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Error of INDEL mode during VQSR process

Hello,
I'm trying to do VQSR on exome data of 50,000 samples. Since this dataset is too big, I used GenomicsDBImport to merge. Whole exome merging is also slower than expected, so I did this per chromosome.
SNP mode for VQSR went on smoothly while the INDEL mode has several problems.
I used the command below at first:

```
time $gatk VariantRecalibrator \
-R $reference \
-V $outdir/population/${outname}.HC.snps.VQSR.vcf.gz \
-resource:mills,known=true,training=true,truth=true,prior=12.0 $GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
-an DP -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum\
-mode INDEL \
--max-gaussians 6 \
--rscript-file $outdir/population/${outname}.HC.indels.plots.R \
--tranches-file $outdir/population/${outname}.HC.indels.tranches \
-O $outdir/population/${outname}.HC.snps.indels.recal && \
time $gatk ApplyVQSR \
-R $reference \
-V $outdir/population/${outname}.HC.snps.VQSR.vcf.gz \
--truth-sensitivity-filter-level 99.0 \
--tranches-file $outdir/population/${outname}.HC.snps.indels.tranches \
--recal-file $outdir/population/${outname}.HC.snps.indels.recal \
-mode INDEL \
-O $outdir/population/${outname}.HC.VQSR.vcf.gz && echo "** SNPs and Indels VQSR (${sample}.HC.VQSR.vcf.gz finish) done **"
```
There are two warnings:
WARN VariantDataManager - WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.
WARN VariantRecalibratorEngine - Evaluate datum returned a NaN
And the program stopped due to "No data found"

I searched on this forum for solution and removed "-MQRankSum". The recalibration process passed this time although the first warning is still there:
WARN VariantDataManager - WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.

But the ApplyVQSR process stopped, due to:

```
13:55:06.069 INFO ApplyVQSR - Deflater: IntelDeflater
13:55:06.069 INFO ApplyVQSR - Inflater: IntelInflater
13:55:06.070 INFO ApplyVQSR - GCS max retries/reopens: 20
13:55:06.070 INFO ApplyVQSR - Requester pays: disabled
13:55:06.070 INFO ApplyVQSR - Initializing engine
13:55:06.517 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.recal
13:55:06.593 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.VQSR.vcf.gz
13:55:06.776 INFO ApplyVQSR - Done initializing engine
13:55:06.778 INFO ApplyVQSR - Shutting down engine
[December 11, 2019 1:55:06 PM CET] org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1933574144
***********************************************************************

A USER ERROR has occurred: Couldn't read file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches. Error was: /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches with exception: /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
```

I do not understand what this "exception" is. Could you give me some suggestion on how to solve this?
On the other hand, I know the limitation for VQSR is above 30 exomes, in some cases it is the reason for "No data found" error. Although I did VQSR for each chromosome separately, I think 50,000 samples is enough.
Is there some method to merge these chromosomes together and do the VQSR afterwards?

Thanks!
Shichao

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @mashimaro

    • The `No data found' issue has been solved on this forum multiple times. The forum is always a good place to start to get a better understanding of the commonly occurring issues, you should get some useful threads. :smile:

    • A USER ERROR has occurred: Couldn't read file error seems like the GATK tool is not able to access the files. Are you running this on a shared file system? That could possibly be the reason for such permissions issue. Also which version of GATK are you using? Can you please provide the entire stack trace?

  • mashimaromashimaro GermanyMember
    > @bhanuGandham said:
    > HI @mashimaro
    >
    > * The `No data found' issue has been solved on this forum multiple times. The forum is always a good place to start to get a better understanding of the commonly occurring issues, you should get some useful threads. :smile:
    >
    >
    > * A USER ERROR has occurred: Couldn't read file error seems like the GATK tool is not able to access the files. Are you running this on a shared file system? That could possibly be the reason for such permissions issue. Also which version of GATK are you using? Can you please provide the entire stack trace?

