q2-scnic - error - read_table() got an unexpected keyword argument 'squeeze'

[kindergarten]

I got following error

Plugin error from SCNIC:
read_table() got an unexpected keyword argument 'squeeze'

while running (q2-scnic in qiime2-2024.5)

qiime SCNIC make-modules-on-correlations
--i-correlation-table fake_correls.qza
--i-feature-table fake_data.qza
--p-min-r .35
--o-collapsed-table fake_data.collapsed.qza
--o-correlation-network fake_net.modules.qza
--o-module-membership fake_membership.qza

qiime2-q2cli-err-ns6oyf6c-1.txt (2.6 KB)

log file is attached.

I would appreciate if you could help me resolve this issue. Thanks.

[colinvwood (Colin Wood)]

Hello @kindergarten,

It looks like you found a bug! We recently updated pandas to above 2.0 and a lot of things changed. The error is complaining about a parameter to the pandas read_table function that doesn't exist anymore. I'll open an issue for this and hopefully it can get fixed soon. In the meantime you should be able to install an older qiime2 environment to avoid this issue. The 24.2 release or anything before that will have the right version of pandas.

[colinvwood (Colin Wood)]

Hello @kindergarten,

Here is a link to the issue on github if you want to follow its status. I'm unsure if the plugin is regularly maintained so I wouldn't necessarily expect it to be resolved soon.

[kindergarten]

No error with q2-SCNIC in qiime2-2023.5. Thanks.