Small database paths problem

[X Morgan]

Hi team, I downloaded iphop’s current databases yesterday (Aug_2023_pub_rw) and when I was running iphop v 1.3.2 , I got two errors:

FileNotFoundError: [Errno 2] No such file or directory: '/redacted/iphop/Aug_2023_pub_rw/db_infos/gtdbtk.ar122.decorated.tree'

and

FileNotFoundError: [Errno 2] No such file or directory: '/redacted/iphop/Aug_2023_pub_rw/db/GTDBtkr202_and_newrepr_s2_mat.pkl'

I didn’t rename the files because I was afraid something else would break but this was easy to fix with symlinks and then everything worked fine.

In directory db: GTDBtkr202_and_newrepr_s2_mat.pkl -> GTDBtk_and_newrepr_s2_mat.pkl

In directory db_infos: gtdbtk.ar122.decorated.tree -> gtdbtk.ar53.decorated.tree

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[Simon Roux]

Hi,

Sorry about this issue. Which part of iphop do you try to run when you get this error message ? Most of these errors should have been fixed in 1.3.3, so the easiest solution should be to update iphop, but there is one known issue with “add_to_db” which in some cases requires copying over the file gtdbtk.ar53.decorated.tree, but the pkl file should not cause any problem

Best,

Simon

[X Morgan]

Thanks, good to know that’s been fixed in the update. I should have checked for updates before running!

I got that error while running 'iphop predict --fa_file genomes.fa -t 32 --out output_dir --db_dir /iphop/Aug_2023_pub_rw/, after having successfully run iphop download --db_dir /path/iphop --split.

[Simon Roux]

Got it. Let me know if upgrading to 1.3.3 works out, but it should solve this issue.