Bonjour
J'essaie de faire tourner GATK HaplotypeCaller, mais je me retrouve avec cette erreur
Using GATK jar /shared/ifbstor1/software/miniconda/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-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 /shared/ifbstor1/software/miniconda/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar HaplotypeCaller -R ref/Felis_catus.Felis_catus_9.0.dna.toplevel.fa.gz -I mark/Delux.bam -O hap_caller/Delux.gvcf -ERC GVCF
09:36:58.720 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ifbstor1/software/miniconda/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 14, 2022 9:36:59 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
09:37:00.016 INFO HaplotypeCaller - ------------------------------------------------------------
09:37:00.035 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.3.0
09:37:00.035 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
09:37:00.036 INFO HaplotypeCaller - Executing as cploix@cpu-node-8 on Linux v3.10.0-1160.6.1.el7.x86_64 amd64
09:37:00.036 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08
09:37:00.037 INFO HaplotypeCaller - Start Date/Time: April 14, 2022 9:36:58 AM CEST
09:37:00.037 INFO HaplotypeCaller - ------------------------------------------------------------
09:37:00.037 INFO HaplotypeCaller - ------------------------------------------------------------
09:37:00.038 INFO HaplotypeCaller - HTSJDK Version: 2.24.1
09:37:00.038 INFO HaplotypeCaller - Picard Version: 2.25.4
09:37:00.038 INFO HaplotypeCaller - Built for Spark Version: 2.4.5
09:37:00.038 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:37:00.038 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:37:00.038 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:37:00.038 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:37:00.038 INFO HaplotypeCaller - Deflater: IntelDeflater
09:37:00.038 INFO HaplotypeCaller - Inflater: IntelInflater
09:37:00.039 INFO HaplotypeCaller - GCS max retries/reopens: 20
09:37:00.039 INFO HaplotypeCaller - Requester pays: disabled
09:37:00.039 INFO HaplotypeCaller - Initializing engine
09:37:01.418 INFO HaplotypeCaller - Shutting down engine
[April 14, 2022 9:37:01 AM CEST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=259588096
java.lang.IllegalArgumentException: Something went wrong with sequence dictionary detection, check that reference has a valid sequence dictionary
at org.broadinstitute.hellbender.utils.Utils.nonNull(Utils.java:643)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:149)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:796)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:731)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:79)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Ma commande
sbatch -J GATK_Delux -o logs/GATK_Delux.out -e logs/GATK_Delux.err --mem=16G --wrap=" \
gatk HaplotypeCaller \
-R ref/Felis_catus.Felis_catus_9.0.dna.toplevel.fa.gz \
-I mark/Delux.bam \
-O hap_caller/Delux.gvcf"
Merci