GenomicsDBImport Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception:
Hello,
I am also getting this error. Has anyone found a remedy? I am working with the g.vcf and index files from HaplotypeCaller I have also re-indexed the files in case they had somehow been corrupted, and still get the error:
A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///GATK/gdbi/File because of the following error:
Unable to parse header with error: /GATK/gdbi/File, for input source: /GATK/gdbi/File
After using the command:
gatk GenomicsDBImport --java-options'-Xmx15g -Xms15g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true'-R ${ref} --genomicsdb-workspace-path ${gdbi_dir} --L1:1-10000 --sample-name-map ${sample_map} --tmp-dir ${tmp_dir} --reader-threads3 --batch-size50
The full error output is (paths shortened for brevity):
The full error output is (paths shortened for brevity):
mkdir: cannot create directory ‘/GATK/gdbi/tmp’: File exists
Using GATK jar /gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 -Xmx15g -Xms15g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar GenomicsDBImport -R /reference/ref.fa --genomicsdb-workspace-path /GATK/gdbi/gdbi --L 1:1-10000 --sample-name-map /GATK/gdbi/gdbi/vcf_files_list.txt --tmp-dir /GATK/gdbi/tmp --reader-threads 3 --batch-size 50
12:41:31.925 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:41:32.042 INFO GenomicsDBImport - ------------------------------------------------------------
12:41:32.045 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.5.0.0
12:41:32.045 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
12:41:32.045 INFO GenomicsDBImport - Executing as h12n18 on Linux v4.18.0-513.24.1.el8_9.x86_64 amd64
12:41:32.045 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v17.0.8-internal+0-adhoc..src
12:41:32.046 INFO GenomicsDBImport - Start Date/Time: April 29, 2024 at 12:41:31 PM EDT
12:41:32.046 INFO GenomicsDBImport - ------------------------------------------------------------
12:41:32.046 INFO GenomicsDBImport - ------------------------------------------------------------
12:41:32.046 INFO GenomicsDBImport - HTSJDK Version: 4.1.0
12:41:32.047 INFO GenomicsDBImport - Picard Version: 3.1.1
12:41:32.047 INFO GenomicsDBImport - Built for Spark Version: 3.5.0
12:41:32.047 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:41:32.047 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:41:32.047 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:41:32.047 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:41:32.047 INFO GenomicsDBImport - Deflater: IntelDeflater
12:41:32.047 INFO GenomicsDBImport - Inflater: IntelInflater
12:41:32.047 INFO GenomicsDBImport - GCS max retries/reopens: 20
12:41:32.047 INFO GenomicsDBImport - Requester pays: disabled
12:41:32.048 INFO GenomicsDBImport - Initializing engine
12:41:32.198 INFO IntervalArgumentCollection - Processing 10000 bp from intervals
12:41:32.338 INFO GenomicsDBImport - Done initializing engine
12:41:32.566 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.5.1-84e800e
12:41:32.568 INFO GenomicsDBImport - Vid Map JSON file will be written to /GATK/gdbi/gdbi/vidmap.json
12:41:32.568 INFO GenomicsDBImport - Callset Map JSON file will be written to /GATK/gdbi/gdbi/callset.json
12:41:32.568 INFO GenomicsDBImport - Complete VCF Header will be written to /GATK/gdbi/gdbi/vcfheader.vcf
12:41:32.568 INFO GenomicsDBImport - Importing to workspace - /GATK/gdbi/gdbi
12:41:32.876 INFO GenomicsDBImport - Starting batch input file preload
12:41:35.699 INFO GenomicsDBImport - Finished batch preload
12:41:35.700 INFO GenomicsDBImport - Importing batch 1 with 50 samples
12:41:38.299 INFO GenomicsDBImport - Done importing batch 1/2
12:41:38.300 INFO GenomicsDBImport - Starting batch input file preload
12:41:39.680 INFO GenomicsDBImport - Shutting down engine
[April 29, 2024 at 12:41:39 PM EDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=16106127360
***********************************************************************
A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///GATK/gdbi/File because of the following error:
Unable to parse header with error: /GATK/gdbi/File, for input source: file:///GATK/gdbi/File
***********************************************************************
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///GATK/gdbi/File because of the following error:
Unable to parse header with error: /GATK/gdbi/File, for input source: file:///GATK/gdbi/File
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.lambda$getFeatureReadersInParallel$9(GenomicsDBImport.java:941)
at java.base/java.util.LinkedHashMap.forEach(LinkedHashMap.java:721)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.getFeatureReadersInParallel(GenomicsDBImport.java:936)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.createSampleToReaderMap(GenomicsDBImport.java:724)
at org.genomicsdb.importer.GenomicsDBImporter.lambda$iterateOverChromosomeIntervals$4(GenomicsDBImporter.java:711)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.util.concurrent.ExecutionException: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///GATK/gdbi/File because of the following error:
Unable to parse header with error: /GATK/gdbi/File, for input source: file:///GATK/gdbi/File
at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.lambda$getFeatureReadersInParallel$9(GenomicsDBImport.java:938)
... 8 more
Caused by: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///GATK/gdbi/File because of the following error:
Unable to parse header with error: /GATK/gdbi/File, for input source: file:///GATK/gdbi/File
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.getReaderFromPath(GenomicsDBImport.java:1026)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.lambda$getFeatureReadersInParallel$8(GenomicsDBImport.java:929)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
... 3 more
Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /GATK/gdbi/File, for input source: file:///GATK/gdbi/File
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:265)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:104)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:129)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.getReaderFromPath(GenomicsDBImport.java:977)
... 5 more
Caused by: java.nio.file.NoSuchFileException: /GATK/gdbi/File
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
at java.base/java.nio.file.Files.newByteChannel(Files.java:432)
at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:422)
at java.base/java.nio.file.Files.newInputStream(Files.java:160)
at htsjdk.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:105)
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:255)
... 9 more
-
Your sample name map file /GATK/gdbi/gdbi/vcf_files_list.txt seems to contain invalid entries. Can you check and fix invalid entries and try running again. Tool is looking for an input file that does not exist.
Caused by: java.nio.file.NoSuchFileException: /GATK/gdbi/File
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