Hi, 

I am trying to run ModelSegments but it doesn't seem to be able to read my allelic counts file. The command seems to freeze at this time and never progresses past. I have tried to alter the memory with the Java options to no success. 

Any help would be great! 

a) GATK version used: v4.1.9.0

b) Command: gatk --java-options "-Xmx6g" ModelSegments \
--denoised-copy-ratios Copy_ratios/JRG-3119.denoisedCR.tsv \
--allelic-counts Allelic_counts/JRG-3119.allelicCounts.tsv \
--output ModelSegments \
--output-prefix JRG-3119_test_PBS

(Have also tried increasing memory to 8GB and decreasing to 4GB to no success). 

c) Log: Using GATK jar /cm/shared/apps/gatk/4.1.9.0/gatk-package-4.1.9.0-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 -Xmx6g -jar /cm/shared/apps/gatk/4.1.9.0/gatk-package-4.1.9.0-local.jar ModelSegments --denoised-copy-ratios Copy_ratios/JRG-3119.denoisedCR.tsv --allelic-counts Allelic_counts/JRG-3119.allelicCounts.tsv --output ModelSegments --output-prefix JRG-3119_test_PBS
19:39:22.024 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cm/shared/apps/gatk/4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 10, 2022 7:39:22 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
19:39:22.336 INFO  ModelSegments - ------------------------------------------------------------
19:39:22.336 INFO  ModelSegments - The Genome Analysis Toolkit (GATK) v4.1.9.0
19:39:22.336 INFO  ModelSegments - For support and documentation go to https://software.broadinstitute.org/gatk/
19:39:22.336 INFO  ModelSegments - Executing as rj214@node093 on Linux v3.10.0-1160.62.1.el7.x86_64 amd64
19:39:22.336 INFO  ModelSegments - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_322-b06
19:39:22.336 INFO  ModelSegments - Start Date/Time: May 10, 2022 7:39:21 PM BST
19:39:22.337 INFO  ModelSegments - ------------------------------------------------------------
19:39:22.337 INFO  ModelSegments - ------------------------------------------------------------
19:39:22.337 INFO  ModelSegments - HTSJDK Version: 2.23.0
19:39:22.337 INFO  ModelSegments - Picard Version: 2.23.3
19:39:22.337 INFO  ModelSegments - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:39:22.337 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:39:22.337 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:39:22.337 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:39:22.337 INFO  ModelSegments - Deflater: IntelDeflater
19:39:22.338 INFO  ModelSegments - Inflater: IntelInflater
19:39:22.338 INFO  ModelSegments - GCS max retries/reopens: 20
19:39:22.338 INFO  ModelSegments - Requester pays: disabled
19:39:22.338 INFO  ModelSegments - Initializing engine
19:39:22.338 INFO  ModelSegments - Done initializing engine
19:39:22.430 INFO  ModelSegments - Reading file (Copy_ratios/JRG-3119.denoisedCR.tsv)...
19:39:22.883 INFO  ModelSegments - Reading file (Allelic_counts/JRG-3119.allelicCounts.tsv)...