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Mutation_analysis Error: Intervals must have position width #6
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Hi, Thanks for using MMARGE. You can prepare files for each strain, as long as you have the vcf files. To debug your error message, could you share your FBNJ and output-FVBE2 mutation files with me? |
Do you want the -ind FBNJ files and the annotation file (ann_FVBNJ_Treatment)? |
Yes that would be great. It is probably enough if you send me the annotation file and chromosome 1 from the FBNJ folder. These files should not too big and you might be able to send them by email? |
Hi Vlink/Marge,
Please find the files in below link:
https://drive.google.com/drive/folders/1QeZUF2Te1I-wyo6ygFVPaHyEby9fbUMS?usp=sharing
Thanks,
Rohit
…On Wed, Jun 17, 2020 at 2:57 PM vlink ***@***.***> wrote:
Yes that would be great.
It is probably enough if you send me the annotation file and chromosome 1
from the FBNJ folder. These files should not too big and you might be able
to send them by email?
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I am not sure if I fixed the bug, but I believe that you probably use a newer version of the IntervalTree module and they changed the way they index it. Thanks, |
when i am trying to use the new version of (analysis_tree.pm) it throws an error |
Hi Team, Do you have an updated config_MMARGE.pm which supports analysis_tree.pm? Thanks, |
Can you try this version? |
Its working now. |
Hi Team,
I have couple of questions regarding MMARGE pipeline.
I am trying to run the following command and see this error:
MMARGE.pl mutation_analysis -file ann_FVBNJ_Treatment -ind FBNJ output-FVBE2 -plot plot-FVBE2 -core 6
Error: Intervals must have positive width at /MMARGE/MMARGE_v1.0//bin/analysis_tree.pm line 1079.
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