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Question: mpileup error: reference sequence is not being fetched correctly?
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gravatar for mkim3
2.2 years ago by
mkim3 • 10
mkim3 • 10 wrote:

Hi, I ran mpileup using Arabidopsis reference sequence but got an error message in the log file which is below.

[mpileup] 1 samples in 1 input files

<mpileup> Set max per-file depth to 8000

[fai_fetch_seq] The sequence "Pt" not found

[fai_fetch_seq] The sequence "Mt" not found

[fai_fetch_seq] The sequence "4" not found

[fai_fetch_seq] The sequence "2" not found

[fai_fetch_seq] The sequence "3" not found

[fai_fetch_seq] The sequence "5" not found

[fai_fetch_seq] The sequence "1" not found

I have all Ns in reference sequence column when I look at the output file. Can you tell me what I am doing wrong?

Thanks, Minsoo
dbkey genome reference mpileup samtools • 1.2k views
ADD COMMENT • link •
modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by mkim3 • 10
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like a reference genome mismatch problem. There are three Arabidopsis builds at http://usegalaxy.org. If working somewhere else, there could be none or the same or others.

To resolve the problem, make sure that genome/build you select on the MACS2 form is an exact match for the reference genome for the prior mapping steps used to generate the BAM(s).

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you Jen for the help!

ADD REPLY • link written 2.2 years ago by mkim3 • 10
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