Mysterious Funcotator issue

Answered

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Robert Bremel

• May 21, 2021 01:22

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:

Docker 4.2.0

b) Exact command used:

./gatk Funcotator -R mydata/refs/Homo_sapiens_assembly38.fasta -V mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_filtered_hg38.vcf -O mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_funcotator_hg38.maf --output-file-format MAF --data-sources-path mydata/dataSourcesFolder/funcotator_dataSources.v1.6.20190124s/ --verbosity ERROR --ref-version hg38
c) Entire error log:

docker exec PAAD_00034_HeuristicJaguar_funky_gatk ./gatk Funcotator
-R mydata/refs/Homo_sapiens_assembly38.fasta
-V mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_filtered_hg38.vcf
-O mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_funcotator_hg38.maf
--output-file-format MAF
--data-sources-path mydata/dataSourcesFolder/funcotator_dataSources.v1.6.20190124s/
--verbosity ERROR
--ref-version hg38

21:05:56.448 ERROR GencodeFuncotationFactory -
Problem creating a GencodeFuncotation on transcript ENST00000467404.6 for variant: chr1:6785517-6785520(CGAG* -> C):
Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case.
Transcript: ENST00000467404.6
Variant: [VC Unknown @ chr1:6785517-6785520 Q. of type=INDEL alleles=[CGAG*, C] attr={AS_FilterStatus=SITE, AS_SB_TABLE=[99, 74|3, 3], DP=184, ECNT=1, GERMQ=93, MBQ=[20, 20], MFRL=[140, 137], MMQ=[60, 60], MPOS=41, NALOD=1.02, NLOD=2.71, POPAF=6.00, RPA=[4, 3], RU=GAG, STR=true, STRQ=1, TLOD=10.52} GT=GT:AD:AF:DP:F1R2:F2R1:SB 0/0:15,0:0.088:15:8,0:7,0:9,6,0,0 0/1:158,6:0.041:164:50,4:100,2:90,68,3,3 filters=slippage
[May 20, 2021 9:08:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 8.04 minutes.
Runtime.totalMemory()=5592055808
java.lang.StringIndexOutOfBoundsException: String index out of range: 421
at java.lang.String.substring(String.java:1963)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.initializeForInsertion(ProteinChangeInfo.java:256)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.<init>(ProteinChangeInfo.java:93)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.create(ProteinChangeInfo.java:371)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSequenceComparison(GencodeFuncotationFactory.java:2054)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotationForProteinCodingFeature(GencodeFuncotationFactory.java:1235)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createExonFuncotation(GencodeFuncotationFactory.java:1086)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnSingleTranscript(GencodeFuncotationFactory.java:1020)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:847)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:831)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:508)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:509)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:564)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:243)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:147)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:907)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:861)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/gatk-package-4.2.0.0-local.jar

 

EMBEDDED in vcf file itself

 

GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_filtered_hg38.vcf --stats mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_unfiltered_hg38.vcf.stats --variant mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_unfiltered_hg38.vcf --reference mydata/refs/Homo_sapiens_assembly38.fasta --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.2.0.0",Date="May 20, 2021 8:01:52 PM GMT">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --normal-sample PAAD_00034-72324_DN_HeuristicJaguar --output mydata/PAAD_00034_HeuristicJaguar/analysis/PAAD_00034-944f1_DT_HeuristicJaguar_mutect2_unfiltered_hg38.vcf --intervals mydata/refs/hg38_exons.interval_list --interval-padding 30 --input mydata/PAAD_00034_HeuristicJaguar/bsqr/PAAD_00034-944f1_DT_HeuristicJaguar_Tbwa_dedup_bsqr_hg38.bam --input mydata/PAAD_00034_HeuristicJaguar/bsqr/PAAD_00034-72324_DN_HeuristicJaguar_Nbwa_dedup_bsqr_hg38.bam --reference mydata/refs/Homo_sapiens_assembly38.fasta --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --max-read-length 2147483647 --min-read-length 30 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.2.0.0",Date="May 20, 2021 2:55:04 PM GMT">