    Hi @bhanuGandham
    Thanks for your reply.
    Yes, I searched the forum and found that this was due to the limited sample size and could be solved by removing "MQRankSum". My question is 50,000 seemed to be big enough even though I only performed VQSR on one chromosome.

    I used GATK 4.1.4.0 and the full stack trace looks like this:

    Using GATK jar /home/pang/program/gatk/gatk-package-4.1.4.0-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 /home/pang/program/gatk/gatk-package-4.1.4.0-local.jar VariantRecalibrator -R /home/pang/program/gatk/GATK_bundle/Homo_sapiens_assembly38.fasta -V /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.VQSR.vcf.gz -resource:mills,known=true,training=true,truth=true,prior=12.0 /home/pang/program/gatk/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -an DP -an QD -an FS -an SOR -an ReadPosRankSum -mode INDEL --max-gaussians 6 --rscript-file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.indels.plots.R --tranches-file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.indels.tranches -O /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.recal
    12:11:02.084 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/pang/program/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Dec 17, 2019 12:11:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    12:11:02.298 INFO VariantRecalibrator - ------------------------------------------------------------
    12:11:02.298 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.4.0
    12:11:02.298 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:11:02.298 INFO VariantRecalibrator - Executing as [email protected] on Linux v3.10.0-1062.4.3.el7.x86_64 amd64
    12:11:02.299 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_232-b09
    12:11:02.299 INFO VariantRecalibrator - Start Date/Time: December 17, 2019 12:11:02 PM CET
    12:11:02.299 INFO VariantRecalibrator - ------------------------------------------------------------
    12:11:02.299 INFO VariantRecalibrator - ------------------------------------------------------------
    12:11:02.299 INFO VariantRecalibrator - HTSJDK Version: 2.20.3
    12:11:02.299 INFO VariantRecalibrator - Picard Version: 2.21.1
    12:11:02.300 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:11:02.300 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:11:02.300 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:11:02.300 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:11:02.300 INFO VariantRecalibrator - Deflater: IntelDeflater
    12:11:02.300 INFO VariantRecalibrator - Inflater: IntelInflater
    12:11:02.300 INFO VariantRecalibrator - GCS max retries/reopens: 20
    12:11:02.300 INFO VariantRecalibrator - Requester pays: disabled
    12:11:02.300 INFO VariantRecalibrator - Initializing engine
    12:11:02.804 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/program/gatk/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
    12:11:02.977 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.VQSR.vcf.gz
    12:11:03.156 INFO VariantRecalibrator - Done initializing engine
    12:11:03.161 INFO TrainingSet - Found mills track: Known = true Training = true Truth = true Prior = Q12.0
    12:11:03.206 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
    12:11:03.272 INFO ProgressMeter - Starting traversal
    12:11:03.272 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:11:08.997 INFO ProgressMeter - chr4:186619977 0.1 38201 400429.8
    12:11:08.997 INFO ProgressMeter - Traversal complete. Processed 38201 total variants in 0.1 minutes.
    12:11:09.000 INFO VariantDataManager - DP: mean = 13855.36 standard deviation = 10753.11
    12:11:09.002 INFO VariantDataManager - QD: mean = 17.50 standard deviation = 7.21
    12:11:09.004 INFO VariantDataManager - FS: mean = 1.85 standard deviation = 4.33
    12:11:09.006 INFO VariantDataManager - SOR: mean = 1.10 standard deviation = 1.07
    12:11:09.008 INFO VariantDataManager - ReadPosRankSum: mean = 0.00 standard deviation = 0.55
    12:11:09.035 INFO VariantDataManager - Annotation order is: [DP, QD, FS, SOR, ReadPosRankSum]
    12:11:09.035 INFO VariantDataManager - Training with 853 variants after standard deviation thresholding.
    12:11:09.036 WARN VariantDataManager - WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.
    12:11:09.040 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
    12:11:09.141 INFO VariantRecalibratorEngine - Finished iteration 0.
    12:11:09.177 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.18547
    12:11:09.207 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.05580
    12:11:09.224 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.00673
    12:11:09.237 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00588
    12:11:09.248 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00924
    12:11:09.260 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01748
    12:11:09.271 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01057
    12:11:09.284 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01054
    12:11:09.297 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00440
