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ERROR: Couldn't create GenomicsDBFeatureReader #6616

Closed wdermauw closed 4 years ago

wdermauw commented 4 years ago

Hi

After creating a GenomicsDB with 36 gvcf withGenomicsDBimport, I used GEnotypeGVCF on the GenomicsDB folder but get the following error: "ERROR: Couldn't create GenomicsDBFeatureReader". See below for the complete output.

FYI, I don't get this error when importing only six samples in GenomicsDB and then running GenotypeGVCF.

FYI, also added "TILEDB_DISABLE_FILE_LOCKING=1" to environment (export TILEDB_DISABLE_FILE_LOCKING=1) before executing GenomicsDBimport command but that dit not help either.

Any suggestion would be highly appreciated.

GenotypeVCF not working on 36 samples

(base) xxxxxx@galaxy:~$ gatk --java-options "-Xmx30g" GenomicsDBImport \

-V output/B7_2.g.vcf.gz \ -V output/B7_6.g.vcf.gz \ -V output/B8_7.g.vcf.gz \ -V output/B8_5.g.vcf.gz \ -V output/B8_17.g.vcf.gz \ -V output/B8_9.g.vcf.gz \ -V output/B7_9.g.vcf.gz \ -V output/B7_10.g.vcf.gz \ -V output/B8_13.g.vcf.gz \ -V output/B7_15.g.vcf.gz \ -V output/B8_8.g.vcf.gz \ -V output/B8_10.g.vcf.gz \ -V output/B8_11.g.vcf.gz \ -V output/F_A.g.vcf.gz \ -V output/B7_3.g.vcf.gz \ -V output/B8_19.g.vcf.gz \ -V output/A8.g.vcf.gz \ -V output/B7_4.g.vcf.gz \ -V output/B8_4.g.vcf.gz \ -V output/B8_4g.g.vcf.gz \ -V output/B8_16.g.vcf.gz \ -V output/A9_1.g.vcf.gz \ -V output/X2.g.vcf.gz \ -V output/X1.g.vcf.gz \ -V output/7_5_2.g.vcf.gz \ -V output/C3.g.vcf.gz \ -V output/C1.g.vcf.gz \ -V output/C2.g.vcf.gz \ -V output/C3.g.vcf.gz \ -V output/A9-10.g.vcf.gz \ -V output/P3.g.vcf.gz \ -V output/P4.g.vcf.gz \ -V output/X4.g.vcf.gz \ -V output/X5.g.vcf.gz \ -V output/X6.g.vcf.gz \ -V output/X7.g.vcf.gz \ --genomicsdb-workspace-path ABchroneALL \ --intervals pseudochromosome_1 \ --intervals pseudochromosome_2 \ --intervals pseudochromosome_3 \ --batch-size 6 Using GATK jar /data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-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 -Xmx30g -jar /data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar GenomicsDBImport -V output/B7_2.g.vcf.gz -V output/B7_6.g.vcf.gz -V output/B8_7.g.vcf.gz -V output/B8_5.g.vcf.gz -V output/B8_17.g.vcf.gz -V output/B8_9.g.vcf.gz -V output/B7_9.g.vcf.gz -V output/B7_10.g.vcf.gz -V output/B8_13.g.vcf.gz -V output/B7_15.g.vcf.gz -V output/B8_8.g.vcf.gz -V output/B8_10.g.vcf.gz -V output/B8_11.g.vcf.gz -V output/F_A.g.vcf.gz -V output/B7_3.g.vcf.gz -V output/B8_19.g.vcf.gz -V output/A8.g.vcf.gz -V output/B7_4.g.vcf.gz -V output/B8_4.g.vcf.gz -V output/B8_4g.g.vcf.gz -V output/B8_16.g.vcf.gz -V output/A9_1.g.vcf.gz -V output/TRZ.g.vcf.gz -V output/RAINBOW.g.vcf.gz -V output/7_5_2.g.vcf.gz -V output/Athens.g.vcf.gz -V output/C1.g.vcf.gz -V output/C2.g.vcf.gz -V output/C3.g.vcf.gz -V output/A9-10.g.vcf.gz -V output/P3.g.vcf.gz -V output/P4.g.vcf.gz -V output/Spg.g.vcf.gz -V output/EtAB.g.vcf.gz -V output/TuR.g.vcf.gz -V output/TuG.g.vcf.gz --genomicsdb-workspace-path ABchroneALL --intervals pseudochromosome_1 --batch-size 6 07:56:24.538 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 27, 2020 7:56:24 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 07:56:24.849 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:24.850 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.6.0 07:56:24.850 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.oAB/gatk/ 