htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa
java -jar ../picard.jar CreateSequenceDictionary REFERENCE=GRCh38.primary_assembly.genome.fa OUTPUT=GRCh38.primary_assembly.genome.dict INFO 2020-02-12 17:46:43 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CreateSequenceDictionary -REFERENCE GRCh38.primary_assembly.genome.fa -OUTPUT GRCh38.primary_assembly.genome.dict **********
17:46:44.534 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Feb 12 17:46:44 IST 2020] CreateSequenceDictionary OUTPUT=GRCh38.primary_assembly.genome.dict REFERENCE=GRCh38.primary_assembly.genome.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Feb 12 17:47:07 IST 2020] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.39 minutes. Runtime.totalMemory()=3614965760
Install Picard
https://github.com/broadinstitute/picard/releases/tag/2.21.8
Then run following command:
java -jar ../picard.jar CreateSequenceDictionary REFERENCE=GRCh38.primary_assembly.genome.fa OUTPUT=GRCh38.primary_assembly.genome.dict
INFO 2020-02-12 17:46:43 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -REFERENCE GRCh38.primary_assembly.genome.fa -OUTPUT GRCh38.primary_assembly.genome.dict
**********
17:46:44.534 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Feb 12 17:46:44 IST 2020] CreateSequenceDictionary OUTPUT=GRCh38.primary_assembly.genome.dict REFERENCE=GRCh38.primary_assembly.genome.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Feb 12 17:47:07 IST 2020] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.39 minutes.
Runtime.totalMemory()=3614965760