Comments (12)
milot-mirdita
commented on August 18, 2024
That looks like an MMseqs2 bug, the target alignment it prints is completely broken.
Could you upload the query/target sequence(s)?
I'll try to reproduce the issue locally, it might already be fixed in release 11, then I would only need to update the containers.
By the way, if you want a set of stickers (see https://twitter.com/thesteinegger/status/1201076220957315074), send me your address to milot at mirdita de.
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milot-mirdita
commented on August 18, 2024
I actually only need your unnamed query seq and the 5MRF_1 target seq. That should already be enough to reproduce the issue.
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josemduarte
commented on August 18, 2024
Query sequence is:
CAUCUAAGUAACUUAAGGAUAAGAAAUCAACAGAGAUAUUAUGAGUAUUGGUGAGAGAAAAUAAUAAAGGUCUAAUAAGUAUUAUGUGAAAAAAAUGUAAGAAAAUAGGAUAACAAAUUCUAAGACUAAAUACUAUUAAUAAGUAUAGUAAGUACCGUAAGGGAAAGUAUGAAAAUGAUUAUUUUAUAAGCAAUCAUGAAUAUAUUAUAUUAUAUUAAUGAUGUACCUUUUGUAUAAUGGGUCAGCAAGUAAUUAAUAUUAGUAAAACAAUAAGUUAUAAAUAAAUAGAAUAAUAUAUAUAUAUAAAAAAAUAUAUUAAAAUAUUUAAUUAAUAUUAAUUGACCCGAAAGCAAACGAUCUAACUAUGAUAAGAUGGAUAAACGAUCGAACAGGUUGAUGUUGCAAUAUCAUCUGAUUAAUUGUGGUUAGUAGUGAAAGACAAAUCUGGUUUGCAGAUAGCUGGUUUUCUAUGAAAUAUAUGUAAGUAUAGCCUUUAUAAAUAAUAAUUAUUAUAUAAUAUUAUAUUAAUAUUAUAUAAAGAAUGGUACAGCAAUUAAUAUAUAUUAGGGAACUAUUAAAGUUUUAUUAAUAAUAUUAAAUCUCGAAAUAUUUAAUUAUAUAUAAUAAAGAGUCAGAUUAUGUGCGAUAAGGUAAAUAAUCUAAAGGGAAACAGCCCAGAUUAAGAUAUAAAGUUCCUAAUAAAUAAUAAGUGAAAUAAAUAUUAAAAUAUUAUAAUAUAAUCAGUUAAUGGGUUUGACAAUAACCAUUUUUUAAUGAACAUGUAACAAUGCACUGAUUUAUAAUAAAUAAAAAAAAAUAAUAUUUAAAAUCAAAUAUAUAUAUAUUUGUUAAUAGAUAAUAUACGGAUCUUAAUAAUAAGAAUUAUUUAAUUCCUAAUAUGGAAUAUUAUAUUUUUAUAAUAAAAAUAUAAAUACUGAAUAUCUAAAUAUUAUUAUUACUUUUUUUUUAAUAAUAAUAAUAUGGUAAUAGAACAUUUAAUGAUAAUAUAUAUUAGUUAUUAAUUAAUAUAUGUAUUAAUUAAAUAGAGAAUGCUGACAUGAGUAACGAAAAAAAGGUAUAAACCUUUUCACCUAAAACAUAAGGUUUAACUAUAAAAGUACGGCCCCUAAUUAAAUUAAUAAGAAUAUAAAUAUAUUUAAGAUGGGAUAAUCUAUAUUAAUAAAAAUUUAUCUUAAAAUAUAUAUAUUAUUAAUAAUUAUAUUAAUUAAUUAAUAAUAUAUAUAAUUAUAUUAUAUAUUAUAUAUUUUUUAUAUAAUAUAAACUAAUAAAGAUCAGGAAAUAAUUAAUGUAUACCGUAAUGUAGACCGACUCAGGUAUGUAAGUAGAGAAUAUGAAGGUGAAUUAGAUAAUUAAAGGGAAGGAACUCGGCAAAGAUAGCUCAUAAGUUAGUCAAUAAAGAGUAAUAAGAACAAAGUUGUACAACUGUUUACUAAAAACACCGCACUUUGCAGAAACGAUAAGUUUAAGUAUAAGGUGUGAACUCUGCUCCAUGCUUAAUAUAUAAAUAAAAUUAUUUAACGAUAAUUUAAUUAAAUUUAGGUAAAUAGCAGCCUUAUUAUGAGGGUUAUAAUGUAGCGAAAUUCCUUGGCCUAUAAUUGAGGUCCCGCAUGAAUGACGUAAUGAUACAACAACUGUCUCCCCUUUAAGCUAAGUGAAAUUGAAAUCGUAGUGAAGAUGCUAUGUACCUUCAGCAAGACGGAAAGACCCUAUGCAGCUUUACUGUAAUUAGAUAGAUCGAAUUAUUGUUUAUUAUAUUCAGCAUAUUAAGUAAUCCUAUUAUUAGGUAAUCGUUUAGAUAUUAAUGAGAUACUUAUUAUAAUAUAAUGAUAAUUCUAAUCUUAUAAAUAAUUAUUAUUAUUAUUAUUAAUAAUAA
and sequence of 5MRF_1 is:
>5MRF_1
GUAAAAAGUAGAAUAAUAGAUUUGAAAUAUUUAUUAUAUAGAUUUAAAGAGAUAAUCAUGGAGUAUAAUAAUUAAAUUUA
AUAAAUUUAAUAUAACUAUUAAUAGAAUUAGGUUACUAAUAAAUUAAUAACAAUUAAUUUUAAAACCUAAAGGUAAACCU
UUAUAUUAAUAAUGUUAUUUUUUAUUAUUUUUAUAAUAAGAAUAAUUAUUAAUAAUAAUAAACUAAGUGAACUGAAACAU
CUAAGUAACUUAAGGAUAAGAAAUCAACAGAGAUAUUAUGAGUAUUGGUGAGAGAAAAUAAUAAAGGUCUAAUAAGUAUU
AUGUGAAAAAAAUGUAAGAAAAUAGGAUAACAAAUUCUAAGACUAAAUACUAUUAAUAAGUAUAGUAAGUACCGUAAGGG
AAAGUAUGAAAAUGAUUAUUUUAUAAGCAAUCAUGAAUAUAUUAUAUUAUAUUAAUGAUGUACCUUUUGUAUAAUGGGUC
AGCAAGUAAUUAAUAUUAGUAAAACAAUAAGUUAUAAAUAAAUAGAAUAAUAUAUAUAUAUAAAAAAAUAUAUUAAAAUA
UUUAAUUAAUAUUAAUUGACCCGAAAGCAAACGAUCUAACUAUGAUAAGAUGGAUAAACGAUCGAACAGGUUGAUGUUGC
AAUAUCAUCUGAUUAAUUGUGGUUAGUAGUGAAAGACAAAUCUGGUUUGCAGAUAGCUGGUUUUCUAUGAAAUAUAUGUA
AGUAUAGCCUUUAUAAAUAAUAAUUAUUAUAUAAUAUUAUAUUAAUAUUAUAUAAAGAAUGGUACAGCAAUUAAUAUAUA
UUAGGGAACUAUUAAAGUUUUAUUAAUAAUAUUAAAUCUCGAAAUAUUUAAUUAUAUAUAAUAAAGAGUCAGAUUAUGUG
CGAUAAGGUAAAUAAUCUAAAGGGAAACAGCCCAGAUUAAGAUAUAAAGUUCCUAAUAAAUAAUAAGUGAAAUAAAUAUU
AAAAUAUUAUAAUAUAAUCAGUUAAUGGGUUUGACAAUAACCAUUUUUUAAUGAACAUGUAACAAUGCACUGAUUUAUAA
UAAAUAAAAAAAAAUAAUAUUUAAAAUCAAAUAUAUAUAUAUUUGUUAAUAGAUAAUAUACGGAUCUUAAUAAUAAGAAU
UAUUUAAUUCCUAAUAUGGAAUAUUAUAUUUUUAUAAUAAAAAUAUAAAUACUGAAUAUCUAAAUAUUAUUAUUACUUUU
UUUUUAAUAAUAAUAAUAUGGUAAUAGAACAUUUAAUGAUAAUAUAUAUUAGUUAUUAAUUAAUAUAUGUAUUAAUUAAA
UAGAGAAUGCUGACAUGAGUAACGAAAAAAAGGUAUAAACCUUUUCACCUAAAACAUAAGGUUUAACUAUAAAAGUACGG
CCCCUAAUUAAAUUAAUAAAAAUAUAAAUAUAUUUAAGAUGGGAUAAUCUAUAUUAAUAAAAAUUUAUCUUAAAAUAUAU
