Fetch from COG-UK failing

[joverlee521]

Automated pipeline for open ingest has been failing since Friday, July 5th with errors during the fetch from COG-UK.

[batch] [2024-07-05T18:19:00+00:00] ccurulr:l :( 2(82)8 )F aFialileedd  ttoo  ccoonnnneectc tt ot oc ocgo-gu-ku.ks.3s.3c.lcilmibm.ba.ca.cu.ku kp oprotr t4 4434:3 :C oCnonnencetcitoino nt itmiemde do uotu
[batch] [2024-07-05T18:19:00+00:00] t
[batch] [2024-07-05T18:19:00+00:00] [Fri Jul  5 18:18:59 2024]
[batch] [2024-07-05T18:19:00+00:00] Error in rule fetch_cog_uk_accessions:
[batch] [2024-07-05T18:19:00+00:00]     jobid: 17
[batch] [2024-07-05T18:19:00+00:00]     output: data/cog_uk_accessions.tsv
[batch] [2024-07-05T18:19:00+00:00]     shell:
[batch] [2024-07-05T18:19:00+00:00]         
[batch] [2024-07-05T18:19:00+00:00]         ./bin/fetch-from-cog-uk-accessions > data/cog_uk_accessions.tsv
[batch] [2024-07-05T18:19:00+00:00]         
[batch] [2024-07-05T18:19:00+00:00]         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[batch] [2024-07-05T18:19:00+00:00] Removing output files of failed job fetch_cog_uk_accessions since they might be corrupted:
[batch] [2024-07-05T18:19:00+00:00] data/cog_uk_accessions.tsv

[AngieHinrichs]

See https://github.com/COG-UK/dipi-group/issues/213

[joverlee521]

Ah, thank you for the pointer @AngieHinrichs 👍

[joverlee521]

I verified the COG-UK files are available and today's automated workflow has progressed past the fetch rules.