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hhalignment: did not find [x] match states in sequence [i] #277
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Also to note, this does work on other input sequences |
Do you have the full command line call that was passed to HHblits? |
Thanks for the reply and trying to reproduce. Unfortunately little more info from my end
Sorry that I forgot to include this line in the gist:
which appear to be correct:
Tried running again, and the same result. A number of other input sequences have now worked without issue. |
Can you check the uniclust too:
|
I reproduced your issue. Weirdly it only happens in this specific combination of BFD and UC 2018_08. Either database alone, or a newer UC version does not result in this error. |
Thanks for looking into this further, and glad it ended up being reproducible. I guess for me the easiest solution will be to update the uniclust DB? |
That's probably the easiest solution for now. We will need some time to investigate the root cause. |
Hi! Is there a better solution to this problem at present? When I run the job here, the above error message also appears @milot-mirdita @ |
Same error here. Is there a better solution to this problem? |
I just ran into it too. Is there a specific newer version of UniClust that does the job? |
I also have seen several instances of this hhblits error with different sequences using AlphaFold. I doubt the problem is with UniClust and updating that database will likely just make the errors occur with different sequences. |
This also happened to one protein sequence I'm working on, while no similar problem for other sequences. |
I second this problem with the 2.2.0 version: ERROR: Error in /tmp/hh-suite/src/hhalignment.cpp:3539: MergeMasterSlave:
|
I also have this issue: Expected Behaviorhhblits does not crash on this sequence:
and using uniclust30_2018_08 database. Current Behaviorhhblits crashes with the error:
There are also some other sequences crashing like this, can provide them if useful Steps to Reproduce (for bugs)Please make sure to execute the reproduction steps.
HH-suite Output (for bugs)Please make sure to post the complete output of the tool you called. Please use gist.github.com. ContextProviding context helps us come up with a solution and improve our documentation for the future. Your EnvironmentInclude as many relevant details about the environment you experienced the issue in.
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Janek, I ran your command just now on my computer with your sequence and it finished without any error... I got 6298 lines in a3m output. Maybe there's a problem with the computational resources you are using, or the binaries (did you compile them for the machine?)? bfd is quite big... I ran it on a single 256GB RAM machine, which is not big as for today's standards, with local storage. That's what I was able to check. Unfortunately, I didn't get any error. |
Thanks Kamil for checking this. I can see that you checked on UniRef30_2020_06 while I used uniclust30_2018_08, as others in this feed, probably that is why it works for you. We want to use uniclust30_2018_08 because AlphaFold uses it. Can you check with uniclust30_2018_08? BTW. it's not related to memory, longer sequences with bigger alignment run just fine on our setup. @DS-unib also gets this error on the same sequence and database. I have four more sequences behaving like this (out of hundreds that run fine). |
Hold on, or is the UniRef30_2020_06 basically updated version of uniclust30_2018_08? |
I believe yes - they are calling it uniclust but the files are named Uniref30... also, there's even newer version from 2021: |
Oh, and indeed, with uniclust'18 it crashed with exactly the same error as yours. :/ |
I tested UniRef30_2020_06 on around 1,000 sequences and as Tom Goddard predicted above, it now crashes with the same error just on different sequences, like this one:
Will check UniRef30_2021_03 tonight. |
UniRef30_2021_03 gives similar errors just on different sequences. |
The multi-database feature of HH-suite seems the be the problem. If you search against the Uniref30 and the BFD separately it works without crashing. Please do not use this feature. |
Thanks! I hope DeepMind is reading this, as the command is from AlphaFold. |
Another option would to merge both databases into one (which shouldn't be
difficult since it is ffindex based) and modify af2 script to run it on the
merged DB.
Janek's question inspired me to check, for a few Pfam DUFs, whether adding
BFD to profile building procedure brings new, informative mappings to
proteins of known structures - it didn't - but maybe my choices were
unfortunate. In the next recalculation of my all vs all mappings database
I'll try to use fused databases for a more systematic comparison. Updating
to uniref2021 itself boosted the scores a bit. But af2 probably makes use
of more nuanced profile properties than simply similarity to known
structures/domains so BFD might be beneficial especially in the cases of
some orphan sequences, like viral ones...
pt., 6 maj 2022 o 11:58 Jan Kosinski ***@***.***> napisał(a):
… The multi-database feature of HH-suite seems the be the problem. If you
search against the Uniref30 and the BFD separately it works without
crashing. Please do not use this feature.
Thanks! I hope DeepMind is reading this, as the command is from AlphaFold.
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Hi @martin-steinegger , how can I run Alphafold with searching against either Uniref30 or BFD ? Alphafold requires both the options --uniclust30_database_path and --bfd_database_path to run to the best of my knowledge. Thanks. |
@jkosinski could you share how to edit the AlphaFold hh-suite call here to prevent this error? |
Well, I haven't edited the code to enable this. I guess the easiest would
have to run hhblits twice and combine the alignments into one file
named bfd_uniclust_hits.a3m, but I don't know if that would be equivalent.
Does anyone know?
Don't tell anyone but what I did in the end was quite silly:
- first run with the newest UniRef30_2021_03 specified in the
--uniclust30_database_path
- re-run the crashed jobs with the default database provided by AlphaFold.
Out of 5,000 sequences that I have run, I got only one crashed on both with
the above error.
But this is definitely not a nice solution ;-)
…On Thu, Jul 21, 2022 at 5:07 PM grandrea ***@***.***> wrote:
@jkosinski <https://github.com/jkosinski> could you share how to edit the
AlphaFold hh-suite call here to prevent this error?
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I downloaded the latest UniRef30_2022_02, and hhblits also reported this error. |
I have been testing with this issue and I think the cause is in UniRef30. The bdf+uniclust30_2018_08 works without any problems, while the bfd+UniRef30_2022_02 always shows the same error. |
See soedinglab/hh-suite#277 for details.
See soedinglab/hh-suite#277 for details.
hi, we are also seeing the same issue when running a recent AlphaFold and using UniRef30_2021_03 |
❗ Make to check out our User Guide.
I am trying to run alphafold (using the docker image in the current readme), but an error is encountered when running the HHblits step. Apologies if this is actually an alphafold issue – do let me know and I will close this issue and post there.
I am not sure what this error message means/what it implies – if you could help me understand further I would be happy to look into this in more detail if I can.
Expected Behavior
hhblits completes alignment
Current Behavior
Error hit at
hh-suite/src/hhalignment.cpp:3539
The error lines are (full output in gist below):
Steps to Reproduce (for bugs)
dltA.fa:
HH-suite Output (for bugs)
https://gist.github.com/johnlees/535f1012fbbded1ffaa499f40cbd4bdf
Context
Running via alphafold docker image and databases
Your Environment
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