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MSA query stuck at "PENDING 0%" for a particular sequence. #49

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jnrsloth opened this issue Sep 22, 2021 · 2 comments
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MSA query stuck at "PENDING 0%" for a particular sequence. #49

jnrsloth opened this issue Sep 22, 2021 · 2 comments

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@jnrsloth
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Not sure if I'm doing something incorrectly.
A particular sequence doing a batch run using the alphafold2_batch or a single run with the AlphaFold2_mmseqs2 notebook seems to cause the MMSeq2 query step to hang.
My current run has been stuck at 0% on the MSA (MMSeq2 (Uniref+environmental)) step for the past 1h 43 minutes and it's been stuck for longer in the past before I kill the process.
The raw sequence is; MAQVQLVESGGGLVQAGGSLRLSCAVSGRPFSEYNLGWFRQAPGKEREFVARIRSSGTTVYTDSVKGRFSASRDNFLATT
LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSG
KKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKELAKNMGYLQLNSLEPEDTAVYY
CAMSRVDTDSPAFYDYWGQGTQVTVSTPRS

Other variations on this sequence have worked flawlessly with these settings, so I'm not sure what is wrong with this sequence.
Running the notebook off a colab instance, not locally.

LaM-8_NA73-O.txt
file extension changed from fasta to txt so that github would allow the upload

@milot-mirdita
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milot-mirdita commented Sep 22, 2021

That sequence was already processed before the last server update and is now in an invalid state after the last restart.

Could you append a single amino acid to break the cache? I cant restart the server right now.

@jnrsloth
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That fixed it, perfect!

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