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genome_updater FIX failed

Hello guys, I am using genome_updater.sh to download viral sequences. All worked well, but it never can fix (-i option) the missing files (1005 files failed to download). Any idea?

Thank you

genome_updater.sh -d "refseq" -g "viral" -c "all" -f "genomic.fna.gz"

-o "all_virus_genomes" -t 4 -i

┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐    ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐
│ ┬├┤ ││││ ││││├┤     │ │├─┘ ││├─┤ │ ├┤ ├┬┘
└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴  ─┴┘┴ ┴ ┴ └─┘┴└─
                                     v0.2.5 
-------------------------------------------
Mode: FIX - DOWNLOAD
Working directory: /remote-storage/NCBI-ViralRefSeq/all_virus_genomes/
-------------------------------------------
Checking for missing files in the current version [2021-12-02_11-37-59]
 - 9 missing files
 - Downloading 9 files with 4 threads
 - 0/9 files successfully downloaded


Checking for extra files [2021-12-02_11-37-59]

 - None


# 11845/12850 files successfully obtained
 - 1005 file(s) failed to download. Please re-run your command with -i to fix it again
# Log file: /remote-storage/NCBI-ViralRefSeq/all_virus_genomes/2021-12-02_11-37-59/2021-12-02_14-36-35.log
# Finished! Current version: /remote-storage/NCBI-ViralRefSeq/all_virus_genomes/2021-12-02_11-37-59
ncbi viruses genome_updater.sh sequences
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updated by pirovc • pirovc • written by emiliomastriani • emiliomastriani

1 answer

There is nothing much you can do, the download may be failing due to many reasons (NCBI file missing, connection issue, etc). You could try it again later to see if it works. You can also try to re-run it with the parameter -p to report all failed urls into a file (*_url_failed.txt).

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written by pirovc • pirovc

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