    12:11:09.308 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00213
    12:11:09.310 INFO VariantRecalibratorEngine - Convergence after 51 iterations!
    12:11:09.320 INFO VariantRecalibratorEngine - Evaluating full set of 4325 variants...
    12:11:09.340 INFO VariantDataManager - Selected worst 321 scoring variants --> variants with LOD <= -5.0000.
    12:11:09.340 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
    12:11:09.343 INFO VariantRecalibratorEngine - Finished iteration 0.
    12:11:09.345 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.25150
    12:11:09.347 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.00660
    12:11:09.349 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.00010
    12:11:09.349 INFO VariantRecalibratorEngine - Convergence after 15 iterations!
    12:11:09.349 INFO VariantRecalibratorEngine - Evaluating full set of 4325 variants...
    12:11:09.397 INFO TrancheManager - Finding 4 tranches for 4325 variants
    12:11:09.404 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
    12:11:09.414 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
    12:11:09.414 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-Infinity known=(853 @ 0.0000) novel=(3472 @ 0.0000) truthSites(853 accessible, 853 called), name=anonymous]
    12:11:09.414 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
    12:11:09.416 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 87; running score is 0.001
    12:11:09.416 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-6296837026772337700.0000 known=(852 @ 0.0000) novel=(3386 @ 0.0000) truthSites(853 accessible, 852 called), name=anonymous]
    12:11:09.416 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
    12:11:09.421 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 205; running score is 0.011
    12:11:09.421 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=-1765392875374067460.0000 known=(844 @ 0.0000) novel=(3276 @ 0.0000) truthSites(853 accessible, 844 called), name=anonymous]
    12:11:09.421 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
    12:11:09.423 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 966; running score is 0.101
    12:11:09.423 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=-670228339559492990.0000 known=(767 @ 0.0000) novel=(2592 @ 0.0000) truthSites(853 accessible, 767 called), name=anonymous]
    12:11:09.424 INFO VariantRecalibrator - Writing out recalibration table...
    12:11:09.630 INFO VariantRecalibrator - Writing out visualization Rscript file...
    12:11:09.663 INFO VariantRecalibrator - Building DP x QD plot...
    12:11:09.667 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:10.030 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:10.345 INFO VariantRecalibrator - Building DP x FS plot...
    12:11:10.349 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:10.750 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:11.031 INFO VariantRecalibrator - Building DP x SOR plot...
    12:11:11.037 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:11.427 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:11.667 INFO VariantRecalibrator - Building DP x ReadPosRankSum plot...
    12:11:11.668 INFO VariantRecalibratorEngine - Evaluating full set of 3721 variants...
    12:11:12.177 INFO VariantRecalibratorEngine - Evaluating full set of 3721 variants...
    12:11:12.470 INFO VariantRecalibrator - Building QD x FS plot...
    12:11:12.471 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:12.891 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:13.249 INFO VariantRecalibrator - Building QD x SOR plot...
    12:11:13.250 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:13.685 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:13.986 INFO VariantRecalibrator - Building QD x ReadPosRankSum plot...
    12:11:13.987 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:14.390 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:14.700 INFO VariantRecalibrator - Building FS x SOR plot...
    12:11:14.701 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:15.130 INFO VariantRecalibratorEngine - Evaluating full set of 3600 variants...
    12:11:15.430 INFO VariantRecalibrator - Building FS x ReadPosRankSum plot...
    12:11:15.432 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:15.849 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:16.131 INFO VariantRecalibrator - Building SOR x ReadPosRankSum plot...
    12:11:16.131 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:16.560 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
    12:11:16.805 INFO VariantRecalibrator - Executing: Rscript /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.indels.plots.R
    12:11:30.594 INFO VariantRecalibrator - Tranches plot will not be generated since we are running in INDEL mode
    12:11:30.702 INFO VariantRecalibrator - Shutting down engine
    [December 17, 2019 12:11:30 PM CET] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.48 minutes.
    Runtime.totalMemory()=3642228736
    Tool returned:
    true

