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Mutation_analysis Error: Intervals must have position width #6

Closed rsetlem closed 4 years ago

rsetlem commented 4 years ago

Hi Team,

I have couple of questions regarding MMARGE pipeline.

  1. Can MMARGE prepare files for other strains such as C3HHEJ, FVBNJ, 129S1?
  2. Motif mutation analysis 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.
vlink commented 4 years ago

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?

rsetlem commented 4 years ago

Do you want the -ind FBNJ files and the annotation file (ann_FVBNJ_Treatment)? Is there any way I can share the files with you?

vlink commented 4 years ago

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?

rsetlem commented 4 years ago

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 notifications@github.com 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?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vlink/marge/issues/6#issuecomment-645590862, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGBWT5EDVCI3XBFFNTIVDBLRXEN2BANCNFSM4N7YSUIA .

vlink commented 4 years ago

I am not sure if I fixed the bug, but I believe that you probably use a newer version of the IntervalTree module and they changed the way they index it. Could you try this new version of the MMARGE module and let me know if that fixed your issue before I update the package?

Thanks, Verena analysis_tree.pm.zip

rsetlem commented 4 years ago

when i am trying to use the new version of (analysis_tree.pm) it throws an error Can't locate config_MMARGE.pm which is not present in the MMARGE folders (bin)

rsetlem commented 4 years ago

Hi Team,

Do you have an updated config_MMARGE.pm which supports analysis_tree.pm?

Thanks, Rohit

vlink commented 4 years ago

Can you try this version? analysis_tree.pm.zip

rsetlem commented 4 years ago

Its working now. Thanks, Rohit