Hello.
Whilst counts coverage of paired end fragments, using the CollectReadCounts function (GATK v. 4.1.3.0), I got the following an error. It states:

java.lang.IllegalArgumentException: Records contained at least one interval that did not validate against the sequence dictionary.

I quite don't understand the problem. Did I prepare the BAM file in a wrong way? What is the cause of this and what can be done?

Full error log:

"

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 /opt/software/conda2/envs/GATK/share/gatk4-4.1.3.0-0/gatk-package-4.1.3.0-local.jar CollectReadCounts -I example_sorted_filtered_wRG.bam -L tutorial_11682/targets_C.preprocessed_2.interval_list --interval-merging-rule OVERLAPPING_ONLY -O example.hdf5
16:55:10.607 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/software/conda2/envs/GATK/share/gatk4-4.1.3.0-0/gatk-package-4.1.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Feb 12, 2020 4:55:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:55:10.890 INFO CollectReadCounts - ------------------------------------------------------------
16:55:10.891 INFO CollectReadCounts - The Genome Analysis Toolkit (GATK) v4.1.3.0
16:55:10.891 INFO CollectReadCounts - For support and documentation go to https://software.broadinstitute.org/gatk/
16:55:10.891 INFO CollectReadCounts - Executing as praposo@b1s4 on Linux v3.10.0-957.21.3.el7.x86_64 amd64
16:55:10.892 INFO CollectReadCounts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
16:55:10.892 INFO CollectReadCounts - Start Date/Time: 12 February 2020 16:55:10 GMT
16:55:10.892 INFO CollectReadCounts - ------------------------------------------------------------
16:55:10.892 INFO CollectReadCounts - ------------------------------------------------------------
16:55:10.893 INFO CollectReadCounts - HTSJDK Version: 2.20.1
16:55:10.893 INFO CollectReadCounts - Picard Version: 2.20.5
16:55:10.893 INFO CollectReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:55:10.894 INFO CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:55:10.894 INFO CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:55:10.894 INFO CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:55:10.894 INFO CollectReadCounts - Deflater: IntelDeflater
16:55:10.894 INFO CollectReadCounts - Inflater: IntelInflater
16:55:10.894 INFO CollectReadCounts - GCS max retries/reopens: 20
16:55:10.894 INFO CollectReadCounts - Requester pays: disabled
16:55:10.894 INFO CollectReadCounts - Initializing engine
16:55:11.303 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/AD/praposo/WGS/gatk/tutorial_11682/targets_C.preprocessed_2.interval_list
16:55:12.833 INFO IntervalArgumentCollection - Processing 110882629 bp from intervals
16:55:12.884 INFO CollectReadCounts - Done initializing engine
16:55:12.889 INFO CollectReadCounts - Collecting read counts...
16:55:12.889 INFO ProgressMeter - Starting traversal
16:55:12.889 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:55:22.896 INFO ProgressMeter - 4:25413371 0.2 518000 3106136.3
16:55:32.910 INFO ProgressMeter - 9:122989414 0.3 1019000 3053946.1
16:55:42.914 INFO ProgressMeter - 16:88856680 0.5 1641000 3279376.5
16:55:48.410 INFO CollectReadCounts - 163541 read(s) filtered by: ((((WellformedReadFilter AND MappedReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND NotDuplicateReadFilter) AND MappingQualityReadFilter)
163541 read(s) filtered by: MappingQualityReadFilter

16:55:48.411 INFO ProgressMeter - 22:50715748 0.6 2027207 3424239.7
16:55:48.411 INFO ProgressMeter - Traversal complete. Processed 2027207 total reads in 0.6 minutes.
16:55:48.411 INFO CollectReadCounts - Writing read counts to /home/AD/praposo/WGS/gatk/example.hdf5...
16:55:48.538 INFO CollectReadCounts - Shutting down engine
[12 February 2020 16:55:48 GMT] org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts done. Elapsed time: 0.63 minutes.
Runtime.totalMemory()=3325558784
java.lang.IllegalArgumentException: Records contained at least one interval that did not validate against the sequence dictionary.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:724)
at org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils.validateIntervals(CopyNumberArgumentValidationUtils.java:54)
at org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection.<init>(AbstractLocatableCollection.java:47)
at org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleLocatableCollection.<init>(AbstractSampleLocatableCollection.java:34)
at org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.<init>(SimpleCountCollection.java:60)
at org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.onTraversalSuccess(CollectReadCounts.java:197)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1050)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

"

The command used:

gatk CollectReadCounts -I example_sorted_filtered_wRG.bam -L tutorial_11682/targets_C.preprocessed_2.interval_list --interval-merging-rule OVERLAPPING_ONLY -O example.hdf5

Thank you in advance,
Pedro Raposo