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how to make seqid2taxid.map #259

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DAWNkKim opened this issue Jun 27, 2023 · 1 comment
Open

how to make seqid2taxid.map #259

DAWNkKim opened this issue Jun 27, 2023 · 1 comment

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@DAWNkKim
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Hello,

While trying to building the index with the script provided in the manual:
centrifuge-download -o taxonomy taxonomy
centrigue-download -o library -m -d "archaea,bacteria,viral" refseq > seqid2taxid.map

I obtained the following errors:
image

I could find reports of similar issues in #201, #245, etc, but I couldn't find a workaround.

also I tried -d "archaea" as the error only occurred with "viral", but the seqid2taxid.map file size was zero and empty.

What I want to check is HBV and I have AB033550.fa file downloaded from NCBI. Is there any way to create a seqid2taixd.map with the refseq I have?

Thanks in advance!

@LilyAnderssonLee
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@josemunozc's solution within #201 works fine to me to download viral genomes.

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