Hi,
What does this error msg try to tell me? Is the 'reference dictionary' the refseq? If yes, why can't it load it (the file is OK, sourced from the bundle, successfully used with bwa and Picard).
Full command used (full path replaced with <PATH> for legibility:
java -Xmx2g -jar <PATH>/GenomeAnalysisTK.jar -I AA26_md.bam -R <PATH>/bundle/human_g1k_v37.fasta -T RealignerTargetCreator -o AA26_forIndelRealigner.intervals --known <PATH>/bundle/Mills_and_1000G_gold_standard.indels.b37.vcf --known <PATH>/bundle/1000G_phase1.indels.b37.vcf
Or is it caused by my wrong syntax for the --known vcf's OK? (omitting both has no effect on the error, but could simply be the same msg for other reasons)
The reference fasta and PATH seem OK (see below), so why the error? Am I missing something??
Many thanks in advance!
K
head -3 and grep '>' of my <PATH>/bundle/human_g1k_v37.fasta:
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
9 dna:chromosome chromosome:GRCh37:9:1:141213431:1
10 dna:chromosome chromosome:GRCh37:10:1:135534747:1
11 dna:chromosome chromosome:GRCh37:11:1:135006516:1
12 dna:chromosome chromosome:GRCh37:12:1:133851895:1
13 dna:chromosome chromosome:GRCh37:13:1:115169878:1
14 dna:chromosome chromosome:GRCh37:14:1:107349540:1
15 dna:chromosome chromosome:GRCh37:15:1:102531392:1
16 dna:chromosome chromosome:GRCh37:16:1:90354753:1
17 dna:chromosome chromosome:GRCh37:17:1:81195210:1
18 dna:chromosome chromosome:GRCh37:18:1:78077248:1
19 dna:chromosome chromosome:GRCh37:19:1:59128983:1
20 dna:chromosome chromosome:GRCh37:20:1:63025520:1
21 dna:chromosome chromosome:GRCh37:21:1:48129895:1
22 dna:chromosome chromosome:GRCh37:22:1:51304566:1
X dna:chromosome chromosome:GRCh37:X:1:155270560:1
Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
MT gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome
GL000207.1 dna:supercontig supercontig::GL000207.1:1:4262:1
GL000226.1 dna:supercontig supercontig::GL000226.1:1:15008:1
GL000229.1 dna:supercontig supercontig::GL000229.1:1:19913:1
GL000231.1 dna:supercontig supercontig::GL000231.1:1:27386:1
GL000210.1 dna:supercontig supercontig::GL000210.1:1:27682:1
GL000239.1 dna:supercontig supercontig::GL000239.1:1:33824:1
GL000235.1 dna:supercontig supercontig::GL000235.1:1:34474:1
GL000201.1 dna:supercontig supercontig::GL000201.1:1:36148:1
GL000247.1 dna:supercontig supercontig::GL000247.1:1:36422:1
GL000245.1 dna:supercontig supercontig::GL000245.1:1:36651:1
GL000197.1 dna:supercontig supercontig::GL000197.1:1:37175:1
GL000203.1 dna:supercontig supercontig::GL000203.1:1:37498:1
GL000246.1 dna:supercontig supercontig::GL000246.1:1:38154:1
GL000249.1 dna:supercontig supercontig::GL000249.1:1:38502:1
GL000196.1 dna:supercontig supercontig::GL000196.1:1:38914:1
GL000248.1 dna:supercontig supercontig::GL000248.1:1:39786:1
GL000244.1 dna:supercontig supercontig::GL000244.1:1:39929:1
GL000238.1 dna:supercontig supercontig::GL000238.1:1:39939:1
GL000202.1 dna:supercontig supercontig::GL000202.1:1:40103:1
GL000234.1 dna:supercontig supercontig::GL000234.1:1:40531:1
GL000232.1 dna:supercontig supercontig::GL000232.1:1:40652:1
GL000206.1 dna:supercontig supercontig::GL000206.1:1:41001:1
GL000240.1 dna:supercontig supercontig::GL000240.1:1:41933:1
GL000236.1 dna:supercontig supercontig::GL000236.1:1:41934:1
GL000241.1 dna:supercontig supercontig::GL000241.1:1:42152:1
GL000243.1 dna:supercontig supercontig::GL000243.1:1:43341:1
GL000242.1 dna:supercontig supercontig::GL000242.1:1:43523:1
GL000230.1 dna:supercontig supercontig::GL000230.1:1:43691:1
GL000237.1 dna:supercontig supercontig::GL000237.1:1:45867:1
GL000233.1 dna:supercontig supercontig::GL000233.1:1:45941:1
GL000204.1 dna:supercontig supercontig::GL000204.1:1:81310:1
GL000198.1 dna:supercontig supercontig::GL000198.1:1:90085:1
GL000208.1 dna:supercontig supercontig::GL000208.1:1:92689:1
GL000191.1 dna:supercontig supercontig::GL000191.1:1:106433:1
GL000227.1 dna:supercontig supercontig::GL000227.1:1:128374:1
GL000228.1 dna:supercontig supercontig::GL000228.1:1:129120:1
GL000214.1 dna:supercontig supercontig::GL000214.1:1:137718:1
GL000221.1 dna:supercontig supercontig::GL000221.1:1:155397:1
GL000209.1 dna:supercontig supercontig::GL000209.1:1:159169:1
GL000218.1 dna:supercontig supercontig::GL000218.1:1:161147:1
GL000220.1 dna:supercontig supercontig::GL000220.1:1:161802:1
GL000213.1 dna:supercontig supercontig::GL000213.1:1:164239:1
GL000211.1 dna:supercontig supercontig::GL000211.1:1:166566:1
GL000199.1 dna:supercontig supercontig::GL000199.1:1:169874:1
GL000217.1 dna:supercontig supercontig::GL000217.1:1:172149:1
GL000216.1 dna:supercontig supercontig::GL000216.1:1:172294:1
GL000215.1 dna:supercontig supercontig::GL000215.1:1:172545:1
GL000205.1 dna:supercontig supercontig::GL000205.1:1:174588:1
GL000219.1 dna:supercontig supercontig::GL000219.1:1:179198:1
GL000224.1 dna:supercontig supercontig::GL000224.1:1:179693:1
GL000223.1 dna:supercontig supercontig::GL000223.1:1:180455:1
GL000195.1 dna:supercontig supercontig::GL000195.1:1:182896:1
GL000212.1 dna:supercontig supercontig::GL000212.1:1:186858:1
GL000222.1 dna:supercontig supercontig::GL000222.1:1:186861:1
GL000200.1 dna:supercontig supercontig::GL000200.1:1:187035:1
GL000193.1 dna:supercontig supercontig::GL000193.1:1:189789:1
GL000194.1 dna:supercontig supercontig::GL000194.1:1:191469:1
GL000225.1 dna:supercontig supercontig::GL000225.1:1:211173:1
GL000192.1 dna:supercontig supercontig::GL000192.1:1:547496:1