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soedinglab / MMseqs2-App

MMseqs2 app to run on your workstation or servers
https://search.foldseek.com
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pairaln mode does not support the binary version of the taxonomy files #53

Open athbaltzis opened 2 years ago

athbaltzis commented 2 years ago

Hi guys! While trying to set up a mmseqs web server to run colabfold for a multimer, I came across the following issue that hampers the creation of the final pair.a3m alignment file:

mmseqs-web-worker_1     | pairaln /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/qdb /opt/mmseqs-web/databases/uniref30_2103_db.idx /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign_pair --db-load-mode 2
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Input taxonomy database "/opt/mmseqs-web/databases/uniref30_2103_db.idx" is missing files:
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_mapping
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_nodes.dmp
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_names.dmp
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_merged.dmp
mmseqs-web-worker_1     | align /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/qdb /opt/mmseqs-web/databases/uniref30_2103_db.idx /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign_pair /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign_pair_bt --db-load-mode 2 -e inf -a
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Input /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign_pair does not exist
mmseqs-web-worker_1     | pairaln /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/qdb /opt/mmseqs-web/databases/uniref30_2103_db.idx /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_exp_realign_pair_bt /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_final --db-load-mode 2
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Input taxonomy database "/opt/mmseqs-web/databases/uniref30_2103_db.idx" is missing files:
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_mapping
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_nodes.dmp
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_names.dmp
mmseqs-web-worker_1     | - /opt/mmseqs-web/databases/uniref30_2103_db.idx_merged.dmp
mmseqs-web-worker_1     | result2msa /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/qdb /opt/mmseqs-web/databases/uniref30_2103_db.idx /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_final /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/pair.a3m --db-load-mode 2 --msa-format-mode 5
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Input /opt/mmseqs-web/jobs/qOfRdtYp0THSGaDxs9TXTh4GNdmpLvMSERS4oQ/res_final does not exist

It seems that the pairaln mode of mmseqs2 does not support the binary version of the taxonomy files (uniref30_2103_db_taxonomy) and requires the taxonomy flat file databases. I use this mmseqs commit: 96b2009982ce686e0b78e226c75c59fd286ba450. Could an update to the latest version solve this issue? Is there any workaround to create the flat file databases for uniref30_2013?

Thanks in advance!

milot-mirdita commented 2 years ago

Can you try with a newer commit? This look about right.

Can you please post a ls -lah of the databases folder?

wosmanitx commented 2 years ago

Hi, I am having the same problem:

