What is this error?

I'm running IndelRealigner and I got this error

, HLA-B13:02:09, HLA-B13:08, HLA-B13:15, HLA-B13:25, HLA-B14:01:01, HLA-B14:02:01, HLA-B14:07N, HLA-B15:01:01:01, HLA-B15:01:01:02N, HLA-B15:01:01:03, HLA-B15:02:01, HLA-B15:03:01, HLA-B15:04:01, HLA-B15:07:01, HLA-B15:108, HLA-B15:10:01, HLA-B15:11:01, HLA-B15:13:01, HLA-B15:16:01, HLA-B15:17:01:01, HLA-B15:17:01:02, HLA-B15:18:01, HLA-B15:220, HLA-B15:25:01, HLA-B15:27:01, HLA-B15:32:01, HLA-B15:42, HLA-B15:58, HLA-B15:66, HLA-B15:77, HLA-B15:83, HLA-B18:01:01:01, HLA-B18:01:01:02, HLA-B18:02, HLA-B18:03, HLA-B18:17N, HLA-B18:26, HLA-B18:94N, HLA-B27:04:01, HLA-B27:05:02, HLA-B27:05:18, HLA-B27:06, HLA-B27:07:01, HLA-B27:131, HLA-B27:24, HLA-B27:25, HLA-B27:32, HLA-B35:01:01:01, HLA-B35:01:01:02, HLA-B35:01:22, HLA-B35:02:01, HLA-B35:03:01, HLA-B35:05:01, HLA-B35:08:01, HLA-B35:14:02, HLA-B35:241, HLA-B35:41, HLA-B37:01:01, HLA-B37:01:05, HLA-B38:01:01, HLA-B38:02:01, HLA-B38:14, HLA-B39:01:01:01, HLA-B39:01:01:02L, HLA-B39:01:01:03, HLA-B39:01:03, HLA-B39:01:16, HLA-B39:01:21, HLA-B39:05:01, HLA-B39:06:02, HLA-B39:10:01, HLA-B39:13:02, HLA-B39:14, HLA-B39:34, HLA-B39:38Q, HLA-B40:01:01, HLA-B40:01:02, HLA-B40:02:01, HLA-B40:03, HLA-B40:06:01:01, HLA-B40:06:01:02, HLA-B40:10:01, HLA-B40:150, HLA-B40:40, HLA-B40:72:01, HLA-B40:79, HLA-B41:01:01, HLA-B41:02:01, HLA-B42:01:01, HLA-B42:02, HLA-B42:08, HLA-B44:02:01:01, HLA-B44:02:01:02S, HLA-B44:02:01:03, HLA-B44:02:17, HLA-B44:02:27, HLA-B44:03:01, HLA-B44:03:02, HLA-B44:04, HLA-B44:09, HLA-B44:138Q, HLA-B44:150, HLA-B44:23N, HLA-B44:26, HLA-B44:46, HLA-B44:49, HLA-B44:56N, HLA-B45:01:01, HLA-B45:04, HLA-B46:01:01, HLA-B46:01:05, HLA-B47:01:01:01, HLA-B47:01:01:02, HLA-B48:01:01, HLA-B48:03:01, HLA-B48:04, HLA-B48:08, HLA-B49:01:01, HLA-B49:32, HLA-B50:01:01, HLA-B51:01:01, HLA-B51:01:02, HLA-B51:02:01, HLA-B51:07:01, HLA-B51:42, HLA-B52:01:01:01, HLA-B52:01:01:02, HLA-B52:01:01:03, HLA-B52:01:02, HLA-B53:01:01, HLA-B53:11, HLA-B54:01:01, HLA-B54:18, HLA-B55:01:01, HLA-B55:01:03, HLA-B55:02:01, HLA-B55:12, HLA-B55:24, HLA-B55:48, HLA-B56:01:01, HLA-B56:03, HLA-B56:04, HLA-B57:01:01, HLA-B57:03:01, HLA-B57:06, HLA-B57:11, HLA-B57:29, HLA-B58:01:01, HLA-B58:31N, HLA-B59:01:01:01, HLA-B59:01:01:02, HLA-B67:01:01, HLA-B67:01:02, HLA-B67:02, HLA-B73:01, HLA-B78:01:01, HLA-B81:01, HLA-B82:02:01, HLA-C01:02:01, HLA-C01:02:11, HLA-C01:02:29, HLA-C01:02:30, HLA-C01:03, HLA-C01:06, HLA-C01:08, HLA-C01:14, HLA-C01:21, HLA-C01:30, HLA-C01:40, HLA-C02:02:02:01, HLA-C02:02:02:02, HLA-C02:10, HLA-C02:11, HLA-C02:16:02, HLA-C02:69, HLA-C02:85, HLA-C02:86, HLA-C02:87, HLA-C03:02:01, HLA-C03:02:02:01, HLA-C03:02:02:02, HLA-C03:02:02:03, HLA-C03:03:01, HLA-C03:04:01:01, HLA-C03:04:01:02, HLA-C03:04:02, HLA-C03:04:04, HLA-C03:05, HLA-C03:06, HLA-C03:100, HLA-C03:13:01, HLA-C03:20N, HLA-C03:219, HLA-C03:261, HLA-C03:40:01, HLA-C03:41:02, HLA-C03:46, HLA-C03:61, HLA-C04:01:01:01, HLA-C04:01:01:02, HLA-C04:01:01:03, HLA-C04:01:01:04, HLA-C04:01:01:05, HLA-C04:01:62, HLA-C04:03:01, HLA-C04:06, HLA-C04:09N, HLA-C04:128, HLA-C04:161, HLA-C04:177, HLA-C04:70, HLA-C04:71, HLA-C05:01:01:01, HLA-C05:01:01:02, HLA-C05:08, HLA-C05:09:01, HLA-C05:93, HLA-C06:02:01:01, HLA-C06:02:01:02, HLA-C06:02:01:03, HLA-C06:23, HLA-C06:24, HLA-C06:46N, HLA-C07:01:01:01, HLA-C07:01:01:02, HLA-C07:01:02, HLA-C07:01:19, HLA-C07:01:27, HLA-C07:01:45, HLA-C07:02:01:01, HLA-C07:02:01