Tried:

1. Checked, have used 4.2.0 about two weeks ago with same workflow, worked fine
2. Deleted the the line in the .vcf that ostensibly triggered the string index error and re-indexed -- same error, but no ENST flagged?
3. Used the unfiltered version of same file -- same string index 421 error at same ENST
4. ran ValidateVariants --  OK  (with minimal arguments)
5. can send .vcf if that helps (can't see how to attach to this query)

 

 

 

 

Ostensible offending line in vcf

 

chr1 6785517 . CGAG C . slippage AS_FilterStatus=SITE;AS_SB_TABLE=99,74|3,3;DP=184;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=140,137;MMQ=60,60;MPOS=41;NALOD=1.02;NLOD=2.71;POPAF=6.00;RPA=4,3;RU=GAG;STR;STRQ=1;TLOD=10.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:15,0:0.088:15:8,0:7,0:9,6,0,0 0/1:158,6:0.041:164:50,4:100,2:90,68,3,3

 

 

0

• 

  Genevieve Brandt (she/her)

  • May 25, 2021 20:51

  Hi Robert Bremel,

  There is an issue with the Funcotator data sources 1.6 and we are recommending that users do not use these data sources. Here is the issue ticket for more information: https://github.com/broadinstitute/gatk/issues/7265

  Could you try with the 1.7 data sources and then paste your stack trace again if you get the same issue?

  Thank you,

  Genevieve

  0

  Comment actions Permalink
• 

  Robert Bremel

  • May 25, 2021 22:23

  Thanks Genevieve, 

  I will download and install the 1.7 data sources. 

  I thought I was really up to date using 1.6 as 1.2 is in your examples. 

  I found a workaround that I could remove two lines from the .vcf  -- the ostensible offending one and the next one then it worked okay.  I will get around to do a test in the next week or so. 

  _Bob

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • May 26, 2021 03:32

  Hi Bob,

  I was looking at this with my coworker and found that I was actually mistaken, the issue is only with the germline 1.6 resources and not the somatic 1.6 resources. So the resources are not the issue here!

  It looks like you have found another example of this known GATK issue: https://github.com/broadinstitute/gatk/issues/6651. If you want to help out our dev team, you can comment on that issue ticket and provide test data if necessary. Your workaround seems like the best idea as of now, but hopefully we will be able to get a fix for this bug soon!

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Robert Bremel

  • May 26, 2021 12:45

  Thanks again Genevieve,

  I think I have stashed the offending lines somewhere I will see if I can find them.  It was a really unusual indel with three TLOD values each of which was mapping perhaps an indel 100nt in length, so I thought the line length limit may have made sense.  

  Looks like I am having unlucky streak.  We live in a rural area so I set about downloading the v1.7 overnight.  It almost finished?  No evidence of the files anywhere.  I was downloading to an SSD mapped as a docker volume

  Seems as though it almost finished and then things vanished?

   

  _Bob

   

  ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

  03:56:45.563 INFO NioFileCopierWithProgressMeter - Transfer: 87.50% complete. Est. time remaining: 46:19.537 (@1413.35 kbps)

  03:57:45.773 INFO NioFileCopierWithProgressMeter - Transfer: 87.75% complete. Est. time remaining: 45:51.935 (@1399.24 kbps)

  03:58:42.348 INFO NioFileCopierWithProgressMeter - Transfer: 88.00% complete. Est. time remaining: 45:01.062 (@1396.40 kbps)

  03:59:38.357 INFO NioFileCopierWithProgressMeter - Transfer: 88.25% complete. Est. time remaining: 44:07.781 (@1394.73 kbps)

  04:00:33.141 INFO NioFileCopierWithProgressMeter - Transfer: 88.50% complete. Est. time remaining: 43:09.865 (@1395.47 kbps)

  04:01:28.669 INFO NioFileCopierWithProgressMeter - Transfer: 88.75% complete. Est. time remaining: 42:14.593 (@1395.20 kbps)

  04:02:03.698 INFO FuncotatorDataSourceDownloader - Shutting down engine

  [May 26, 2021 4:02:03 AM GMT] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 336.46 minutes.