[root@ip-172-31-50-187 databases]# ls -lah
total 1.6T
drwxr-xr-x 7 root     root      48K Oct 31 15:27 .
drwxr-xr-x 6 root     root      227 Oct 28 17:36 ..
-rw-r--r-- 1 root     root        0 Oct 27 05:55 COLABDB_READY
-rw-r--r-- 1 ec2-user ec2-user  52G Sep 10  2021 colabfold_envdb_202108_aln.tsv
-rw-r--r-- 1 root     root     196M Oct 27 05:15 colabfold_envdb_202108_db.0
-rw-r--r-- 1 root     root     206M Oct 27 05:15 colabfold_envdb_202108_db.1
-rw-r--r-- 1 root     root     200M Oct 27 05:15 colabfold_envdb_202108_db.10
-rw-r--r-- 1 root     root     198M Oct 27 05:15 colabfold_envdb_202108_db.100
-rw-r--r-- 1 root     root     197M Oct 27 05:15 colabfold_envdb_202108_db.101
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-rw-r--r-- 1 root     root     196M Oct 27 05:15 colabfold_envdb_202108_db.57
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lrwxrwxrwx 1 root     root       27 Oct 27 05:31 colabfold_envdb_202108_db_seq_h -> colabfold_envdb_202108_db_h
lrwxrwxrwx 1 root     root       34 Oct 27 05:31 colabfold_envdb_202108_db_seq_h.dbtype -> colabfold_envdb_202108_db_h.dbtype
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-rw-r--r-- 1 ec2-user ec2-user  30G Sep 13  2021 colabfold_envdb_202108_h.tsv
-rw-r--r-- 1 ec2-user ec2-user 128G Sep 13  2021 colabfold_envdb_202108_seq.tsv
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-rw-r--r-- 1 ec2-user ec2-user  38G Sep 10  2021 colabfold_envdb_202108.tsv
-rw-rw-r-- 1 ec2-user ec2-user  119 Apr  1  2022 md5sum
drwxr-xr-x 4 root     root       37 Oct 27 06:15 pdb
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drwxr-xr-x 3 root     root       47 Oct 31 14:57 tmp
drwxr-xr-x 3 root     root       48 Oct 27 03:15 tmp1
drwxr-xr-x 3 root     root       48 Oct 27 05:31 tmp2
drwxr-xr-x 3 root     root       48 Oct 27 05:55 tmp3
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-rw-r--r-- 1 root     root     104M Oct 27 03:14 uniref30_2202_db_aln.67
-rw-r--r-- 1 root     root      45M Oct 27 03:14 uniref30_2202_db_aln.68
-rw-r--r-- 1 root     root      25M Oct 27 03:14 uniref30_2202_db_aln.69
-rw-r--r-- 1 root     root      51M Oct 27 03:14 uniref30_2202_db_aln.7
-rw-r--r-- 1 root     root      52M Oct 27 03:14 uniref30_2202_db_aln.70
-rw-r--r-- 1 root     root     109M Oct 27 03:14 uniref30_2202_db_aln.71
-rw-r--r-- 1 root     root      44M Oct 27 03:14 uniref30_2202_db_aln.72
-rw-r--r-- 1 root     root      24M Oct 27 03:14 uniref30_2202_db_aln.73
-rw-r--r-- 1 root     root      52M Oct 27 03:14 uniref30_2202_db_aln.74
-rw-r--r-- 1 root     root     102M Oct 27 03:14 uniref30_2202_db_aln.75
-rw-r--r-- 1 root     root      44M Oct 27 03:14 uniref30_2202_db_aln.76
-rw-r--r-- 1 root     root      24M Oct 27 03:14 uniref30_2202_db_aln.77
-rw-r--r-- 1 root     root      50M Oct 27 03:14 uniref30_2202_db_aln.78
-rw-r--r-- 1 root     root     110M Oct 27 03:14 uniref30_2202_db_aln.79
-rw-r--r-- 1 root     root     110M Oct 27 03:14 uniref30_2202_db_aln.8
-rw-r--r-- 1 root     root      46M Oct 27 03:14 uniref30_2202_db_aln.80
-rw-r--r-- 1 root     root      25M Oct 27 03:14 uniref30_2202_db_aln.81
-rw-r--r-- 1 root     root      48M Oct 27 03:14 uniref30_2202_db_aln.82
-rw-r--r-- 1 root     root     105M Oct 27 03:14 uniref30_2202_db_aln.83
-rw-r--r-- 1 root     root      47M Oct 27 03:14 uniref30_2202_db_aln.84
-rw-r--r-- 1 root     root      27M Oct 27 03:14 uniref30_2202_db_aln.85
-rw-r--r-- 1 root     root      42M Oct 27 03:14 uniref30_2202_db_aln.86
-rw-r--r-- 1 root     root     113M Oct 27 03:14 uniref30_2202_db_aln.87
-rw-r--r-- 1 root     root      49M Oct 27 03:14 uniref30_2202_db_aln.88
-rw-r--r-- 1 root     root      26M Oct 27 03:14 uniref30_2202_db_aln.89
-rw-r--r-- 1 root     root      44M Oct 27 03:14 uniref30_2202_db_aln.9
-rw-r--r-- 1 root     root      36M Oct 27 03:14 uniref30_2202_db_aln.90
-rw-r--r-- 1 root     root     118M Oct 27 03:14 uniref30_2202_db_aln.91
-rw-r--r-- 1 root     root      51M Oct 27 03:14 uniref30_2202_db_aln.92
-rw-r--r-- 1 root     root      27M Oct 27 03:14 uniref30_2202_db_aln.93
-rw-r--r-- 1 root     root      28M Oct 27 03:14 uniref30_2202_db_aln.94
-rw-r--r-- 1 root     root     123M Oct 27 03:14 uniref30_2202_db_aln.95
-rw-r--r-- 1 root     root      56M Oct 27 03:14 uniref30_2202_db_aln.96
-rw-r--r-- 1 root     root      29M Oct 27 03:14 uniref30_2202_db_aln.97
-rw-r--r-- 1 root     root      19M Oct 27 03:14 uniref30_2202_db_aln.98
-rw-r--r-- 1 root     root     125M Oct 27 03:14 uniref30_2202_db_aln.99
-rw-r--r-- 1 root     root        4 Oct 27 03:14 uniref30_2202_db_aln.dbtype
-rw-r--r-- 1 root     root     730M Oct 27 03:14 uniref30_2202_db_aln.index
-rw-r--r-- 1 root     root        4 Oct 27 03:07 uniref30_2202_db.dbtype
-rw-r--r-- 1 root     root     3.7G Oct 27 03:06 uniref30_2202_db_h
-rw-r--r-- 1 root     root        4 Oct 27 03:07 uniref30_2202_db_h.dbtype
-rw-r--r-- 1 root     root     6.7G Oct 27 03:07 uniref30_2202_db_h.index
-rw-r--r-- 1 root     root     157G Oct 31 15:27 uniref30_2202_db.idx
-rw-r--r-- 1 root     root        4 Oct 31 15:27 uniref30_2202_db.idx.dbtype
-rw-r--r-- 1 root     root      512 Oct 31 15:27 uniref30_2202_db.idx.index
-rw-r--r-- 1 root     root     740M Oct 27 03:07 uniref30_2202_db.index
-rw-r--r-- 1 ec2-user ec2-user 2.1G Apr  1  2022 uniref30_2202_db_mapping
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.0
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.1
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.10
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.100
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.101
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.102
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.103
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.104
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.105
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.106
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.107
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.108
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.109
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.11
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.110
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.111
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.112
