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File is not a supported reference file type

WaqasWaqas canterburyMember
edited June 2017 in Ask the GATK team

I am following a tutorial for variant analysis and to create sequence dictionary they have written following command:

java -jar ~/bin/picard-tools-1.8.5/CreateSequenceDictionary.jar \
    REFERENCE=reference.fasta \
    OUTPUT=reference.dict

I have modified the command which is :

java -jar /usr/bin/picard.jar CreateSequenceDictionary \
    REFERENCE=TAIR10_chr_all.fas \
    OUTPUT=reference.dict

and got following error:

[Wed Jun 21 18:18:43 BST 2017] picard.sam.CreateSequenceDictionary REFERENCE=TAIR10_chr_all.fas OUTPUT=reference.dict    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
[Wed Jun 21 18:18:43 BST 2017] Executing as waqas@waqas-Inspiron-5521 on Linux 4.8.0-54-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11; Picard version: 2.9.2-SNAPSHOT
[Wed Jun 21 18:18:43 BST 2017] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=60293120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: File is not a supported reference file type: /media/waqas/FE8C0AFA8C0AACE9/Canterburry/research work/Tutorials/variant_analysis/genome/TAIR_10/TAIR10_chr_all.fas
    at htsjdk.samtools.reference.ReferenceSequenceFileFactory.lambda$getFastaExtension$0(ReferenceSequenceFileFactory.java:163)
    at java.util.Optional.orElseGet(Optional.java:267)
    at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaExtension(ReferenceSequenceFileFactory.java:163)
    at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:119)
    at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:84)
    at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:72)
    at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:175)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

I have used the same "TAIR10_chr_all.fas" file to index reference genome using bwa with the following command:

bwa index TAIR10_chr_all.fas

and sorted reference genome with the following command

samtools faidx TAIR10_chr_all.fas

In both the cases, i didn't get any error, I wonder why I am getting an error this time. Your kind help will be highly appericated.

Extra details:

java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

I have attached snapshot of picard, please find attached file

Post edited by shlee on
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