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Question: Lift-Over tool in Galaxy error: 'Exception caught attempting conversion: '
1
gravatar for rfabmc
22 months ago by
rfabmc • 10
Spain
rfabmc • 10 wrote:

Dear all,

I'm trying to remap mm9 genome coordinates to mm10 from a .BED file. Galaxy "Lift-Over" tool fails and returns this error:

" Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/tools/extract/liftOver_wrapper.py", line 84, in <module> raise Exception('Exception caught attempting conversion: ' + str( e )) Exception: Exception caught attempting con..."

Metadata is correct and .BED file has the proper build assigned.

Tool also fails in converting from mm9 to any other genome.

Has anyone have any clue?

Thanks!!!
assembly software error galaxy • 724 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by rfabmc • 10

I'm running some tests - feedback soon. Jen

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am able to achieve successful liftover results going from mm9->mm10 and mm9>mm8 at http://usegalaxy.org. I tested with bed3 format (with datatype interval assigned), bed6 (bed datatype) and bed12 (bed datatype) input.

Test results are in this shared history for review. It may help you to determine where the format problem is in your input. My guess is that the data is not in strict BED format. Even if interval format is assigned, the column ordering/values must follow bed format due to this being a UCSC sourced tool with BED column ordering required: https://usegalaxy.org/u/jen/h/test-liftover-esp-mm9-from

I'll leave the history shared for a week or so.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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