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nf-core / fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases
https://nf-co.re/fetchngs
MIT License
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SRA file links deprecated #301

Open tiendu opened 7 months ago

tiendu commented 7 months ago

Description of the bug

I used these IDs as input:

SRR26943528
SRR26943529

I was unable to retrieve the download links. ffq said that NCBI is deprecating SRA file links so that's why no download links available.

Command used and terminal output

No response

Relevant files

No response

System information

No response

allyssonallan commented 3 months ago

That what I saw when I tried...

Command executed:

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX3958387_SRR7026107_1.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR702/007/SRR7026107/SRR7026107_1.fastq.gz

  echo "782827dbf79c833f1c439f2db1aa932a  SRX3958387_SRR7026107_1.fastq.gz" > SRX3958387_SRR7026107_1.fastq.gz.md5
  md5sum -c SRX3958387_SRR7026107_1.fastq.gz.md5

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX3958387_SRR7026107_2.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR702/007/SRR7026107/SRR7026107_2.fastq.gz

  echo "53550f7b015054a1085d9268b626e6f3  SRX3958387_SRR7026107_2.fastq.gz" > SRX3958387_SRR7026107_2.fastq.gz.md5
  md5sum -c SRX3958387_SRR7026107_2.fastq.gz.md5

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP":
      wget: $(echo $(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*$//'))
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

We now have a S3 solution to work with. I don't know if it is a good workaround.

allyssonallan commented 3 months ago

Maybe this prefetch -> fasterq-dump -> gzip works.

https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump

Midnighter commented 3 months ago

The last part is already implemented if you run the pipeline with the option --download_method sratools.