  Runtime.totalMemory()=1351090176

  code: 0

  message: All 0 reopens failed. Waited a total of 0 ms between attempts

  reason: null

  location: null

  retryable: false

  com.google.cloud.storage.StorageException: All 0 reopens failed. Waited a total of 0 ms between attempts

  at com.google.cloud.storage.contrib.nio.CloudStorageRetryHandler.handleReopenForStorageException(CloudStorageRetryHandler.java:156)

  at com.google.cloud.storage.contrib.nio.CloudStorageRetryHandler.handleStorageException(CloudStorageRetryHandler.java:119)

  at com.google.cloud.storage.contrib.nio.CloudStorageReadChannel.handleStorageException(CloudStorageReadChannel.java:272)

  at com.google.cloud.storage.contrib.nio.CloudStorageReadChannel.read(CloudStorageReadChannel.java:162)

  at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)

  at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)

  at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)

  at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)

  at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)

  at java.io.BufferedInputStream.read(BufferedInputStream.java:345)

   

  etc.....

   

   

   

   

   

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• 

  Genevieve Brandt (she/her)

  • May 26, 2021 17:20

  In the beginning of the log when GATK starts up, could you share the line that looks like this?

  GCS max retries/reopens: X

  Was your command exactly this? gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

  0

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• 

  Robert Bremel

  • May 26, 2021 19:27

  Hi,

  I copied it from the Funcotator webpage,  Just to be clear -- I am running the Docker version in Docker Desktop on a Windows 10 workstation.  The workstation has 128 GB memory and I believe Docker grabs about 100 GB at the outset and commandeers more if needed.

  This is all I see when I start up an interactive shell 

  
  PS C:\Users\Owner> docker run -v G:/gatk_dock:/gatk/mydata -it broadinstitute/gatk:latest
  (gatk) root@6d4d08142dae:/gatk#

   

  Here is the header from the download

  There is a line in it 

  GCS max retries/reopens: 20

  there is 250 GB free space on the SSD where mydata lives

  What struck me as a little puzzling is that is wasn't clear where the file was to go.  The dataSourcesFolder with v1.6 is in the mydata directory.  Is it to be overwritten?

   

  Using GATK jar /gatk/gatk-package-4.2.0.0-local.jar

  Running:

  java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.2.0.0-local.jar FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

  22:25:36.350 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

  May 25, 2021 10:25:36 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

  INFO: Failed to detect whether we are running on Google Compute Engine.

  22:25:36.603 INFO FuncotatorDataSourceDownloader - ------------------------------------------------------------

  22:25:36.603 INFO FuncotatorDataSourceDownloader - The Genome Analysis Toolkit (GATK) v4.2.0.0

  22:25:36.603 INFO FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/

  22:25:36.604 INFO FuncotatorDataSourceDownloader - Executing as root@d61b3408e462 on Linux v5.4.72-microsoft-standard-WSL2 amd64

  22:25:36.604 INFO FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08

  22:25:36.604 INFO FuncotatorDataSourceDownloader - Start Date/Time: May 25, 2021 10:25:36 PM GMT

  22:25:36.605 INFO FuncotatorDataSourceDownloader - ------------------------------------------------------------

  22:25:36.605 INFO FuncotatorDataSourceDownloader - ------------------------------------------------------------

  22:25:36.606 INFO FuncotatorDataSourceDownloader - HTSJDK Version: 2.24.0

  22:25:36.606 INFO FuncotatorDataSourceDownloader - Picard Version: 2.25.0

  22:25:36.606 INFO FuncotatorDataSourceDownloader - Built for Spark Version: 2.4.5

