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Question: Error in the fetch sequence tool
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gravatar for rao.kottapalli
4.0 years ago by
rao.kottapalli • 0
rao.kottapalli • 0 wrote:

11209 warnings, 1st is: Unable to fetch the sequence from '2' to '2410' for chrom '>Contig1'. Skipped 11209 invalid lines, 1st is #1, ">Contig1 2 2412"

 

Please look at this error and let me know how to resolve this.

 

Thanks

Rao
galaxy • 727 views
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modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by rao.kottapalli • 0
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gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Rao,

I believe that we solved this problem through a submitted bug report last week. But if that was not you, then the solution is to remove the ">" from the input bed/interval dataset. 

Make lines that are formatted like this:

>Contig1 2 2412

Into lines that are formatted like this:

Contig1 2 2412

Best, Jen, Galaxy team
ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

Thank you for your email.

My issue got resolved and I could fetch data from a custom build database.

Thanks Rao

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Tuesday, December 9, 2014 1:17 PM To: Kottapalli, Rao Subject: [galaxy-biostar] A: Error in the fetch sequence tool

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Error in the fetch sequence tool<http: biostar.usegalaxy.org="" p="" 9888="" #9924="">:

Hello Rao,

I believe that we solved this problem through a submitted bug report last week. But if that was not you, then the solution is to remove the ">" from the input bed/interval dataset.

Make lines that are formatted like this:

Into lines that are formatted like this:

Contig1 2 2412

Best, Jen, Galaxy team

ADD REPLY • link written 4.0 years ago by rao.kottapalli • 0
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