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ERROR MESSAGE: Badly formed genome loc

Hello,

I am using IndelRealigner. I get this error:
ERROR MESSAGE: Badly formed genome loc: Contig ENSGALG00000024490|ENSGALT00000041403|3|651|852 given as location, but this contig isn't present in the Fasta sequence dictionary

I checked in the .dict and .bam files, indeed, the last line of .bam file which contains the above contig is missing from .dict file:

.bam file:
@SQ SN:ENSGALG00000024480|ENSGALT00000041393|22|309|366 LN:2220
@SQ SN:ENSGALG00000024481|ENSGALT00000041394|1|231|231 LN:1946
@SQ SN:ENSGALG00000024482|ENSGALT00000041395|25|342|342 LN:3194
@SQ SN:ENSGALG00000024483|ENSGALT00000041396|33|191|213 LN:1252
@SQ SN:ENSGALG00000024484|ENSGALT00000041397|139|203|288 LN:1146
@SQ SN:ENSGALG00000024487|ENSGALT00000041400|1|245|258 LN:294
@SQ SN:ENSGALG00000024488|ENSGALT00000041401|336|531|531 LN:2755
@SQ SN:ENSGALG00000024490|ENSGALT00000041403|3|651|852 LN:1693
@RG ID:1 PL:Illumina PU:3 LB:SX165_1.1 SM:1
@PG ID:bwa PN:bwa VN:0.6.2-r126

and

.dict file:
@SQ SN:ENSGALG00000024480|ENSGALT00000041393|22|309|366 LN:2220 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:a1d6d352f572b6c869d5d4196ba818b1
@SQ SN:ENSGALG00000024481|ENSGALT00000041394|1|231|231 LN:1946 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:9a90cffed9374c371cad87b962e2d9e0
@SQ SN:ENSGALG00000024482|ENSGALT00000041395|25|342|342 LN:3194 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:997affbb2c6e0e90de28446927c5b1cf
@SQ SN:ENSGALG00000024483|ENSGALT00000041396|33|191|213 LN:1252 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:d03d3553e20bb0fe30b87ac359a681f6
@SQ SN:ENSGALG00000024484|ENSGALT00000041397|139|203|288 LN:1146 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:1e9db17274efd2c147be4a339cba7ffd
@SQ SN:ENSGALG00000024487|ENSGALT00000041400|1|245|258 LN:294 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:8d2f3543543c8b3dfb62df3e89fa9791
@SQ SN:ENSGALG00000024488|ENSGALT00000041401|336|531|531 LN:2755 UR:file:/proj/b2011033/private/assembly/GG_gap/scamelus_oases31_newbler_gg_gap.fa M5:fe62d9e99cc89b45fe43d8522ab589cc

My question is that how is it possible that my .bam file contains a contig that does not exist in the .dict file? And how I can solve this problem. I used the picard utility, CreatSequenceDictionary, to recreat the .dict file but the problem is still there.

Thank you very much in advance for any help.

Homa- Uppsala University

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Answers

  • HomaHoma Member

    Yes, I created the .bam files myself, thank you for your explanation, it is more clear to me now what I should do, I will track the problem.

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