  22:25:36.606 INFO FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2

  22:25:36.606 INFO FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

  22:25:36.606 INFO FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

  22:25:36.606 INFO FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

  22:25:36.606 INFO FuncotatorDataSourceDownloader - Deflater: IntelDeflater

  22:25:36.606 INFO FuncotatorDataSourceDownloader - Inflater: IntelInflater

  22:25:36.607 INFO FuncotatorDataSourceDownloader - GCS max retries/reopens: 20

  22:25:36.607 INFO FuncotatorDataSourceDownloader - Requester pays: disabled

  22:25:36.607 INFO FuncotatorDataSourceDownloader - Initializing engine

  22:25:36.607 INFO FuncotatorDataSourceDownloader - Done initializing engine

  22:25:36.607 INFO FuncotatorDataSourceDownloader - Somatic data sources selected.

  22:25:36.618 INFO FuncotatorDataSourceDownloader - Collecting expected checksum...

  22:25:38.605 INFO FuncotatorDataSourceDownloader - Collection complete!

  22:25:38.754 INFO NioFileCopierWithProgressMeter - Initiating copy from gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521s.tar.gz to file:///gatk/funcotator_dataSources.v1.7.20200521s.tar.gz

  22:25:38.754 INFO NioFileCopierWithProgressMeter - File size: 32188531109 bytes (29 GB).

  22:25:38.754 INFO NioFileCopierWithProgressMeter - Please wait. This could take a while...

  22:26:34.409 INFO NioFileCopierWithProgressMeter - Transfer: 0.25% complete. Est. time remaining: 06:09:40.684 (@1413.63 kbps)

  22:27:28.572 INFO NioFileCopierWithProgressMeter - Transfer: 0.50% complete. Est. time remaining: 06:03:25.201 (@1434.36 kbps)

  22:28:24.809 INFO NioFileCopierWithProgressMeter - Transfer: 0.75% complete. Est. time remaining: 06:05:14.546 (@1423.60 kbps)

  22:29:20.546 INFO NioFileCopierWithProgressMeter - Transfer: 1.00% complete. Est. time remaining: 06:06:05.297 (@1416.77 kbps)

  22:30:20.601 INFO NioFileCopierWithProgressMeter - Transfer: 1.25% complete. Est. time remaining: 06:10:35.585 (@1396.00 kbps)

  22:31:16.326 INFO NioFileCopierWithProgressMeter - Transfer: 1.50% complete. Est. time remaining: 06:08:49.045 (@1399.16 kbps)

  22:32:12.392 INFO NioFileCopierWithProgressMeter - Transfer: 1.75% complete. Est. time remaining: 06:07:36.457 (@1400.19 kbps)

  22:33:07.357 INFO NioFileCopierWithProgressMeter - Transfer: 2.00% complete. Est. time remaining: 06:06:10.094 (@1402.15 kbps)

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • May 27, 2021 03:39

  Hi Bob,

  It looks like that command line is fine, though you can specify a specific location for the data resources with the --output argument. The download issue is most likely a spurious connection issue and so you can re-try without changing anything in your command. You could though specify a larger number for the --gcs-max-retries, the default is 20.

  Let me know what you find,

  Genevieve

  0

  Comment actions Permalink
• 

  yinxiu Zhan

  • February 23, 2023 11:03

  Hey there,

  I was wondering whether a solution was found to overcome this problem of GencodeFuncotationFactory. I am experiencing the same problem and deleting the variant works but it's not ideal as I would like to have the variant annotated but without gencode part.

