after sort VCF as command the website showed, but still have question in VariantRecalibrator

sunylsunyl beijingMember

I sort vcf as command"java -jar picard.jar SortVcf \
I=original.vcf \
O=sorted.vcf \
SEQUENCE_DICTIONARY=reference.dict "

I call snp as "https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php" show.
But I counter problems like:
INFO 15:40:14,228 HelpFormatter - ---------------------------------------------------------------------------------
INFO 15:40:15,731 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:40:29,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:41:30,833 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Connection reset
INFO 15:41:30,834 HttpMethodDirector - Retrying request
INFO 15:41:31,098 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Connection reset
INFO 15:41:31,099 HttpMethodDirector - Retrying request
INFO 15:41:31,362 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Connection reset
INFO 15:41:31,363 HttpMethodDirector - Retrying request
INFO 15:41:31,621 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Connection reset
INFO 15:41:31,622 HttpMethodDirector - Retrying request
INFO 15:41:31,897 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Connection reset
INFO 15:41:31,897 HttpMethodDirector - Retrying request

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
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 http://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: Lexicographically sorted human genome sequence detected in input.
ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.
ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.
ERROR You can use the ReorderSam utility to fix this problem: http://gatkforums.broadinstitute.org/discussion/58/companion-utilities-reordersam
ERROR input contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]
ERROR ------------------------------------------------------------------------------------------

I see the VCFfile,the order is the same as human ref contig"1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M ",what's wrong?

Sign In or Register to comment.