AUAUUAUUAAUAAUUAUAUUAAUUAAUUAAUAAUAUAUAUAAUUAUAUUAUAUAUUAUAUAUUUUUUAUAUAAUAUAAAC
UAAUAAAGAUCAGGAAAUAAUUAAUGUAUACCGUAAUGUAGACCGACUCAGGUAUGUAAGUAGAGAAUAUGAAGGUGAAU
UAGAUAAUUAAAGGGAAGGAACUCGGCAAAGAUAGCUCAUAAGUUAGUCAAUAAAGAGUAAUAAGAACAAAGUUGUACAA
CUGUUUACUAAAAACACCGCACUUUGCAGAAACGAUAAGUUUAAGUAUAAGGUGUGAACUCUGCUCCAUGCUUAAUAUAU
AAAUAAAAUUAUUUAACGAUAAUUUAAUUAAAUUUAGGUAAAUAGCAGCCUUAUUAUGAGGGUUAUAAUGUAGCGAAAUU
CCUUGGCCUAUAAUUGAGGUCCCGCAUGAAUGACGUAAUGAUACAACAACUGUCUCCCCUUUAAGCUAAGUGAAAUUGAA
AUCGUAGUGAAGAUGCUAUGUACCUUCAGCAAGACGGAAAGACCCUAUGCAGCUUUACUGUAAUUAGAUAGAUCGAAUUA
UUGUUUAUUAUAUUCAGCAUAUUAAGUAAUCCUAUUAUUAGGUAAUCGUUUAGAUAUUAAUGAGAUACUUAUUAUAAUAU
AAUGAUAAUUCUAAUCUUAUAAAUAAUUAUUAUUAUUAUUAUUAAUAAUAAUAAUAUGCUUUCAAGCAUAGUGAUAAAAC
AUAUUUAUAUGAUAAUCACUUUACUUAAUAGAUAUAAUUCUUAAGUAAUAUAUAAUAUAUAUUUUAUAUAUAUUAUAUAU
AAUAUAAGAGACAAUCUCUAAUUGGUAGUUUUGAUGGGGCGUCAUUAUCAGCAAAAGUAUCUGAAUAAGUCCAUAAAUAA
AUAUAUAAAAUUAUUGAAUAAAAAAAAAAUAAUAUAUAUUAUAUAUAUUAAUUAUAAAUUGAAAUAUGUUUAUAUAAAUU
UAUAUUUAUUGAAUAUAUUUUAGUAAUAGAUAAAAAUAUGUACAGUAAAAUUGUAAGGAAAACAAUAAUAACUUUCUCCU
CUCUCGGUGGGGGUUCACACCUAUUUUUAAUAGGUGUGAACCCCUCUUCGGGGUUCCGGUUCCCUUUCGGGUCCCGGAAC
UUAAAUAAAAAUGGAAAGAAUUAAAUUAAUAUAAUGGUAUAACUGUGCGAUAAUUGUAACACAAACGAGUGAAACAAGUA
CGUAAGUAUGGCAUAAUGAACAAAUAACACUGAUUGUAAAGGUUAUUGAUAACGAAUAAAAGUUACGCUAGGGAUAACAG
GGUAAUAUAGCGAAAGAGUAGAUAUUGUAAGCUAUGUUUGCCACCUCGAUGUCGACUCAACAUUUCCUCUUGGUUGUAAA
AGCUAAGAAGGGUUUGACUGUUCGUCAAUUAAAAUGUUACGUGAGUUGGGUUAAAUACGAUGUGAAUCAGUAUGGUUCCU
AUCUGCUGAAGGAAAUAUUAUCAAAUUAAAUCUCAUUAUUAGUACGCAAGGACCAUAAUGAAUCAACCCAUGGUGUAUCU
AUUGAUAAUAAUAUAAUAUAUUUAAUAAAAAUAAUACUUUAUUAAUAUAUUAUCUAUAUUAGUUUAUAUUUUAAUUAUAU
AUUAUCAUAGUAGAUAAGCUAAGUUGAUAAUAAAUAAAUAUUGAAUACAUAUUAAAUAUGAAGUUGUUUUAAUAAGAUAA
UUAAUCUGAUAAUUUUAUACUAAAAUUAAUAAUUAUAGGUUUUAUAUAUUAUUUAUAAAUAAAUAUAUUAUAAUAAUAAU
AAUUAUUAUUAUUAAUAAAAAAUAUUAAUUAUAAUAUUAAUAAAAUACUAAUUUAUCAGUUAUCUAUAUAAUAUCUAAUC
UAUUAUUCUAUAUACU
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milot-mirdita
commented on August 18, 2024
Seems to be fixed in release 11, I'll have to build new containers.
