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Question: Bedtools job in paused mode
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gravatar for vmuthu
5 months ago by
vmuthu • 20
vmuthu • 20 wrote:

Hi I'm trying to use intersect intervals in Bedtools but the job has been in paused mode since morning. I tried resuming the job multiple times but that didn't help. Appreciate your help in this.

Thanks,

Victor
bed software error format intersect interval • 182 views
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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by vmuthu • 20
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gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

BEDTools > Intersect intervals find overlapping intervals in various ways expects one of these formats as an input: BAM/BED/GFF/VCF

One of your datasets is in Interval format and it failed conversion to BED format because of the extra columns that do not meet BED specification. You'll need to recreate that interval dataset and not try to convert it to BED (before fixing the format, or ever, see below). Currently, the existing data is in an error state and not usable with tools (why your downstream job is paused).

Choices:

  • Modify the interval dataset to only include columns that meet the specification for BED format (content and order), convert to BED, then use this tool.
  • Use a different tool that accepts interval format. For example: Operate on Genomic Intervals > Intersect the intervals of two datasets

FAQs: https://galaxyproject.org/support/#getting-inputs-right

Thanks! Jen, Galaxy team
ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k
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