#12 Error with Atlas INDEL in the WGL

2.0
closed
Danny Challis
bug (5)
2012-12-13
2012-12-13
Alicia Hawes
No

I have had Atlas INDEL fail twice on this MITO sample. We have had
many sets of MITO successfully complete Atlas INDEL, previously in the
WGL.
I decided to run it interactively to see where things were failing.
Here are the results:

[p-wgl@c81sa-11 INDEL]$
/stornext/snfswgl/software/ruby/ruby-1.9.2/bin/ruby
/stornext/snfswgl/next-gen/Illumina/ipipeV2/components/IndelCaller/Atlas-Indel2.rb

-b
/stornext/snfswgl/next-gen/Illumina/Instruments/7001306/121121_SN7001306_0089_BC1EPHACXX/Results/Project_121121_SN7001306_0089_BC1EPHACXX/Sample_C1EPHACXX-4-ID21/C1EPHACXX-4-ID21_realigned.bam

-r
/stornext/snfswgl/next-gen/Illumina/bwa_references/h/hg19_mito_only/NC_012920.1-mitochondrial-genome.fasta

-s 538596 -I -o 538596_INDELs.vcf
Input BAM:
/stornext/snfswgl/next-gen/Illumina/Instruments/7001306/121121_SN7001306_0089_BC1EPHACXX/Results/Project_121121_SN7001306_0089_BC1EPHACXX/Sample_C1EPHACXX-4-ID21/C1EPHACXX-4-ID21_realigned.bam
Reference Genome:
/stornext/snfswgl/next-gen/Illumina/bwa_references/h/hg19_mito_only/NC_012920.1-mitochondrial-genome.fasta
Writing output to: 538596_INDELs.vcf
Using Illumina-exome regression model
Using p cutoff of 0.5
Using minimum variant read requirement of 2
Using minimum variant ratio requirement of 0.06
Using minimum total depth requirement of 5
Using maximum near-read-end ratio requirement of 0.8
Using homozygous variant cutoff of 0.6 for genotyping
Using sample name 538596
/stornext/snfswgl/next-gen/Illumina/ipipeV2/components/IndelCaller/Atlas-Indel2.rb:250:

warning: Insecure world writable dir /stornext/snfswgl in PATH, mode
040777
Progress:
UNKOWN FATAL ERROR: Please contact the developers so they can address
this issue (challis@bcm.edu, fyu@bcm.edu).

Please include the following details:
Illegal reference coordinate(s): 16551, 16572


Any help you can provide would be greatly appreciated.

Thanks,
-ali

Discussion

  • Danny Challis
    Danny Challis
    2012-12-13

    This is a known bug in version 1.0 of Atlas2. It is caused by reads which are mapped past the end of the reference genome. This bug was fixed in revision 91 and is fixed in the current stable version of Atlas2 (1.4.1). In the new version Atlas-Indel2 prints a warning instead of crashing. These warnings can safely be ignored unless you are getting it several thousand times, which would indicate that you may be using an incorrect reference genome version.

     
  • Danny Challis
    Danny Challis
    2012-12-13

    • labels: --> bug
    • status: open --> closed
    • assigned_to: Danny Challis
     


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