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patrickbryant1 / MoLPC

Modelling of Large Protein Complexes
Apache License 2.0
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InvalidArgumentError #6

Closed MohdKhairulNizam closed 2 years ago

MohdKhairulNizam commented 2 years ago

Hi Patrick,

Capture

The test sample ran perfectly but I received this error when trying on my sample

patrickbryant1 commented 2 years ago

Hi, This seems to be an error with the input MSA. Please check that the MSA you input has the right dimensions.

MohdKhairulNizam commented 2 years ago

How do I check if the MSA has the right dimensions and how to fix if the dimension is wrong?

patrickbryant1 commented 2 years ago

Hi, I suggest that you first open the MSA file and ensure it matches the query sequence in length. These are errors that are not related to MoLPC and, unfortunately, I can't help you with these.

Pi3k-Akt commented 2 years ago

Hi @MohdKhairulNizam and @patrickbryant1 , Has this problem been solved? I have the same problem.

MohdKhairulNizam commented 2 years ago

Hi,

Yes, I fixed it by using an alignment file (.a3m) generated using MoLPC pipeline instead of https://toolkit.tuebingen.mpg.de/tools/hhblits. I also found it useful that everytime I ran the notebook, I cleared the previously generated files to avoid conflict. Hope that helps!

Best Wishes,

Nizam

On Thu, 1 Dec 2022 at 11:14, Pi3k-Akt @.***> wrote:

Hi Mohd and Patrick, Has this problem been solved? I have the same problem.

— Reply to this email directly, view it on GitHub https://github.com/patrickbryant1/MoLPC/issues/6#issuecomment-1333106460, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQS2BXQVSYUIKJSSC4WPMRLWLAJYJANCNFSM6AAAAAARJV7S4I . You are receiving this because you authored the thread.Message ID: @.***>

Pi3k-Akt commented 2 years ago

Hi, Yes, I fixed it by using an alignment file (.a3m) generated using MoLPC pipeline instead of https://toolkit.tuebingen.mpg.de/tools/hhblits. I also found it useful that everytime I ran the notebook, I cleared the previously generated files to avoid conflict. Hope that helps! Best Wishes, Nizam … On Thu, 1 Dec 2022 at 11:14, Pi3k-Akt @.> wrote: Hi Mohd and Patrick, Has this problem been solved? I have the same problem. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQS2BXQVSYUIKJSSC4WPMRLWLAJYJANCNFSM6AAAAAARJV7S4I . You are receiving this because you authored the thread.Message ID: @.>

Hi,

Thanks for your reply!

I found that this error is caused by the first FASTA sequence in the MSA file (.a3m) not matching the input file. For me, the MSA file is missing the last "GH" residues. Manually adding these two residues to the MSA file will fix this error.

Thanks again for your help!