6231:35664, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1106:5365:6728, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1201:5887:87680, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1204:9449:99890, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2207:6920:91927, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1113:17505:78862, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2311:19423:17546, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2303:6787:39570, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1116:6350:25293, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1305:15016:58323, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1116:10894:97830, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2306:13179:38191, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1301:11303:99731, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:13726:37821, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:11652:76919, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1208:4895:32748, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1106:9371:79983, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:1798:22917, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1107:1267:20231, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:15189:92031, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2302:9045:63944, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1102:14247:57062, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:7407:36655, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:12584:72228, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1111:18302:40904, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2316:8382:94789, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2109:12845:82338, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:10557:31568, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2210:14790:11210, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1303:7824:5423, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:9909:100689, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2202:16293:94205, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1102:16519:74708, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1305:10365:69588, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:8288:100810, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1311:17645:65928, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:17819:68329, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2206:3160:52730, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1112:18820:52584, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1108:4475:4687, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2205:7334:35631, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2106:9384:64665, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2316:12960:78271, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1104:3451:71528, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2211:21055:28695, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2202:13814:96357, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:17147:10853, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2106:20520:88043, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1214:2637:77724, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:9367:35640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1215:11379:23758, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1304:17507:91188, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:12459:100042, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2216:8585:77239, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1313:12667:24591, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1316:10367:5281, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1315:15333:2359, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:5534:7650, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:4820:93659, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:6528:72676, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:7297:76200, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1315:5361:88165, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:17200:26640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1302:2356:100479, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1101:3217:24975, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2314:1898:42432, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1316:5424:4897, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:16620:81246, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:15822:17446, Mate not found for paired read
Maximum output of [100] errors reached.
[Thu Mar 26 16:44:50 CET 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=505937920
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Please let me know where to send the test BAM file.

Regards,

Bernt


Created 2014-09-04 21:45:51 | Updated 2014-09-04 21:50:59 | Tags: haplotypecaller nullpointerexception

Comments (17)

Hi,

I encountered a NullPointerException in 3.2-2 using the HaplotypeCaller on a BAM that run just fine on 3.1. Here is the stack trace:

java.lang.NullPointerException at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:421) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:395) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.calculateGLsForThisEvent(HaplotypeCallerGenotypingEngine.java:421) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:257) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:941) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)

And here are the program args:

Program Args: -T HaplotypeCaller -R human_genome/human_g1k_v37.fasta -I <my_bam> -ERC GVCF -nct 16 --dbsnp /tmp/4437712/dbsnp_135.b37.vcf --variant_index_type LINEAR --variant_index_parameter 128000 -o /tmp/4437712/<my_sample>.vcf.gz

Let me know if you need more info.


Created 2014-02-23 15:23:48 | Updated | Tags: variantrecalibrator nullpointerexception gatk-walkers

Comments (1)

Hi there,

I've a problem running GATK2.8's VariantRecalibrator, I get Code Exception (java.lang.NullPointerException). Below is the error trace:

INFO 17:05:37,528 GenomeAnalysisEngine - Preparing for traversal INFO 17:14:27,706 VariantDataManager - MQRankSum: mean = -0.09 standard deviation = 0.99 INFO 17:14:27,742 VariantDataManager - ReadPosRankSum: mean = 0.18 standard deviation = 0.96 INFO 17:14:27,820 VariantDataManager - Annotations are now ordered by their information content: [QD, ReadPosRankSum, MQRankSum] INFO 17:14:27,823 VariantDataManager - Training with 2739 variants after standard deviation thresholding. INFO 17:14:27,829 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 17:14:28,389 VariantRecalibratorEngine - Finished iteration 0. INFO 17:14:28,534 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.20522 INFO 17:14:28,601 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46290 INFO 17:14:28,675 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.95604 INFO 17:14:28,759 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 9.00456 INFO 17:14:28,861 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01190 INFO 17:14:28,951 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00796 INFO 17:14:29,041 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00546 INFO 17:14:29,131 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00360 INFO 17:14:29,221 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00218 INFO 17:14:29,239 VariantRecalibratorEngine - Convergence after 46 iterations! INFO 17:14:29,276 VariantRecalibratorEngine - Evaluating full set of 13495 variants... INFO 17:14:29,280 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000. INFO 17:14:32,024 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:359) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:139) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

And this is the command i used:

java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx4g -jar ~/genomekey-data/tools/gatk2.jar -T VariantRecalibrator -R ~/genomekey-data/bwa_references/human_g1k_v37.fasta -input ~/simplex/ngs_test/snp_calling/aln.haplotyper.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 ~/genomekey-data/bundle/current/dbsnp_137.b37.vcf -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 ~/genomekey-data/bundle/current/hapmap_3.3.b37.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 ~/genomekey-data/bundle/current/1000G_omni2.5.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -recalFile ~/simplex/ngs_test/snp_recal/aln.snp.recal -tranche 100 -tranche 99.9 -tranche 99.0 -tranche 90 -tranchesFile ~/simplex/ngs_test/snp_recal/aln.snp.tranches -rscriptFile ~/simplex/ngs_test/snp_recal/aln.snp.plots.R -mode SNP

Please note that i got the same error running GATK 2.6. Any help or suggestions will be appreciated.

