pop from empty list error when taxonomy label not complete

[BenKaehler]

Bug Description
If one of the taxonomies is not complete, for instance

k_Eukaryota; p_Parabasalia; c_Hypotrichomonadea; o_Hypotrichomonadida; f_Hypotrichomonadidae; g_Trichomitus sp.

does not go all the way to species level, you get an uninformative pop from empty list error when you run classify-sklearn.

Comments
It would be better if there was an error message when training the classifier.

References
This issue was discovered here.

[ssavvi]

I am also getting this error. Is there anyway to resolve this . Issue occurs with QIIME2 version 2019.10 onwards .

[ssavvi]

Just ran feature classifier classif- sklearn with silva-138-99-515-806-nb-classifier version and this bug was no longer an issue ! Thanks

[XrandallX]

Hello,

I also received the original message and I tried to correct by the following addition to the code based on the following thread

https://forum.qiime2.org/t/plugin-error-from-feature-classifier-pop-from-empty-list/1431/11

qiime feature-classifier classify-sklearn --i-reads rep-seqs.qza --i-classifier classifier.qza --o-classification result.qza --p-confidence -1 --p-read-orientation same

This is the new error I received regarding the --p- confidence -1 section below

Would anyone have any ideas on how to deal with this please?

Thank you.

Plugin error from feature-classifier:

Parameter 'confidence' received -1 as an argument, which is incompatible with parameter type: Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable')

Debug info has been saved to /tmp/qiime2-q2cli-err-dc8df57b.log

[nbokulich]

Hi @XrandallX ,

Please open a topic on the forum for troubleshooting issues — you are receiving a different error message that is not related to this issue.

[ncep112]

Hello,

I also got this error when I used QIIME 2 version 2022.2. I made a classifier file (silva-138-ssu-nr99-515f-806r-classifier.qza) following the steps in the RESCRIPt tutorial. Using the qiime rescript dereplicate command, I made a consensus classifier file using the -lca option. I thought this command was supposed to fill the lower-level taxonomy with empty place-holders to prevent this issue from happening, so I am not sure what is causing the error. Do you have any advice?

Thank you for your help; it is greatly appreciated!

[ssavvi]

The latest version of the classifier does not produce the error .

…

On Tue, 15 Mar 2022 at 20:33, ncep112 ***@***.***> wrote: Hello, I also got this error when I used QIIME 2 version 2022.2. I made a classifier file (silva-138-ssu-nr99-515f-806r-classifier.qza) following the steps in the RESCRIPt tutorial. Using the *qiime rescript dereplicate* command, I made a consensus classifier file using the -lca option. I thought this command was supposed to fill the lower-level taxonomy with empty place-holders to prevent this issue from happening, so I am not sure what is causing the error. Do you have any advice? Thank you for your help; it is greatly appreciated! — Reply to this email directly, view it on GitHub <#93 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM5KAONNKV2OKCX4MKPO6CDVADX2TANCNFSM4D7Y5XOQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[ncep112]

@ssavvi thanks for the response! I was creating and training my own classifier file instead of using a pre-made one and received this error when I tried to assign taxonomy to my req-seqs.qza file. Did you use a pre-made classifier or create your own?

[ssavvi]

Downloaded a pre made version ( latest )

…

On Tue, 15 Mar 2022 at 20:42, ncep112 ***@***.***> wrote: @ssavvi <https://github.com/ssavvi> thanks for the response! I was creating and training my own classifier file instead of using a pre-made one and received this error when I tried to assign taxonomy to my req-seqs.qza file. Did you use a pre-made classifier or create your own? — Reply to this email directly, view it on GitHub <#93 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM5KAOKO3B7E32TYLN5G6ADVADY4ZANCNFSM4D7Y5XOQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[nbokulich]

Hi @ncep112 and @ssavvi please post all user support questions to the QIIME 2 forum, thank you.

[gregcaporaso]

@nbokulich, do you know if this is a bug that needs to be addressed (e.g., with a better error message)?

[nbokulich]

yes this still has not been addressed, please leave open.

[Thainacortezs]

I had the same issue and what I did was to use a python script to fix the taxon file to adjust the pattern of taxonomic identifications, where all the sequences had the exactly same hierarchical levels. Even if the level wasn't there for some sequences, I just classified as 'unknown'. That way all the sequences had the same amount of classifications. Hope it helps