07:56:24.850 INFO GenomicsDBImport - Executing as xxxxxx@galaxy on Linux v4.4.0-133-generic amd64 07:56:24.850 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 07:56:24.850 INFO GenomicsDBImport - Start Date/Time: 27 May 2020 07:56:24 CEST 07:56:24.850 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:24.850 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:24.851 INFO GenomicsDBImport - HTSJDK Version: 2.21.2 07:56:24.851 INFO GenomicsDBImport - Picard Version: 2.21.9 07:56:24.851 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 07:56:24.851 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 07:56:24.851 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 07:56:24.851 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 07:56:24.851 INFO GenomicsDBImport - Deflater: IntelDeflater 07:56:24.851 INFO GenomicsDBImport - Inflater: IntelInflater 07:56:24.851 INFO GenomicsDBImport - GCS max retries/reopens: 20 07:56:24.851 INFO GenomicsDBImport - Requester pays: disabled 07:56:24.852 INFO GenomicsDBImport - Initializing engine 07:56:25.955 INFO IntervalAABumentCollection - Processing 32654540 bp from intervals 07:56:25.957 INFO GenomicsDBImport - Done initializing engine 07:56:26.238 INFO GenomicsDBImport - Vid Map JSON file will be written to /data/xxxxxx/ABchroneALL/vidmap.json 07:56:26.238 INFO GenomicsDBImport - Callset Map JSON file will be written to /data/xxxxxx/ABchroneALL/callset.json 07:56:26.238 INFO GenomicsDBImport - Complete VCF Header will be written to /data/xxxxxx/ABchroneALL/vcfheader.vcf 07:56:26.238 INFO GenomicsDBImport - Importing to array - /data/xxxxxx/ABchroneALL/genomicsdb_array 07:56:26.238 INFO ProgressMeter - Starting traversal 07:56:26.238 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 07:56:26.670 INFO GenomicsDBImport - Importing batch 1 with 6 samples 08:04:53.380 INFO ProgressMeter - pseudochromosome_1:1 8.5 1 0.1 08:04:53.380 INFO GenomicsDBImport - Done importing batch 1/6 08:04:53.426 INFO GenomicsDBImport - Importing batch 2 with 6 samples 08:10:51.448 INFO ProgressMeter - pseudochromosome_1:1 14.4 2 0.1 08:10:51.448 INFO GenomicsDBImport - Done importing batch 2/6 08:10:51.492 INFO GenomicsDBImport - Importing batch 3 with 6 samples 08:17:48.471 INFO ProgressMeter - pseudochromosome_1:1 21.4 3 0.1 08:17:48.471 INFO GenomicsDBImport - Done importing batch 3/6 08:17:48.510 INFO GenomicsDBImport - Importing batch 4 with 6 samples 08:23:17.675 INFO ProgressMeter - pseudochromosome_1:1 26.9 4 0.1 08:23:17.675 INFO GenomicsDBImport - Done importing batch 4/6 08:23:17.709 INFO GenomicsDBImport - Importing batch 5 with 6 samples 08:31:44.254 INFO ProgressMeter - pseudochromosome_1:1 35.3 5 0.1 08:31:44.255 INFO GenomicsDBImport - Done importing batch 5/6 08:31:44.286 INFO GenomicsDBImport - Importing batch 6 with 6 samples 08:38:39.554 INFO ProgressMeter - pseudochromosome_1:1 42.2 6 0.1 08:38:39.554 INFO GenomicsDBImport - Done importing batch 6/6 08:38:39.556 INFO ProgressMeter - pseudochromosome_1:1 42.2 6 0.1 08:38:39.556 INFO ProgressMeter - Traversal complete. Processed 6 total batches in 42.2 minutes. 08:38:39.556 INFO GenomicsDBImport - Import of all batches to GenomicsDB completed! 08:38:39.556 INFO GenomicsDBImport - Shutting down engine [27 May 2020 08:38:39 CEST] oAB.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 42.25 minutes. Runtime.totalMemory()=2545942528 Tool returned: true

