Hi all!
I have a problem with this tool of GATK: RealignerTargetCreator. At the beginning I found this error:
FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /home/reference/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx because an IOException occurred with message: Funzione non implementata.
RMDTrackBuilder - Unable to write to /home/reference/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx for the index file, creating index in memory only
So I added this argument: --disable_auto_index_creation_and_locking_when_reading_rods
And I didn't find the same error. But now I have this problem:
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Line 222: there aren't enough columns for line chrUn_gl000217,length=172149,assembly=hg19> (we expected 9 tokens, and saw 1 ), for input source: /home/reference/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
I am using as reference hg 19. I downloaded the Mills vcf and index from ftp://ftp.broadinstitute.org/bundle/2.8/hg19.
Thank you in advance,
best