:02, HLA-C07:02:01:03, HLA-C07:02:01:04, HLA-C07:02:01:05, HLA-C07:02:05, HLA-C07:02:06, HLA-C07:02:64, HLA-C07:04:01, HLA-C07:04:02, HLA-C07:06, HLA-C07:149, HLA-C07:18, HLA-C07:19, HLA-C07:26, HLA-C07:30, HLA-C07:32N, HLA-C07:384, HLA-C07:385, HLA-C07:386, HLA-C07:391, HLA-C07:392, HLA-C07:49, HLA-C07:56:02, HLA-C07:66, HLA-C07:67, HLA-C08:01:01, HLA-C08:01:03, HLA-C08:02:01:01, HLA-C08:02:01:02, HLA-C08:03:01, HLA-C08:04:01, HLA-C08:112, HLA-C08:20, HLA-C08:21, HLA-C08:22, HLA-C08:24, HLA-C08:27, HLA-C08:36N, HLA-C08:40, HLA-C08:41, HLA-C08:62, HLA-C12:02:02, HLA-C12:03:01:01, HLA-C12:03:01:02, HLA-C12:08, HLA-C12:13, HLA-C12:19, HLA-C12:22, HLA-C12:99, HLA-C14:02:01, HLA-C14:03, HLA-C14:21N, HLA-C14:23, HLA-C15:02:01, HLA-C15:05:01, HLA-C15:05:02, HLA-C15:13, HLA-C15:16, HLA-C15:17, HLA-C15:96Q, HLA-C16:01:01, HLA-C16:02:01, HLA-C16:04:01, HLA-C17:01:01:01, HLA-C17:01:01:02, HLA-C17:01:01:03, HLA-C17:03, HLA-C18:01, HLA-DQA101:01:02, HLA-DQA101:02:01:01, HLA-DQA101:02:01:02, HLA-DQA101:02:01:03, HLA-DQA101:02:01:04, HLA-DQA101:03:01:01, HLA-DQA101:03:01:02, HLA-DQA101:04:01:01, HLA-DQA101:04:01:02, HLA-DQA101:05:01, HLA-DQA101:07, HLA-DQA101:10, HLA-DQA101:11, HLA-DQA102:01, HLA-DQA103:01:01, HLA-DQA103:02, HLA-DQA103:03:01, HLA-DQA104:01:02:01, HLA-DQA104:01:02:02, HLA-DQA104:02, HLA-DQA105:01:01:01, HLA-DQA105:01:01:02, HLA-DQA105:03, HLA-DQA105:05:01:01, HLA-DQA105:05:01:02, HLA-DQA105:05:01:03, HLA-DQA105:11, HLA-DQA106:01:01, HLA-DQB102:01:01, HLA-DQB102:02:01, HLA-DQB103:01:01:01, HLA-DQB103:01:01:02, HLA-DQB103:01:01:03, HLA-DQB103:02:01, HLA-DQB103:03:02:01, HLA-DQB103:03:02:02, HLA-DQB103:03:02:03, HLA-DQB103:05:01, HLA-DQB105:01:01:01, HLA-DQB105:01:01:02, HLA-DQB105:03:01:01, HLA-DQB105:03:01:02, HLA-DQB106:01:01, HLA-DQB106:02:01, HLA-DQB106:03:01, HLA-DQB106:09:01, HLA-DRB101:01:01, HLA-DRB101:02:01, HLA-DRB103:01:01:01, HLA-DRB103:01:01:02, HLA-DRB104:03:01, HLA-DRB107:01:01:01, HLA-DRB107:01:01:02, HLA-DRB108:03:02, HLA-DRB109:21, HLA-DRB110:01:01, HLA-DRB111:01:01, HLA-DRB111:01:02, HLA-DRB111:04:01, HLA-DRB112:01:01, HLA-DRB112:17, HLA-DRB113:01:01, HLA-DRB113:02:01, HLA-DRB114:05:01, HLA-DRB114:54:01, HLA-DRB115:01:01:01, HLA-DRB115:01:01:02, HLA-DRB115:01:01:03, HLA-DRB115:01:01:04, HLA-DRB115:02:01, HLA-DRB115:03:01:01, HLA-DRB115:03:01:02, HLA-DRB1*16:02:01]

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

I could not found what was the problem.
What is this mean? What should I do?

Best Answer

Answers

  • EADGEADG KielMember ✭✭✭

    HI @seungminkim,

    let me guess you are using Hg38 ? This output seems to be the name of some of the alt contigs. Can you provide the commandLine/ GATK-Version which you used ? And in addition can you stick to the formating tipps ?:)

    Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.
    

    Greetings EADG

  • Hi @EADG
    I'm using Hg38 GATK reference Homo_sapiens_assembly38.fasta
    I used bowtie-build & tophat for ERR187525.fastq and used picard tools for the bam file.
    My GATK version is 3.8.0.
    My command was

    java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R Homo_sapiens_assembly38.fasta -I accepted_hits_addrg_fixm_sorted_md.bam --known Homo_sapiens_assembly38.known_indels.vcf -o chr1_addrg_fixm_sorted_md_IndelRealigner.intervals

    I couldn't figure out what was the problem. Please help.

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