GenomicsDBImport: An index is required, but none found with file ending .idx
REQUIRED for all errors and issues:
a) GATK version used:
v4.4.0.0
b) Exact command used:
/gatk/gatk GenomicsDBImport --java-options "-Xmx160G -Xms160G" -R "${REF}" -L "${BED}" --merge-input-intervals --genomicsdb-workspace-path "${DBI_path}/joint_list_DBI_work" --batch-size 10 --reader-threads 10 --consolidate --tmp-dir "${tmp_dir}" --sample-name-map "${map_path}"
c) Entire program log:
01:51:12.456 INFO GenomicsDBImport - ------------------------------------------------------------
01:51:12.459 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.4.0.0
01:51:12.459 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
01:51:12.459 INFO GenomicsDBImport - Executing as on Linux v3.10.0-1160.53.1.el7.x86_64 amd64
01:51:12.459 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10-Ubuntu-0ubuntu118.04.1
01:51:12.459 INFO GenomicsDBImport - Start Date/Time: November 16, 2023 at 1:51:12 AM GMT
01:51:12.459 INFO GenomicsDBImport - ------------------------------------------------------------
01:51:12.459 INFO GenomicsDBImport - ------------------------------------------------------------
01:51:12.460 INFO GenomicsDBImport - HTSJDK Version: 3.0.5
01:51:12.460 INFO GenomicsDBImport - Picard Version: 3.0.0
01:51:12.460 INFO GenomicsDBImport - Built for Spark Version: 3.3.1
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
01:51:12.461 INFO GenomicsDBImport - Deflater: IntelDeflater
01:51:12.461 INFO GenomicsDBImport - Inflater: IntelInflater
01:51:12.462 INFO GenomicsDBImport - GCS max retries/reopens: 20
01:51:12.462 INFO GenomicsDBImport - Requester pays: disabled
01:51:12.462 INFO GenomicsDBImport - Initializing engine
01:51:12.754 INFO GenomicsDBImport - Shutting down engine
[November 16, 2023 at 1:51:12 AM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=171798691840
***********************************************************************
01:51:12.459 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.4.0.0
01:51:12.459 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
01:51:12.459 INFO GenomicsDBImport - Executing as on Linux v3.10.0-1160.53.1.el7.x86_64 amd64
01:51:12.459 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10-Ubuntu-0ubuntu118.04.1
01:51:12.459 INFO GenomicsDBImport - Start Date/Time: November 16, 2023 at 1:51:12 AM GMT
01:51:12.459 INFO GenomicsDBImport - ------------------------------------------------------------
01:51:12.459 INFO GenomicsDBImport - ------------------------------------------------------------
01:51:12.460 INFO GenomicsDBImport - HTSJDK Version: 3.0.5
01:51:12.460 INFO GenomicsDBImport - Picard Version: 3.0.0
01:51:12.460 INFO GenomicsDBImport - Built for Spark Version: 3.3.1
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
01:51:12.461 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
01:51:12.461 INFO GenomicsDBImport - Deflater: IntelDeflater
01:51:12.461 INFO GenomicsDBImport - Inflater: IntelInflater
01:51:12.462 INFO GenomicsDBImport - GCS max retries/reopens: 20
01:51:12.462 INFO GenomicsDBImport - Requester pays: disabled
01:51:12.462 INFO GenomicsDBImport - Initializing engine
01:51:12.754 INFO GenomicsDBImport - Shutting down engine
[November 16, 2023 at 1:51:12 AM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=171798691840
***********************************************************************
A USER ERROR has occurred: Failed to create reader from file:///storage1/fs1/jin810/Active/CH-F0012_germline_3_increased_mem/CH-F0012-001U_BP_germline_reEND.g.vcf because of the following error:
An index is required, but none found with file ending .idx, for input source: file:///storage1/fs1/jin810/Active/CH-F0012_germline_3_increased_mem/CH-F0012-001U_BP_germline_reEND.g.vcf
I am not sure how to generate .idx index. I can only generate .gzi or .csi indexes. Could any help with this? Thanks!
-
Hi Leo
You can use IndexFeatureFile tool from GATK to generate an idx index for your gvcf file.
Regards.
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