Hi there, 

I am using GATK v4.0.11.0 and having an issue with GenomicsDBImport. I've tried giving it intervals in the actual command and as a list so that I can make a database for my entire genome, but it won't go beyond chromosome 1. 

Here is the first of two commands I've tried:

gatk --java-options "-Xmx72g" GenomicsDBImport \
--sample-name-map ${Name}_sample_map \
--genomicsdb-workspace-path /cluster/home/cgoeckeritz/bwa_full/moms/gatk/${Name}_DB/${Name}_database \
--intervals /cluster/home/cgoeckeritz/bwa_full/moms/gatk/intervals.list \
--reader-threads 8

The intervals file looks is just one chromosome per line:

chr1A

chr2A

chr3A

chr4A

chr5A

chr6A

chr7A

chr8A

chr9A

chr10A

chr11A

chr12A

chr13A

chr14A

chr15A

chr16A

chr17A

Here's the second command I've tried, but I get the same problem:

gatk --java-options "-Xmx284g" GenomicsDBImport \
--sample-name-map ${Name}_sample_map \
--genomicsdb-workspace-path /cluster/home/cgoeckeritz/bwa_full/moms/gatk/${Name}_DB/${Name}_database_B \
-L chr1A \
-L chr2A \
-L chr3A \
-L chr4A \
-L chr5A \
-L chr6A \
-L chr7A \
-L chr8A \
-L chr9A \
-L chr10A \
-L chr11A \
-L chr12A \
-L chr13A \
-L chr14A \
-L chr15A \
-L chr16A \
-L chr17A \
--reader-threads 24

The program log outputs the following:

/cluster/software/gatk-4.0.11.0/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?

  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):

/cluster/software/gatk-4.0.11.0/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?

  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):

/cluster/software/gatk-4.0.11.0/gatk:117: SyntaxWarning: "is" with a literal. Did you mean "=="?

  if len(args) is 1 and args[0] == "--list":

/cluster/software/gatk-4.0.11.0/gatk:301: SyntaxWarning: "is" with a literal. Did you mean "=="?

  if call(["gsutil", "-q", "stat", gcsjar]) is 0:

/cluster/software/gatk-4.0.11.0/gatk:305: SyntaxWarning: "is" with a literal. Did you mean "=="?

  if call(["gsutil", "cp", jar, gcsjar]) is 0:

/cluster/software/gatk-4.0.11.0/gatk:458: SyntaxWarning: "is not" with a literal. Did you mean "!="?

  if not len(properties) is 0:

/cluster/software/gatk-4.0.11.0/gatk:462: SyntaxWarning: "is not" with a literal. Did you mean "!="?

  if not len(filesToAdd) is 0:

Using GATK jar /cluster/software/gatk-4.0.11.0/gatk-package-4.0.11.0-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 -Xmx284g -jar /cluster/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar GenomicsDBImport --sample-name-map Mspectabilis_588917_sample_map --genomicsdb-workspace-path /cluster/home/cgoeckeritz/bwa_full/moms/gatk/Mspectabilis_588917_DB/Mspectabilis_588917_database_B -L chr1A -L chr2A -L chr3A -L chr4A -L chr5A -L chr6A -L chr7A -L chr8A -L chr9A -L chr10A -L chr11A -L chr12A -L chr13A -L chr14A -L chr15A -L chr16A -L chr17A --reader-threads 24

10:39:32.368 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cluster/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

10:39:34.002 INFO  GenomicsDBImport - ------------------------------------------------------------

10:39:34.002 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.11.0

10:39:34.002 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/

10:39:34.002 INFO  GenomicsDBImport - Executing as cgoeckeritz@hpc0006 on Linux v4.18.0-477.21.1.el8_8.x86_64 amd64

10:39:34.002 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_332-b09

10:39:34.002 INFO  GenomicsDBImport - Start Date/Time: August 12, 2024 10:39:32 AM CDT

10:39:34.002 INFO  GenomicsDBImport - ------------------------------------------------------------

10:39:34.003 INFO  GenomicsDBImport - ------------------------------------------------------------

10:39:34.003 INFO  GenomicsDBImport - HTSJDK Version: 2.16.1

10:39:34.003 INFO  GenomicsDBImport - Picard Version: 2.18.13

10:39:34.003 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2

10:39:34.003 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

10:39:34.003 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

10:39:34.004 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

10:39:34.004 INFO  GenomicsDBImport - Deflater: IntelDeflater

10:39:34.004 INFO  GenomicsDBImport - Inflater: IntelInflater

10:39:34.004 INFO  GenomicsDBImport - GCS max retries/reopens: 20

10:39:34.004 INFO  GenomicsDBImport - Requester pays: disabled

10:39:34.004 INFO  GenomicsDBImport - Initializing engine

10:39:34.376 INFO  IntervalArgumentCollection - Processing 643565055 bp from intervals

10:39:34.378 INFO  GenomicsDBImport - Done initializing engine

10:39:34.480 INFO  GenomicsDBImport - Vid Map JSON file will be written to /cluster/home/cgoeckeritz/bwa_full/moms/gatk/Mspectabilis_588917_DB/Mspectabilis_588917_database_B/vidmap.json

10:39:34.480 INFO  GenomicsDBImport - Callset Map JSON file will be written to /cluster/home/cgoeckeritz/bwa_full/moms/gatk/Mspectabilis_588917_DB/Mspectabilis_588917_database_B/callset.json

10:39:34.480 INFO  GenomicsDBImport - Complete VCF Header will be written to /cluster/home/cgoeckeritz/bwa_full/moms/gatk/Mspectabilis_588917_DB/Mspectabilis_588917_database_B/vcfheader.vcf

10:39:34.481 INFO  GenomicsDBImport - Importing to array - /cluster/home/cgoeckeritz/bwa_full/moms/gatk/Mspectabilis_588917_DB/Mspectabilis_588917_database_B/genomicsdb_array

10:39:34.482 INFO  ProgressMeter - Starting traversal

10:39:34.482 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute

10:39:34.575 INFO  GenomicsDBImport - Starting batch input file preload

10:39:35.146 INFO  GenomicsDBImport - Finished batch preload

10:39:35.146 INFO  GenomicsDBImport - Importing batch 1 with 34 samples

14:52:20.481 INFO  GenomicsDBImport - Starting batch input file preload

14:52:20.942 INFO  GenomicsDBImport - Finished batch preload

14:52:20.943 INFO  GenomicsDBImport - Importing batch 1 with 34 samples

14:52:20.946 INFO  GenomicsDBImport - Starting batch input file preload

14:52:20.946 INFO  GenomicsDBImport - Shutting down engine

[August 12, 2024 2:52:20 PM CDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 252.81 minutes.

Runtime.totalMemory()=1663041536

org.broadinstitute.hellbender.exceptions.GATKException: Cannot call query with different interval, expected:chr1A:1-33734251 queried with: chr2A:1-35818875

        at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$InitializedQueryWrapper.query(GenomicsDBImport.java:816)

        at com.intel.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:136)

        at com.intel.genomicsdb.importer.GenomicsDBImporter.lambda$null$2(GenomicsDBImporter.java:563)

        at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1604)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

        at java.lang.Thread.run(Thread.java:750)

It seems the concerning part of the log is 'Cannot call query with different interval', but I'm unsure what this means, or how to fix it... Any help would be very appreciated!

Thanks so much for your time, 
Charity