Thanks, Shazly


Created 2013-12-31 03:59:15 | Updated | Tags: variantrecalibration nullpointerexception

Comments (3)

I am following the GATK best practices workflow on Linux. I am using chr21.fa as reference from NCBI and .vcf files are taken from resource bundle and dbsnp.vcf is from NCBI. I am working on the VariantRecalibrator step. It gives me NullPointerException. I am attaching the console error that I have got which contains the command also and raw_variants.vcf which is generated in previous step by HaplotypeCaller tool in txt format. Please let me know what can be the issue.


Created 2013-10-27 23:57:57 | Updated | Tags: haplotypecaller nullpointerexception likelihoodcalculationengine

Comments (22)

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:379) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:353) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.calculateGLsForThisEvent(GenotypingEngine.java:338) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:205) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:778) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:140) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:724)

Program Args: -nct 5 -T HaplotypeCaller -R ../ref/ref.fa -L chr10 -I <48 bam files> -o chr10.raw.vcf


Created 2012-11-22 15:48:43 | Updated 2012-11-22 15:49:11 | Tags: unifiedgenotyper queue qscript nullpointerexception

Comments (2)

I'm building a variant calling qscript (it's available here), heavily based on the the MethodsDevelopmentCallingPipeline.scala. I cannot however run into trouble when setting the "this.scatterCount" of the GenotyperBase to more than 1 - in which case I get a NullPointerException (I include the full error message below).

I use the following command line:

java -Djava.io.tmpdir=tmp -jar dist/Queue.jar -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/NewVariantCalling.scala -i NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -R /bubo/nobackup/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.2/b37/human_g1k_v37.fasta -res /bubo/nobackup/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.2/b37/ **-sg 2** -nt 8 -run -l DEBUG -startFromScratch

As you can see, I'm using the files from the gatk bundle, and I guess these should be alright for this purpose? Just to be clear I use the "-res" parameter to point to the directory where all the resource files are located, dbsnp, hapmap, etc. and the -sg parameter is what controls the scatter/gather count.

I've tried to search in the code for what might be causing this, and I can conclude that the org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc is called with str (its parameter) being an empty string, which is what causes contig to be null, which in turn creates the NullPointerException on line 408 when this line is executed: stop = getContigInfo(contig).getSequenceLength();

This, I guess, is the obvious stuff, but this far I haven't been able to figure this out any further that this. I'm not sure if this is caused by a bug in my script, or by a bug in the GATK. Right now I'm thinking the latter of the two, since I have used the scatter/gather function in other scripts without any trouble.

Any ideas of where to continue from here, or confirmation that this is indeed something related to the GATK code would be much appreciated.

Cheers, Johan

ERROR 16:22:50,781 FunctionEdge - Error: LocusScatterFunction: List(/bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam.bai, /bubo/nobackup/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.2/b37/dbsnp_137.b37.vcf, /bubo/nobackup/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.2/b37/human_g1k_v37.fasta, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bai, /bubo/nobackup/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.2/b37/dbsnp_137.b37.vcf.idx, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam) > List(/bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/.queue/scatterGather/.qlog/project.snpcall-sg/temp_1_of_2/scatter.intervals, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/.queue/scatterGather/.qlog/project.snpcall-sg/temp_2_of_2/scatter.intervals) 
java.lang.NullPointerException
        at org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:408)
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:84)
        at org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:97)
        at org.broadinstitute.sting.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:538)
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:520)
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalBindings(IntervalUtils.java:499)
        at org.broadinstitute.sting.queue.extensions.gatk.GATKIntervals.locs(GATKIntervals.scala:60)
        at org.broadinstitute.sting.queue.extensions.gatk.LocusScatterFunction.run(LocusScatterFunction.scala:39)
        at org.broadinstitute.sting.queue.engine.InProcessRunner.start(InProcessRunner.scala:28)
        at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:83)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:432)
        at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:154)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:145)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

Created 2012-09-05 23:34:52 | Updated 2013-01-07 20:43:29 | Tags: phasebytransmission error nullpointerexception

Comments (16)

Hi all,

Has anyone else gotten the following:

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:306) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:35) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) 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:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

My command line was: java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -f "mom+dad=child" -R hg19.fa

Cheers,

Paul