gatk PreprocessIntervals failing

[tylergross97]

Has anyone encountered this error before?

Error executing process > 'preprocessIntervalList (preprocessIntervalList)'

Caused by:
  Process `preprocessIntervalList (preprocessIntervalList)` terminated with an error exit status (2)

Command executed:

  gatk PreprocessIntervals \
      -R GRCh38.d1.vd1.fa \
      -L /vscratch/grp-rpili/nextNEOpi/41/5bf34ede3dc7635aa8ddd2cadfbd65/S07604514_Regions.interval_list \
      --bin-length 0 \
      --padding 250 \
      --interval-merging-rule OVERLAPPING_ONLY \
      -O S07604514_Regions_merged_padded.interval_list

Command exit status:
  2

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Using GATK jar /opt/gatk/gatk-package-4.6.1.0-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 -jar /opt/gatk/gatk-package-4.6.1.0-local.jar PreprocessIntervals -R GRCh38.d1.vd1.fa -L /vscratch/grp-rpili/nextNEOpi/41/5bf34ede3dc7635aa8ddd2cadfbd65/S07604514_Regions.interval_list --bin-length 0 --padding 250 --interval-merging-rule OVERLAPPING_ONLY -O S07604514_Regions_merged_padded.interval_list
  09:39:26.125 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk/gatk-package-4.6.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  SLF4J(W): Class path contains multiple SLF4J providers.
  SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@530ee28b]
  SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@3a3f96ab]
  SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
  SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@530ee28b]
  09:39:26.327 INFO  PreprocessIntervals - ------------------------------------------------------------
  09:39:26.331 INFO  PreprocessIntervals - The Genome Analysis Toolkit (GATK) v4.6.1.0
  09:39:26.331 INFO  PreprocessIntervals - For support and documentation go to https://software.broadinstitute.org/gatk/
  09:39:26.331 INFO  PreprocessIntervals - Executing as tgross2@cpn-h22-29.core.ccr.buffalo.edu on Linux v6.8.0-58-generic amd64
  09:39:26.331 INFO  PreprocessIntervals - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+7-Ubuntu-124.10
  09:39:26.331 INFO  PreprocessIntervals - Start Date/Time: May 16, 2025 at 9:39:25 AM GMT-04:00
  09:39:26.331 INFO  PreprocessIntervals - ------------------------------------------------------------
  09:39:26.331 INFO  PreprocessIntervals - ------------------------------------------------------------
  09:39:26.332 INFO  PreprocessIntervals - HTSJDK Version: 4.1.3
  09:39:26.333 INFO  PreprocessIntervals - Picard Version: 3.3.0
  09:39:26.333 INFO  PreprocessIntervals - Built for Spark Version: 3.5.0
  09:39:26.335 INFO  PreprocessIntervals - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  09:39:26.335 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  09:39:26.336 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  09:39:26.336 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  09:39:26.336 INFO  PreprocessIntervals - Deflater: IntelDeflater
  09:39:26.336 INFO  PreprocessIntervals - Inflater: IntelInflater
  09:39:26.336 INFO  PreprocessIntervals - GCS max retries/reopens: 20
  09:39:26.336 INFO  PreprocessIntervals - Requester pays: disabled
  09:39:26.336 INFO  PreprocessIntervals - Initializing engine
  09:39:26.538 INFO  PreprocessIntervals - Shutting down engine
  [May 16, 2025 at 9:39:26 AM GMT-04:00] org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=285212672
  ***********************************************************************
  
  A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "/vscratch/grp-rpili/nextNEOpi/41/5bf34ede3dc7635aa8ddd2cadfbd65/S07604514_Regions.interval_list" is not valid for this input.

[riederd]

Hi,
I assume you are using WGS not WES data. If son, can you try the latest version, I reverted the changes that create the intervals for WGS which may lead to this error.

[tylergross97]

Thanks for your response. I am actually using WES data.