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milot-mirdita
commented on August 18, 2024
The containers are on the latest version again now. The issue should be resolved there.
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josemduarte
commented on August 18, 2024
Thanks @milot-mirdita !
I've tried building a server from scratch and it doesn't seem to be pulling the latest mmseqs version. Logs say that my mmseqs is on: 6d92cd21676ccc36531f2852f7eb747f6389435f (which corresponds to release 10)
What I do is :
- clone this repo
- add some dbs in databases directory
- run docker-compose
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milot-mirdita
commented on August 18, 2024
You might need to run something like:
docker-compose down
docker-compose pull
To make sure that the base images are up to date.
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milot-mirdita
commented on August 18, 2024
You might need to run something like:
docker-compose down
docker-compose pull
To make sure that the base images are up to date.
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josemduarte
commented on August 18, 2024
I've tried that:
# docker-compose pull
Pulling mmseqs-web-redis (redis:alpine)...
alpine: Pulling from library/redis
Digest: sha256:cb9783b1c39bb34f8d6572406139ab325c4fac0b28aaa25d5350495637bb2f76
Status: Image is up to date for redis:alpine
Pulling mmseqs-web-api (soedinglab/mmseqs2-app-backend:version-4)...
version-4: Pulling from soedinglab/mmseqs2-app-backend
Digest: sha256:0282aa7dcc1b05b4ad62f021a2c50b4cf77a97e2a55bc2b86f0e1a618850859e
Status: Image is up to date for soedinglab/mmseqs2-app-backend:version-4
Pulling mmseqs-web-webserver (soedinglab/mmseqs2-app-frontend:version-4)...
version-4: Pulling from soedinglab/mmseqs2-app-frontend
Digest: sha256:654eb66a041ad260d83b5bda946124ccf56a2c18dacdf6be677e7263e7db2d55
Status: Image is up to date for soedinglab/mmseqs2-app-frontend:version-4
Pulling mmseqs-web-worker (soedinglab/mmseqs2-app-backend:version-4)...
version-4: Pulling from soedinglab/mmseqs2-app-backend
Digest: sha256:0282aa7dcc1b05b4ad62f021a2c50b4cf77a97e2a55bc2b86f0e1a618850859e
Status: Image is up to date for soedinglab/mmseqs2-app-backend:version-4
but the version reported by the app is still 6d92cd21676ccc36531f2852f7eb747f6389435f
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milot-mirdita
commented on August 18, 2024
Sorry, that makes sense. I've forgotten to tag a release so it won’t actually make new tagged images.
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milot-mirdita
commented on August 18, 2024
I tagged the containers correctly now and docker-compose should work after updating the repository.
The electron app seems to still be broken, but that doesn't affect docker.
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josemduarte
commented on August 18, 2024
Fantastic, thank you @milot-mirdita ! All works well now! I'll close the issue.
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Related Issues (20)
- local colabfold_batch cannot communicate with local mmseq2 web api HOT 19
- Full target/query alignment being truncated in web UI HOT 3
- docker install error: ghcr.io pull error HOT 7
- pairaln mode does not support the binary version of the taxonomy files HOT 5
- mmseqs-server: errors when called from colabfold_batch HOT 2
- App does not work with latest mmseqs version HOT 2
- Pass --max-seqs through GUI or server API?
- Implement three diferent states for visualizing query structure in Structure Viewer
- Possible to add single or multiple sequences to existing database
- Temporary redirect issue HOT 6
- Foldseek all database view rework
- Running it in kubernetes HOT 4
- Historical jobs not loaded: "Job failed. Please try again later."
- jobs stuck in PENDING status with local mmseqs-web API HOT 2
- "docker-compose run db-setup PDB" not working HOT 2
- host not found in upstream "mmseqs-web-api HOT 7
- "405 Not Allowed" returned for the queries HOT 4
- Foldseek jobs are not persistent from GUI HOT 5
- Local Foldseek searches are no longer working HOT 6
- docker-compose run db-setup XXX fails due to no space left on device
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