installing databases failed

[jacob-israel]

Are you using the latest release? Yes , I am using the latest funannotate version.

Describe the bug when trying to install the interpro databases, an error appears and that's it. I can't install BUSCO databases like dikarya.The first databases download and install correctly, but since I try to install the interpro database, it fails and I can't install another database.

What command did you issue? $ funannotate setup -f -i interpro or $ funannotate setup -i all --update

[Sep 02 09:57 PM]: OS: Ubuntu 24.04, 16 cores, ~ 528 GB RAM. Python: 3.12.3 [Sep 02 09:57 PM]: Running 1.8.5 [Sep 02 09:57 PM]: Database location: /data2TB/databases/funannotate [Sep 02 09:57 PM]: Retrieving download links from GitHub Repo [Sep 02 09:57 PM]: Parsing Augustus pre-trained species and porting to funannotate [Sep 02 09:57 PM]: Downloading InterProScan Mapping file [Sep 02 09:57 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz Bytes: 37913043 [Sep 02 10:00 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list Bytes: 2527016 Traceback (most recent call last): File "/usr/local/bin/funannotate", line 8, in sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.12/dist-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/usr/local/lib/python3.12/dist-packages/funannotate/setupDB.py", line 704, in main interproDB(DatabaseInfo, args.force, args=args) File "/usr/local/lib/python3.12/dist-packages/funannotate/setupDB.py", line 436, in interproDB for x in elem.getchildren(): ^^^^^^^^^^^^^^^^ AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

Logfiles

OS/Install Information

• Ubuntu Linux Server 24.04 LTS

[hyphaltip]

works for me as of now w/ version 1.8.17 which is live code -- can you confirm the network connection works for you

funannotate setup -f -i interpro
-------------------------------------------------------
[Sep 02 08:45 PM]: OS: Rocky Linux 8.8, 96 cores, ~ 527 GB RAM. Python: 3.8.15
[Sep 02 08:45 PM]: Running 1.8.17
[Sep 02 08:45 PM]: Database location: /srv/projects/db/funannotate/1.8
[Sep 02 08:45 PM]: Retrieving download links from GitHub Repo
[Sep 02 08:45 PM]: Parsing Augustus pre-trained species and porting to funannotate
[Sep 02 08:46 PM]: Downloading InterProScan Mapping file
[Sep 02 08:46 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz Bytes: 37913043
[Sep 02 08:47 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list Bytes: 2527016
[Sep 02 08:47 PM]: InterProScan XML: version=101.0 date=2024-07-25 records=45,899

[jacob-israel]

@hyphaltip yes I confirm the network connections works for me.

funannotate setup -f -i interpro

[Sep 03 08:36 PM]: OS: Ubuntu 24.04, 16 cores, ~ 528 GB RAM. Python: 3.12.3 [Sep 03 08:36 PM]: Running 1.8.5 [Sep 03 08:36 PM]: Database location: /data2TB/databases/funannotate [Sep 03 08:36 PM]: Retrieving download links from GitHub Repo [Sep 03 08:36 PM]: Parsing Augustus pre-trained species and porting to funannotate [Sep 03 08:36 PM]: Downloading InterProScan Mapping file [Sep 03 08:36 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz Bytes: 37913043 [Sep 03 08:39 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list Bytes: 2527016 Traceback (most recent call last): File "/usr/local/bin/funannotate", line 8, in sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.12/dist-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/usr/local/lib/python3.12/dist-packages/funannotate/setupDB.py", line 704, in main interproDB(DatabaseInfo, args.force, args=args) File "/usr/local/lib/python3.12/dist-packages/funannotate/setupDB.py", line 436, in interproDB for x in elem.getchildren(): ^^^^^^^^^^^^^^^^ AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

[hyphaltip]

I guess I would suggest upgrading from github live perhaps as I can't replicate this error wth the current code. I'm not sure what changed to support this parsing.

[gkanogiannis]

All ftp.ebi.ac.uk links in downloads.json need to be https, otherwise some downloads stuck at 99%