Download issue

[Xinpeng021001]

Hi,

Thank you for developing the great tool! Currently, I'm trying to download the whole JGI+NCBI fungi database, but there are some issues:

JGI:
Cannot find the xml

NCBI:

GCA_009193545.1 failed to find the genome ID
10%|███████▉
| 150/1574 [08:17<1:18:49, 3.32s/it]

I guess for the JGI, they changed the API rule to download. Could you please check if possible? Thank you again for developing this great tool.

Best.
Xinpeng

[Xinpeng021001]

Searching NCBI for MycoCosm overlap
100%|████████████████████████████████| 4590/4590 [00:00<00:00, 33979.84it/s]
1298 overlapping genomes
Downloading MycoCosm data
Redundancy check
1726 genomes to assimilate
Logging into JGI
Retrieving xml directories
CocheC4_6 failed to retrieve XML
Rhoto_IFO0880_4 failed to retrieve XML
Aspni7 failed to retrieve XML
Trici4 failed to retrieve XML

[xonq]

thanks for bringing this to my attention, I'll have to look into this during the weekend

[xonq]

Hey @Xinpeng021001 sorry for the long delay - I'm not able to reproduce this issue. There may be some genomes where XMLs cannot be retrieved, but overall I'm not running into errors downloading. Thoughts that come to mind:

• Are you using the correct login credentials?
• Have you retried again to see if this was a transient JGI server issue?
• Are you still running into this issue?

[Xinpeng021001]

Thank you for your reply and efforts! I'll re-check it asap.

[xonq]

I'm closing this issue, I will reopen if you report you are still running into trouble.

[xonq]

Indeed, JGI's API completely changed. This is being reworked in v2.0.0