Question

Cannot get efetch to download genome - what is wrong?

2

Entering edit mode

6.7 years ago

BioBing ▴ 150

Hi all,

I am trying to download a genome assembly (Bioproject: PRJEB20069, assembly: GCA_900241095.1) in FASTA format using the Entrez utilities from the command line, but it continues to fail:

efetch -db=nuccore -format=fasta -id=GCA_900241095.1 > output.fa

I have tried varies things (using the BioProject number, getting information using esearch etc.) but nothing seems to work.

Can any of you see what I am doing wrong?

Thank you!

Best wishes, Birgitte

entrez genome efetch fasta • 3.9k views

ADD COMMENT • link updated 6.7 years ago by h.mon 35k • written 6.7 years ago by BioBing ▴ 150

1

Entering edit mode

There is no such accession in nuccore:

$ wget  -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=GCA_900241095.1"


https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult>
  <Count>0</Count>
  <RetMax>0</RetMax>
  <RetStart>0</RetStart>
  <IdList/>
  <TranslationSet/>
  <QueryTranslation>(GCA_900241095.1[All Fields])</QueryTranslation>
  <ErrorList>
    <PhraseNotFound>GCA_900241095.1</PhraseNotFound>
  </ErrorList>
  <WarningList>
    <OutputMessage>No items found.</OutputMessage>
  </WarningList>
</eSearchResult>

ADD REPLY • link 6.7 years ago by Pierre Lindenbaum 164k

h.mon · Answer 1 · 2018-04-04

2

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6.7 years ago

GenoMax 147k

You may want to try this too

esearch -db bioproject -query "PRJEB20069" \
  | elink -target assembly \
  | efetch -format docsum \
  | xtract -pattern DocumentSummary -element FtpPath_GenBank \
  | xargs -n 1 sh -c 'wget "$0"/*fna.gz'

ADD COMMENT • link updated 6.7 years ago by h.mon 35k • written 6.7 years ago by GenoMax 147k

0

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This is perfect! Thank you'!

ADD REPLY • link 6.7 years ago by BioBing ▴ 150

0

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That's some serious ncbi-fu stuff. I've just break it into several lines just to make it more readable.

ADD REPLY • link 6.7 years ago by h.mon 35k

score 1 · Answer 2 · 2018-04-03

1

Entering edit mode

6.7 years ago

BioBing ▴ 150

You are right! Thanks!

I think I found a way to download it using:

esearch -db bioproject -query "PRJEB20069" | elink -target nuccore| efetch -format fasta > output.fa

ADD COMMENT • link 6.7 years ago by BioBing ▴ 150

score 1 · Answer 3 · 2018-04-03

1

Entering edit mode

6.7 years ago

h.mon 35k

I think you are downloading more than just the assembly. To download only the assembly scaffolds:

esearch -db nucleotide -query "LS041563[PACC]:LS041565[PACC]" \
  | efetch -format fasta