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Unknown error when running Baserecalibrator

I am trying to perform SNP calling on the chicken genome, I downloaded the gallus gallus vcf file from Ensembl for the base recalibrator step, and when I run the command
java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R chicken_ref.fa -I aln_sorted_realigned.bam --knownSites Gallus_gallus.vcf -o recal_data.table

I get an output of hundreds/thousands of accession numbers followed by error, I have copied the last part of my error output below:
3.1|, gi|358468664|ref|NW_003780214.1|, gi|358468663|ref|NW_003780215.1|, gi|358468662|ref|NW_003780216.1|, gi|358468661|ref|NW_003780217.1|, gi|358468660|ref|NW_003780218.1|, gi|358468659|ref|NW_003780219.1|, gi|358468658|ref|NW_003780220.1|, gi|358468657|ref|NW_003780221.1|, gi|358468656|ref|NW_003780222.1|, gi|358468655|ref|NW_003780223.1|, gi|358468654|ref|NW_003780224.1|, gi|358468653|ref|NW_003780225.1|, gi|358468652|ref|NW_003780226.1|, gi|358468651|ref|NW_003780227.1|, gi|358468650|ref|NW_003780228.1|, gi|358468649|ref|NW_003780229.1|, gi|358468648|ref|NW_003780230.1|, gi|358468647|ref|NW_003780231.1|, gi|358468646|ref|NW_003780232.1|, gi|358468645|ref|NW_003780233.1|, gi|358468644|ref|NW_003780234.1|, gi|358468643|ref|NW_003780235.1|, gi|358468642|ref|NW_003780236.1|, gi|358468641|ref|NW_003780237.1|, gi|358468640|ref|NW_003780238.1|, gi|358468639|ref|NW_003780239.1|, gi|358468638|ref|NW_003780240.1|, gi|358468637|ref|NW_003780241.1|, gi|358468636|ref|NW_003780242.1|, gi|358468635|ref|NW_003780243.1|, gi|358468634|ref|NW_003780244.1|, gi|358468633|ref|NW_003780245.1|, gi|358468632|ref|NW_003780246.1|, gi|358468631|ref|NW_003780247.1|, gi|358468630|ref|NW_003780248.1|, gi|358468629|ref|NW_003780249.1|, gi|358468628|ref|NW_003780250.1|, gi|358468627|ref|NW_003780251.1|, gi|358468626|ref|NW_003780252.1|, gi|358468625|ref|NW_003780253.1|, gi|358468624|ref|NW_003780254.1|, gi|358468623|ref|NW_003780255.1|, gi|358468622|ref|NW_003780256.1|, gi|358468621|ref|NW_003780257.1|, gi|358468620|ref|NW_003780258.1|, gi|358468619|ref|NW_003780259.1|, gi|358468618|ref|NW_003780260.1|, gi|358468617|ref|NW_003780261.1|, gi|358468616|ref|NW_003780262.1|, gi|358468615|ref|NW_003780263.1|, gi|358468614|ref|NW_003780264.1|, gi|358468613|ref|NW_003780265.1|, gi|358468612|ref|NW_003780266.1|, gi|358468611|ref|NW_003780267.1|, gi|358468610|ref|NW_003780268.1|, gi|358468609|ref|NW_003780269.1|, gi|358468608|ref|NW_003780270.1|]

ERROR ------------------------------------------------------------------------------------------

Issue · Github
by Sheila

Issue Number
269
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

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