  Just to be more precise:

  gatk4 version 4.3.0.0-0

  Command: 

  gatk Funcotator             -L /hpcnfs/scratch/temporary/vcf_xzhan/WG00333_v2.20181024.designed.bed             -R /hpcnfs/scratch/temporary/gvozza_030223/hg19/hg19.fasta             -V file.vcf.gz             -O GERS01ON9S-1N.maf             --annotation-default Matched_Norm_Sample_Barcode:GERS01ON9S-1N             --remove-filtered-variants true             --output-file-format MAF             --data-sources-path /hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g            --ref-version hg19

  Log:

  Using GATK jar /opt/conda/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar

  Running:

      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /opt/conda/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Funcotator -L /hpcnfs/scratch/temporary/vcf_xzhan/WG00333_v2.20181024.designed.bed -R /hpcnfs/scratch/temporary/gvozza_030223/hg19/hg19.fasta -V file.vcf.gz -O GERS01ON9S-1N.maf --annotation-default Matched_Norm_Sample_Barcode:GERS01ON9S-1N --remove-filtered-variants true --output-file-format MAF --data-sources-path /hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g --ref-version hg19

  10:30:35.622 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

  10:30:35.816 INFO  Funcotator - ------------------------------------------------------------

  10:30:35.816 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.3.0.0

  10:30:35.816 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/

  10:30:35.816 INFO  Funcotator - Executing as ieo6129@cn01.cluster.loc on Linux v3.10.0-1160.el7.x86_64 amd64

  10:30:35.816 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+7-b1751.21

  10:30:35.817 INFO  Funcotator - Start Date/Time: February 23, 2023 at 10:30:35 AM UTC

  10:30:35.817 INFO  Funcotator - ------------------------------------------------------------

  10:30:35.817 INFO  Funcotator - ------------------------------------------------------------

  10:30:35.817 INFO  Funcotator - HTSJDK Version: 3.0.1

  10:30:35.817 INFO  Funcotator - Picard Version: 2.27.5

  10:30:35.817 INFO  Funcotator - Built for Spark Version: 2.4.5

  10:30:35.817 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2

  10:30:35.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

  10:30:35.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

  10:30:35.818 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

  10:30:35.818 INFO  Funcotator - Deflater: IntelDeflater

  10:30:35.818 INFO  Funcotator - Inflater: IntelInflater

  10:30:35.818 INFO  Funcotator - GCS max retries/reopens: 20

  10:30:35.818 INFO  Funcotator - Requester pays: disabled

  10:30:35.818 INFO  Funcotator - Initializing engine

  10:30:35.978 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/file.vcf.gz

  10:30:36.066 INFO  FeatureManager - Using codec BEDCodec to read file file:///hpcnfs/scratch/temporary/vcf_xzhan/WG00333_v2.20181024.designed.bed

  10:30:36.386 INFO  IntervalArgumentCollection - Processing 2206522 bp from intervals

  10:30:36.393 INFO  Funcotator - Done initializing engine

  10:30:36.393 INFO  Funcotator - Validating sequence dictionaries...

  10:30:36.394 INFO  Funcotator - Processing user transcripts/defaults/overrides...

  10:30:36.394 INFO  Funcotator - Initializing data sources...

  10:30:36.396 INFO  DataSourceUtils - Initializing data sources from directory: /hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g

  10:30:36.410 INFO  DataSourceUtils - Data sources version: 1.7.2020521g

  10:30:36.411 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200521g.tar.gz

  10:30:36.411 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521.tar.gz

  10:30:36.450 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf

  10:30:36.468 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/GCF_000001405.25.gz -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/dbsnp/hg19/GCF_000001405.25.gz

  10:30:37.398 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/acmg_lof.tsv -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg19/acmg_lof.tsv

  10:30:37.426 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/gencode.v34lift37.annotation.REORDERED.gtf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

  10:30:37.427 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/gencode.v34lift37.pc_transcripts.fa -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/gencode/hg19/gencode.v34lift37.pc_transcripts.fa

  10:30:37.443 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/acmg_v3.1_Feb162023_test_cleaned.txt -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg19/acmg_v3.1_Feb162023_test_cleaned.txt

  10:30:37.467 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/clinvar_20230218.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/clinvar/hg19/clinvar_20230218.vcf

  10:30:37.468 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...