(base) xxxxxx@galaxy:~$ gatk --java-options "-Xmx30g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" GenotypeGVCFs -R Reference/File_S16_uT_3_Pseudochromosomes.fasta -V gendb://ABchroneALL -O ABchroneALL.vcf.gz Using GATK jar /data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-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 -Xmx30g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar GenotypeGVCFs -R Reference/File_S16_uT_3_Pseudochromosomes.fasta -V gendb://ABchroneALL -O ABchroneALL.vcf.gz 09:48:14.426 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/xxxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 27, 2020 9:48:14 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:48:14.871 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:48:14.871 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.6.0 09:48:14.872 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.oAB/gatk/ 09:48:14.872 INFO GenotypeGVCFs - Executing as xxxxxx@galaxy on Linux v4.4.0-133-generic amd64 09:48:14.872 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 09:48:14.872 INFO GenotypeGVCFs - Start Date/Time: 27 May 2020 09:48:14 CEST 09:48:14.872 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:48:14.872 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:48:14.873 INFO GenotypeGVCFs - HTSJDK Version: 2.21.2 09:48:14.873 INFO GenotypeGVCFs - Picard Version: 2.21.9 09:48:14.873 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:48:14.874 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:48:14.874 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:48:14.874 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:48:14.874 INFO GenotypeGVCFs - Deflater: IntelDeflater 09:48:14.874 INFO GenotypeGVCFs - Inflater: IntelInflater 09:48:14.874 INFO GenotypeGVCFs - GCS max retries/reopens: 20 09:48:14.874 INFO GenotypeGVCFs - Requester pays: disabled 09:48:14.874 INFO GenotypeGVCFs - Initializing engine 09:48:16.015 INFO GenotypeGVCFs - Shutting down engine [27 May 2020 09:48:16 CEST] oAB.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2301100032

A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader

oAB.broadinstitute.hellbender.exceptions.UserException: Couldn't create GenomicsDBFeatureReader at oAB.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(FeatureDataSource.java:410) at oAB.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:326) at oAB.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:282) at oAB.broadinstitute.hellbender.engine.VariantLocusWalker.initializeDrivingVariants(VariantLocusWalker.java:76) at oAB.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:67) at oAB.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:706) at oAB.broadinstitute.hellbender.engine.VariantLocusWalker.onStartup(VariantLocusWalker.java:63) at oAB.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at oAB.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseAABs(CommandLineProgram.java:191) at oAB.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at oAB.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163) at oAB.broadinstitute.hellbender.Main.mainEntry(Main.java:206) at oAB.broadinstitute.hellbender.Main.main(Main.java:292) Caused by: java.io.IOException: GenomicsDB JNI Error: GenomicsDBConfigException : Syntax error in JSON file /data/xxxxxx/ABchroneALL/callset.json at oAB.genomicsdb.reader.GenomicsDBQueryStream.jniGenomicsDBInit(Native Method) at oAB.genomicsdb.reader.GenomicsDBQueryStream.(GenomicsDBQueryStream.java:209) at oAB.genomicsdb.reader.GenomicsDBQueryStream.(GenomicsDBQueryStream.java:182) at oAB.genomicsdb.reader.GenomicsDBQueryStream.(GenomicsDBQueryStream.java:91) at oAB.genomicsdb.reader.GenomicsDBFeatureReader.generateHeadersForQuery(GenomicsDBFeatureReader.java:176) at oAB.genomicsdb.reader.GenomicsDBFeatureReader.(GenomicsDBFeatureReader.java:80) at oAB.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(FeatureDataSource.java:407) ... 12 more