    real 0m31.588s
    user 0m43.288s
    sys 0m3.518s
    Using GATK jar /home/pang/program/gatk/gatk-package-4.1.4.0-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 /home/pang/program/gatk/gatk-package-4.1.4.0-local.jar ApplyVQSR -R /home/pang/program/gatk/GATK_bundle/Homo_sapiens_assembly38.fasta -V /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.VQSR.vcf.gz --truth-sensitivity-filter-level 99.0 --tranches-file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches --recal-file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.recal -mode INDEL -O /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.VQSR.vcf.gz
    12:11:33.791 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/pang/program/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Dec 17, 2019 12:11:34 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    12:11:34.005 INFO ApplyVQSR - ------------------------------------------------------------
    12:11:34.005 INFO ApplyVQSR - The Genome Analysis Toolkit (GATK) v4.1.4.0
    12:11:34.005 INFO ApplyVQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:11:34.005 INFO ApplyVQSR - Executing as [email protected] on Linux v3.10.0-1062.4.3.el7.x86_64 amd64
    12:11:34.006 INFO ApplyVQSR - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_232-b09
    12:11:34.006 INFO ApplyVQSR - Start Date/Time: December 17, 2019 12:11:33 PM CET
    12:11:34.006 INFO ApplyVQSR - ------------------------------------------------------------
    12:11:34.006 INFO ApplyVQSR - ------------------------------------------------------------
    12:11:34.006 INFO ApplyVQSR - HTSJDK Version: 2.20.3
    12:11:34.007 INFO ApplyVQSR - Picard Version: 2.21.1
    12:11:34.007 INFO ApplyVQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:11:34.007 INFO ApplyVQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:11:34.007 INFO ApplyVQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:11:34.007 INFO ApplyVQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:11:34.007 INFO ApplyVQSR - Deflater: IntelDeflater
    12:11:34.007 INFO ApplyVQSR - Inflater: IntelInflater
    12:11:34.007 INFO ApplyVQSR - GCS max retries/reopens: 20
    12:11:34.007 INFO ApplyVQSR - Requester pays: disabled
    12:11:34.007 INFO ApplyVQSR - Initializing engine
    12:11:34.459 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.recal
    12:11:34.535 INFO FeatureManager - Using codec VCFCodec to read file file:///home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.VQSR.vcf.gz
    12:11:34.723 INFO ApplyVQSR - Done initializing engine
    12:11:34.729 INFO ApplyVQSR - Shutting down engine
    [December 17, 2019 12:11:34 PM CET] org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR done. Elapsed time: 0.02 minutes.
    Runtime.totalMemory()=1900019712
    ***********************************************************************

    A USER ERROR has occurred: Couldn't read file /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches. Error was: /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches with exception: /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches

    ***********************************************************************
    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

    real 0m3.800s
    user 0m8.410s
    sys 0m0.841s
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited December 2019

    HI @mashimaro

    1. Are you running this on a shared file system?
    2. Can you confirm that this tranches file exists /home/pang/data/public_data/UKBB/exome_population/population/ukb_efe_chr4.HC.snps.indels.tranches?
    3. Sorry I wasn't more clear, can you please use --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' to print the entire stack trace and provide that to us. It will help our dev team narrow down the issue here.
  • mashimaromashimaro GermanyMember
    Hi @bhanuGandham
    Thanks for your advice, with "--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" I found out the reason, and it was due to the shared file system. After I fixed that it worked.

    Best wishes!
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Great! glad to help. Happy holidays!

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