error running kreport2mpa.py script, name 'l_vals' is not defined.

[Sautumn-Lin]

Traceback (most recent call last):
File "/home/zlinbz/miniconda3/envs/bracken/bin/KrakenTools-master/kreport2mpa.py", line 188, in
main()
File "/home/zlinbz/miniconda3/envs/bracken/bin/KrakenTools-master/kreport2mpa.py", line 143, in main
report_vals = process_kraken_report(line)
File "/home/zlinbz/miniconda3/envs/bracken/bin/KrakenTools-master/kreport2mpa.py", line 80, in process_kraken_report
taxid = int(l_vals[-3])
NameError: name 'l_vals' is not defined. Did you mean: 'locals'?

Is there anyone who met this problem and solved it?

[rahel31]

Same error here :

....../KrakenTools-master/kreport2mpa.py", line 80, in process_kraken_report
taxid = int(l_vals[-3])
NameError: global name 'l_vals' is not defined

Did you solve it ? @Sautumn-Lin

[Sautumn-Lin]

yes, I just downloaded another "kreporet2.mpa.py", and it finally can be used. When Iuse computer Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: rahel31 ***@***.***> Sent: Thursday, October 27, 2022 10:15:23 PM To: jenniferlu717/KrakenTools ***@***.***> Cc: LIN Ziqiu ***@***.***>; Mention ***@***.***> Subject: Re: [jenniferlu717/KrakenTools] error running kreport2mpa.py script, name 'l_vals' is not defined. (Issue #57) Same error here : ....../KrakenTools-master/kreport2mpa.py", line 80, in process_kraken_report taxid = int(l_vals[-3]) NameError: global name 'l_vals' is not defined Did you solve it ? @Sautumn-Lin<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSautumn-Lin&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mKb89kFanCOxpHYZwBWfPpxyWl8nABHLAEegqQuNDjo%3D&reserved=0> — Reply to this email directly, view it on GitHub<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjenniferlu717%2FKrakenTools%2Fissues%2F57%23issuecomment-1293591392&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NxBSWpwlCybhJ4oTzWkqmYUHtEe1UsSIOjp5piPk3rs%3D&reserved=0>, or unsubscribe<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA3VPWTQLOUEHYWUF67T2O6DWFKE7XANCNFSM6AAAAAARH4G4IU&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fA29I9X4XvRVoWuf10uLLUufXMVvKDarf5aEcTclp3I%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Sautumn-Lin]

continue… when I use computer later, I can send it to you. Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: LIN Ziqiu ***@***.***> Sent: Friday, October 28, 2022 12:26:21 PM To: jenniferlu717/KrakenTools ***@***.***>; jenniferlu717/KrakenTools ***@***.***> Cc: Mention ***@***.***> Subject: Re: [jenniferlu717/KrakenTools] error running kreport2mpa.py script, name 'l_vals' is not defined. (Issue #57) yes, I just downloaded another "kreporet2.mpa.py", and it finally can be used. When Iuse computer Get Outlook for Android<https://aka.ms/AAb9ysg>

________________________________ From: rahel31 ***@***.***> Sent: Thursday, October 27, 2022 10:15:23 PM To: jenniferlu717/KrakenTools ***@***.***> Cc: LIN Ziqiu ***@***.***>; Mention ***@***.***> Subject: Re: [jenniferlu717/KrakenTools] error running kreport2mpa.py script, name 'l_vals' is not defined. (Issue #57) Same error here : ....../KrakenTools-master/kreport2mpa.py", line 80, in process_kraken_report taxid = int(l_vals[-3]) NameError: global name 'l_vals' is not defined Did you solve it ? @Sautumn-Lin<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSautumn-Lin&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mKb89kFanCOxpHYZwBWfPpxyWl8nABHLAEegqQuNDjo%3D&reserved=0> — Reply to this email directly, view it on GitHub<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjenniferlu717%2FKrakenTools%2Fissues%2F57%23issuecomment-1293591392&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NxBSWpwlCybhJ4oTzWkqmYUHtEe1UsSIOjp5piPk3rs%3D&reserved=0>, or unsubscribe<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA3VPWTQLOUEHYWUF67T2O6DWFKE7XANCNFSM6AAAAAARH4G4IU&data=05%7C01%7Czlinbz%40connect.ust.hk%7Cdab8e51917764d17f34f08dab825b156%7C6c1d415239d044ca88d9b8d6ddca0708%7C1%7C0%7C638024769275676338%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fA29I9X4XvRVoWuf10uLLUufXMVvKDarf5aEcTclp3I%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[rahel31]

Thank you! Maybe you can put it on google drive and share the downloadable link here? It seems I cannot send an e-mail to you or personal message over github...

[Sautumn-Lin]

https://github.com/jenniferlu717/KrakenTools/releases/tag/v1.2
I can not send you the file on this web. You can try downloading it on this link, but I am unsure whether it is the right one.

[rahel31]

Ok, thanks :)

[simonleandergrimm]

@rahel31 Did this work for you? I still get the same error.

@jenniferlu717 did this also happen to others? If so, is there an easy fix on our side?

Traceback (most recent call last):
File "/[...]/kreport2mpa.py", line 188, in
main()
File "/[...]/kreport2mpa.py", line 143, in main
report_vals = process_kraken_report(line)
File "/[...]/illumina_pilot/kreport2mpa.py", line 80, in process_kraken_report
taxid = int(l_vals[-3])
NameError: name 'l_vals' is not defined. Did you mean: 'locals'?

[gazollavolpiano]

Dear @simonleandergrimm, I used the release v1.1 and it worked!

You can find it here: https://github.com/jenniferlu717/KrakenTools/releases/tag/v1.1

Any concerns about using this previous version to avoid that error @jenniferlu717? :)

Thank you!!