kingfisher error

[yuzhenpeng]

hello, wwood,

I used the kingfisher get some error. Could you help me, Thank you.

`kingfisher get -r ERR1739691 -m ena-ascp

07/17/2021 04:23:33 PM INFO: Attempting download method ena-ascp .. 07/17/2021 04:23:33 PM INFO: Using aspera ssh key file: $HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh 07/17/2021 04:23:33 PM INFO: Querying ENA for FTP paths for ERR1739691.. Traceback (most recent call last): File "/public4/home/sc56340/miniconda3/bin/kingfisher", line 261, in main() File "/public4/home/sc56340/miniconda3/bin/kingfisher", line 224, in main kingfisher.download_and_extract( File "/public4/home/sc56340/miniconda3/lib/python3.9/site-packages/kingfisher/init.py", line 213, in download_and_extract result = EnaDownloader().download_with_aspera(run_identifier, '.', File "/public4/home/sc56340/miniconda3/lib/python3.9/site-packages/kingfisher/ena.py", line 56, in download_with_aspera ftp_urls = self.get_ftp_download_urls(run_id) File "/public4/home/sc56340/miniconda3/lib/python3.9/site-packages/kingfisher/ena.py", line 20, in get_ftp_download_urls text = extern.run("curl --silent '{}'".format(query_url)) File "/public4/home/sc56340/miniconda3/lib/python3.9/site-packages/extern/init.py", line 41, in run raise ExternCalledProcessError(process, command) extern.ExternCalledProcessError: Command curl --silent 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERR1739691&result=read_run&fields=fastq_ftp' returned non-zero exit status 1. STDERR was: b STDOUT was: b `

[wwood]

Hi,

I'm hopefully soon going to release some fixes for things like this, but in the meantime does just simply rerunning it work? Sometimes ENA can be a bit finnicky.

[yuzhenpeng]

solved it. maybe my network problem

[yuzhenpeng]

By the way, can you set the ascp with -k 1, which support network outage for continuing download.

[wwood]

I set the default to -k 2 so some checksum is used in case of file corruption, but thanks for the tip. You can change this also with --ascp-args.