cartogene functional enrichment file is not present

[smoorsh]

Feltus and I can't find the topfunn file results. Where are they? Is this related to the error we previously reported?

[ZealousGeneticist]

Hi! I’m Luke, the Creator of CartoFlow. The error absolutely is causing the problem. It seems that sciparse can’t find one of its own modules, which is odd… I wanted to ask, were you able to run the program again with your data?

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On Fri, Jan 19, 2024 at 12:38 PM smoorsh ***@***.***> wrote: Feltus and I can't find the topfunn file results. Where are they? Is this related to the error we previously reported? — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6F7C2PZMJPHXHMGM3L7VXTYPKVQVAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TAOJZGQYTONI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[smoorsh]

Hi! I’m Luke, the Creator of CartoFlow. The error absolutely is causing the problem. It seems that sciparse can’t find one of its own modules, which is odd… I wanted to ask, were you able to run the program again with your data?
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On Fri, Jan 19, 2024 at 12:38 PM smoorsh @.> wrote: Feltus and I can't find the topfunn file results. Where are they? Is this related to the error we previously reported? — Reply to this email directly, view it on GitHub <#2>, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6F7C2PZMJPHXHMGM3L7VXTYPKVQVAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TAOJZGQYTONI . You are receiving this because you are subscribed to this thread.Message ID: @.>

Hey Luke! I did not run it again after receiving the error the first time. Every other file that is supposed to be created after running the program is created, only the toppfun file is missing. Should I try running the data again to see if the toppfun file is created this time? Does the program need to be run once to download all of the folders it claimed I was missing the first time, and then run again to obtain all of the results?

[ZealousGeneticist]

That’s odd, it seemed from the first error message that the a number of files wouldn’t be available to you. I do suggest running it again. The program should be able to do everything immediately, the confusing part is the SciPy package not seeming to work even though it was downloaded fully. I’ve occasionally had a package issue every once in a while and it normally disappears after an hour or two. It might have been an issue downloading the package, but running it again should check and fix that. I’m running some data myself to see if I can replicate this issue on my machine.

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On Fri, Jan 19, 2024 at 1:11 PM smoorsh ***@***.***> wrote: Hi! I’m Luke, the Creator of CartoFlow. The error absolutely is causing the problem. It seems that sciparse can’t find one of its own modules, which is odd… I wanted to ask, were you able to run the program again with your data? … <#m_2947321385474819259_> On Fri, Jan 19, 2024 at 12:38 PM smoorsh *@*.*> wrote: Feltus and I can't find the topfunn file results. Where are they? Is this related to the error we previously reported? — Reply to this email directly, view it on GitHub <#2 <#2>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6F7C2PZMJPHXHMGM3L7VXTYPKVQVAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TAOJZGQYTONI <https://github.com/notifications/unsubscribe-auth/A6F7C2PZMJPHXHMGM3L7VXTYPKVQVAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TAOJZGQYTONI> . You are receiving this because you are subscribed to this thread.Message ID: @.*> Hey Luke! I did not run it again after receiving the error the first time. Every other file that is supposed to be created after running the program is created, only the toppfun file is missing. Should I try running the data again to see if the toppfun file is created this time? Does the program need to be run once to download all of the folders it claimed I was missing the first time, and then run again to obtain all of the results? — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6F7C2I5BCEVSZUU66QEOJLYPKZLTAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBQHA3DQMZXGA> . You are receiving this because you commented.Message ID: ***@***.***>

[ZealousGeneticist]

Hey @smoorsh ! As you may have seen in #1 , I think this last update should have fixed the issues! Please reinstall the newest version of CartoFlow and tell me if it works or not. If it doesn't work, please post the new errors here.

[smoorsh]

Hey @ZealousGeneticist ! I ran Cartoflow again, and while I did not get any errors, I still cannot locate the ToppFun file in the output. Where should I be looking for this file, and what should it be called?

[ZealousGeneticist]

Sorry for the later than usual response. Glad you didn’t get any errors! The ToppFun files will be in a folder called “community”. This will be in both the CartoFlow directory and the genebridge directory. It also has a graph of every subcommunity along with it. I hope this helps!

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On Sat, Jan 27, 2024 at 5:17 PM smoorsh ***@***.***> wrote: Hey @ZealousGeneticist <https://github.com/ZealousGeneticist> ! I ran Cartoflow again, and while I did not get any errors, I still cannot locate the ToppFun file in the output. Where should I be looking for this file, and what should it be called? — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6F7C2LHM67ZENGKW5OF5QLYQV4HXAVCNFSM6AAAAABCCJRDRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTGM2TCOBUGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>