Hello,

I am trying to run the mitochondrial pipeline (GATK version 4.6.1.0) on an HPC system using Cromwell version 87, and am getting the following error: 

A USER ERROR has occurred: Fasta dict file file:///cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/424588285/Homo_sapiens_assembly38.chrM.dict for reference file:///cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/424588285/Homo_sapiens_assembly38.chrM.fasta does not exist. Please see https://gatk.broadinstitute.org/hc/articles/360035531652-FASTA-Reference-genome-format for help creating it.

All the relevant dict and reference files with their paths are present in the input JSON file that was given when initializing the pipeline (command used: java -jar cromwell-87.jar run MitochondriaPipeline.wdl --inputs InputsMitochondriaPipeline.json). It appears the pipeline is rewriting some input files to a separate directory, and the .dict files are not being written there.

Program log:

Using GATK jar /gatk/gatk.jar defined in environment variable GATK_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 /gatk/gatk.jar PrintReads -R /cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/424588285/Homo_sapiens_assembly38.chrM.fasta -L chrM --read-filter MateOnSameContigOrNoMappedMateReadFilter --read-filter MateUnmappedAndUnmappedReadFilter -I /cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/-1741878074/merged_KEN-1055.dedup.sorted.bam --read-index /cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/-1741878074/merged_KEN-1055.dedup.sorted.bam.bai -O merged_KEN-1055.dedup.sorted.bam
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/execution/tmp.VZ9OMt
22:34:30.105 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/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@353c6da1]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@36c07c75]
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@353c6da1]
22:34:30.224 INFO  PrintReads - ------------------------------------------------------------
22:34:30.226 INFO  PrintReads - The Genome Analysis Toolkit (GATK) v4.6.1.0
22:34:30.226 INFO  PrintReads - For support and documentation go to https://software.broadinstitute.org/gatk/
22:34:30.226 INFO  PrintReads - Executing as 
22:34:30.226 INFO  PrintReads - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:34:30.226 INFO  PrintReads - Start Date/Time: October 25, 2024 at 10:34:30 PM GMT
22:34:30.226 INFO  PrintReads - ------------------------------------------------------------
22:34:30.226 INFO  PrintReads - ------------------------------------------------------------
22:34:30.227 INFO  PrintReads - HTSJDK Version: 4.1.3
22:34:30.227 INFO  PrintReads - Picard Version: 3.3.0
22:34:30.227 INFO  PrintReads - Built for Spark Version: 3.5.0
22:34:30.228 INFO  PrintReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:34:30.229 INFO  PrintReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:34:30.229 INFO  PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:34:30.229 INFO  PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:34:30.229 INFO  PrintReads - Deflater: IntelDeflater
22:34:30.229 INFO  PrintReads - Inflater: IntelInflater
22:34:30.229 INFO  PrintReads - GCS max retries/reopens: 20
22:34:30.229 INFO  PrintReads - Requester pays: disabled
22:34:30.229 INFO  PrintReads - Initializing engine
22:34:30.231 INFO  PrintReads - Shutting down engine
[October 25, 2024 at 10:34:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=285212672
***********************************************************************

A USER ERROR has occurred: Fasta dict file file:///cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/424588285/Homo_sapiens_assembly38.chrM.dict for reference file:///cromwell-executions/MitochondriaPipeline/80c0b641-13d6-4da7-bf15-a448baa19d0a/call-SubsetBamToChrM/inputs/424588285/Homo_sapiens_assembly38.chrM.fasta does not exist. Please see https://gatk.broadinstitute.org/hc/articles/360035531652-FASTA-Reference-genome-format for help creating it.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.