GenotypeGVCF working when only six samples are imported in GenomicsDB

gatk GenotypeGVCFs -R Reference/File_S16_uT_chromosomes.fasta -V gendb://GenomicsDB_wd -O test_chromosome_1_6_samples.vcf Using GATK jar /data/xxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-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 /data/xxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar GenotypeGVCFs -R Reference/File_S16_Tetranychus_urticae_3_chromosomes.fasta -V gendb://GenomicsDB_wd -O test_chromosome_1_6_samples.vcf 21:14:37.817 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/xxxxx/miniconda3/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 26, 2020 9:14:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 21:14:38.245 INFO GenotypeGVCFs - ------------------------------------------------------------ 21:14:38.246 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.6.0 21:14:38.246 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:14:38.246 INFO GenotypeGVCFs - Executing as xxxxx@galaxy on Linux v4.4.0-133-generic amd64 21:14:38.246 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 21:14:38.246 INFO GenotypeGVCFs - Start Date/Time: 26 May 2020 21:14:37 CEST 21:14:38.246 INFO GenotypeGVCFs - ------------------------------------------------------------ 21:14:38.246 INFO GenotypeGVCFs - ------------------------------------------------------------ 21:14:38.247 INFO GenotypeGVCFs - HTSJDK Version: 2.21.2 21:14:38.247 INFO GenotypeGVCFs - Picard Version: 2.21.9 21:14:38.247 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:14:38.247 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:14:38.247 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:14:38.247 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:14:38.247 INFO GenotypeGVCFs - Deflater: IntelDeflater 21:14:38.248 INFO GenotypeGVCFs - Inflater: IntelInflater 21:14:38.248 INFO GenotypeGVCFs - GCS max retries/reopens: 20 21:14:38.248 INFO GenotypeGVCFs - Requester pays: disabled 21:14:38.248 INFO GenotypeGVCFs - Initializing engine WARNING: No valid combination operation found for INFO field AC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AN - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field FS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field QD - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field SOR - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AN - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field FS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field QD - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field SOR - the field will NOT be part of INFO fields in the generated VCF records 21:14:39.358 INFO GenotypeGVCFs - Done initializing engine 21:14:39.430 INFO ProgressMeter - Starting traversal 21:14:39.431 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute WARNING: No valid combination operation found for INFO field AC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field AN - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field FS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field QD - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field SOR - the field will NOT be part of INFO fields in the generated VCF records 21:14:44.408 WARN InbreedingCoeff - InbreedingCoeff will not be calculated; at least 10 samples must have called genotypes 21:14:49.472 INFO ProgressMeter - chromosome_1:220314 0.2 39000 233044.5 21:14:59.558 INFO ProgressMeter - chromosome_1:712661 0.3 174000 518732.0 21:15:09.572 INFO ProgressMeter - chromosome_1:1268793 0.5 295000 587240.0 21:15:19.634 INFO ProgressMeter - chromosome_1:1772603 0.7 406000 605924.9 21:15:29.676 INFO ProgressMeter - chromosome_1:2224562 0.8 491000 586327.0 21:15:39.688 INFO ProgressMeter - chromosome_1:2797827 1.0 590000 587483.6 21:15:49.732 INFO ProgressMeter - chromosome_1:3283434 1.2 692000 590611.7 21:15:59.769 INFO ProgressMeter - chromosome_1:3697367 1.3 786000 587027.1 21:16:09.811 INFO ProgressMeter - chromosome_1:4258637 1.5 905000 600796.6 21:16:19.812 INFO ProgressMeter - chromosome_1:4679796 1.7 997000 595929.5 21:16:29.892 INFO ProgressMeter - chromosome_1:5272909 1.8 1123000 609989.0 21:16:39.897 INFO ProgressMeter - chromosome_1:5829289 2.0 1231000 613119.1 21:16:49.935 INFO ProgressMeter - chromosome_1:6383684 2.2 1334000 613314.5 21:16:59.961 INFO ProgressMeter - chromosome_1:6997412 2.3 1435000 612680.6 21:17:11.048 INFO ProgressMeter - chromosome_1:7697582 2.5 1544000 611013.3 21:17:21.141 INFO ProgressMeter - chromosome_1:8295832 2.7 1641000 608867.7 21:17:31.202 INFO ProgressMeter - chromosome_1:9129097 2.9 1754000 612676.2 21:17:41.235 INFO ProgressMeter - chromosome_1:10085011 3.0 1874000 618468.2 21:17:51.251 INFO ProgressMeter - chromosome_1:10960634 3.2 1987000 621520.2

droazen commented 4 years ago

@nalinigans @mlathara your thoughts on this issue?

@wdermauw Did you confirm prior to the failed GenotypeGVCFs run that the ABchroneALL directory existed in the working directory, was readable, non-empty, etc.? The error you are getting is a very generic I/O error, so it's difficult to diagnose the problem without a bit more information.

mlathara commented 4 years ago

@wdermauw Can you paste the contents of /data/xxxxxx/ABchroneALL/callset.json. This error seems to suggest something is amiss with that...maybe one of the sample names was somehow mangled...

Caused by: java.io.IOException: GenomicsDB JNI Error: GenomicsDBConfigException : Syntax error in JSON file /data/xxxxxx/ABchroneALL/callset.json
wdermauw commented 4 years ago

@mlathara @droazen thank you for the quick reply...

i checked the callset.json and you are correct, sample names were somehow mingled...my sincere apologies

after the mapping/variant calling (using a pipeline), I noticed that two g.vcf.gz files had a space in their filename. I removed the space in the file name (X g.vcf.gz->X.g.vcf.gz) and continued with GenomicsDB, but apparently, GenomicsDb extracts the sample name not from the file name but from somewhere else (as in the callset.json file I found that the file mentioned above was called as X� and X�_stream, while this was not the case for all other files)

not using the vcf.gz files having a � symbol in callset.json solved the problem (GenotypeGVCF not throwing an error).

thank you for helping out again, my apologies for the inconvenience caused

droazen commented 4 years ago

Closing as resolved

zhangxiaojian-zxj commented 4 years ago

i have meet the same question . l want to know how to cue this question ? my sincere apologies

zhangxiaojian-zxj commented 4 years ago

Closing as resolved

i have meet the same question . l want to know how to cue this question ? my sincere apologies