[Tue Jul 18 12:22:45 PDT 2017] picard.vcf.FixVcfHeader INPUT=/media/gilchrist/Expansion/Marshall_Lab_Data/Reference_Variants/anopheles_gambiae.vcf OUTPUT=/media/gilchrist/Expansion/Marshall_Lab_Data/Reference_Variants/anopheles_gambiae_fixed.vcf CHECK_FIRST_N_RECORDS=-1 ENFORCE_SAME_SAMPLES=true 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 [Tue Jul 18 12:22:45 PDT 2017] Executing as gilchrist@gilchrist on Linux 4.10.0-28-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11; Picard version: 2.10.3-SNAPSHOT INFO 2017-07-18 12:22:45 FixVcfHeader Reading in records to re-build the header. INFO 2017-07-18 12:22:45 FixVcfHeader Will add an INFO line with id: Variant_seq INFO 2017-07-18 12:22:45 FixVcfHeader Will add an INFO line with id: Reference_seq INFO 2017-07-18 12:22:45 FixVcfHeader Will add an INFO line with id: WTSI-Ag-GVP-0.1_0 INFO 2017-07-18 12:22:47 FixVcfHeader read 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: 2L:27,212,331 INFO 2017-07-18 12:22:49 FixVcfHeader read 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: 2L:48,782,732 INFO 2017-07-18 12:22:50 FixVcfHeader read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: 2R:23,040,352 INFO 2017-07-18 12:22:52 FixVcfHeader read 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: 2R:50,167,721 INFO 2017-07-18 12:22:53 FixVcfHeader read 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: 3L:21,698,690 INFO 2017-07-18 12:22:55 FixVcfHeader read 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: 3R:4,183,077 INFO 2017-07-18 12:22:56 FixVcfHeader read 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: 3R:27,459,604 INFO 2017-07-18 12:22:58 FixVcfHeader read 8,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: UNKN:686,212 INFO 2017-07-18 12:23:00 FixVcfHeader read 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: X:19,875,726 INFO 2017-07-18 12:23:00 FixVcfHeader VCF header re-built. [Tue Jul 18 12:23:00 PDT 2017] picard.vcf.FixVcfHeader done. Elapsed time: 0.24 minutes. Runtime.totalMemory()=795869184 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.IllegalArgumentException: A reference dictionary is required for creating Tribble indices on the fly at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:426) at picard.vcf.FixVcfHeader.doWork(FixVcfHeader.java:187) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)