  10:30:37.468 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf

  10:30:37.468 INFO  DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000

  10:30:37.494 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf

  10:30:37.532 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf

  10:30:37.543 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf

  10:30:37.549 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/GCF_000001405.25.gz -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/dbsnp/hg19/GCF_000001405.25.gz

  10:30:37.549 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000

  10:30:37.587 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/dbsnp/hg19/GCF_000001405.25.gz

  10:30:37.702 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/GCF_000001405.25.gz -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/dbsnp/hg19/GCF_000001405.25.gz

  10:30:37.751 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/dbsnp/hg19/GCF_000001405.25.gz

  10:30:37.798 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000

  10:30:40.389 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz

  10:30:46.194 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz

  10:30:47.113 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/acmg_lof.tsv -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg19/acmg_lof.tsv

  10:30:47.130 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/gencode.v34lift37.annotation.REORDERED.gtf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

  10:30:47.130 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000

  10:30:47.146 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

  10:30:47.228 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/gencode.v34lift37.pc_transcripts.fa -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/gencode/hg19/gencode.v34lift37.pc_transcripts.fa

  10:30:52.375 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/acmg_v3.1_Feb162023_test_cleaned.txt -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg19/acmg_v3.1_Feb162023_test_cleaned.txt

  10:30:53.085 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/clinvar_20230218.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/clinvar/hg19/clinvar_20230218.vcf

  10:30:53.085 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000

  10:30:56.567 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/clinvar/hg19/clinvar_20230218.vcf

  10:30:57.001 INFO  DataSourceUtils - Resolved data source file path: file:///hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/clinvar_20230218.vcf -> file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/clinvar/hg19/clinvar_20230218.vcf

  10:30:57.219 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/temporary/public_databases/funcotator_dataSources.v1.7.20200521g/clinvar/hg19/clinvar_20230218.vcf

  10:30:57.442 INFO  Funcotator - Initializing Funcotator Engine...

  10:31:01.520 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:

  10:31:01.520 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:

  10:31:01.520 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)

  10:31:01.521 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)

  10:31:01.533 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)

  10:31:01.534 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)

  10:31:01.540 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)

  10:31:01.541 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)

  10:31:01.542 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)

  10:31:01.542 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.

  10:31:01.605 INFO  Funcotator - Creating a MAF file for output: file:/hpcnfs/scratch/temporary/vcf_xzhan/annotations/work/c7/841589ca9177576cd2e0c29cd7e691/GERS01ON9S-1N.maf

  10:31:03.917 INFO  ProgressMeter - Starting traversal

  10:31:03.934 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

  10:31:23.380 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000375071.4_2 for variant: chr1:20915589-20915590(TC* -> T): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000375071.4_2  Variant: [VC Unknown @ chr1:20915589-20915590 Q4390.00 of type=INDEL alleles=[TC*, T] attr={AF=0.500606, AO=407, DP=825, FAO=413, FDP=825, FDVR=0, FR=., FRO=412, FSAF=207, FSAR=206, FSRF=213, FSRR=199, FWDB=0.0862731, FXX=0.00121065, GCM=1, HRUN=3, HS_ONLY=0, LEN=1, MLLD=30.4542, OALT=-, OID=., OMAPALT=T, OPOS=20915590, OREF=C, PB=0.5, PBP=1, PPD=0, QD=21.2849, RBI=0.0864893, REFB=0.0116636, REVB=0.00611137, RO=410, SAF=201, SAR=206, SPD=0, SRF=214, SRR=196, SSEN=0, SSEP=0, SSSB=-0.0257873, STB=0.50788, STBP=0.662, TYPE=del, VARB=-0.0120914} GT=GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:4294:825:825:410:412:407:413:0.500606:206:201:214:196:206:207:213:199 filters=

  10:31:23.405 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000375071.4_2 for problem variant: chr1:20915589-20915590(TC* -> T)

   

  thanks in advance for your help

  Best

  Zhan

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