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icbi-lab
gatk PreprocessIntervals failing
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 [email protected] 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.
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.