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.113
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.114
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.115
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.116
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.117
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.118
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.119
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.12
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.120
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.121
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.122
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.123
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.124
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.125
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.126
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.127
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.13
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.14
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.15
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.16
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.17
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.18
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.19
-rw-r--r-- 1 root     root     375M Oct 27 03:12 uniref30_2202_db_seq.2
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.20
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.21
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.22
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.23
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.24
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.25
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.26
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.27
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.28
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.29
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.3
-rw-r--r-- 1 root     root     375M Oct 27 03:12 uniref30_2202_db_seq.30
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.31
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.32
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.33
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.34
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.35
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.36
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.37
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.38
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.39
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.4
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.40
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.41
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.42
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.43
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.44
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.45
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.46
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.47
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.48
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.49
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.5
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.50
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.51
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.52
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.53
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.54
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.55
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.56
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.57
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.58
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.59
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.6
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.60
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.61
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.62
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.63
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.64
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.65
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.66
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.67
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.68
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.69
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.7
-rw-r--r-- 1 root     root     375M Oct 27 03:12 uniref30_2202_db_seq.70
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.71
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.72
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.73
-rw-r--r-- 1 root     root     375M Oct 27 03:12 uniref30_2202_db_seq.74
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.75
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.76
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.77
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.78
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.79
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.8
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.80
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.81
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.82
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.83
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.84
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.85
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.86
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.87
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.88
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.89
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.9
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.90
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.91
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.92
-rw-r--r-- 1 root     root     541M Oct 27 03:12 uniref30_2202_db_seq.93
-rw-r--r-- 1 root     root     375M Oct 27 03:12 uniref30_2202_db_seq.94
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.95
-rw-r--r-- 1 root     root     1.1G Oct 27 03:12 uniref30_2202_db_seq.96
-rw-r--r-- 1 root     root     542M Oct 27 03:12 uniref30_2202_db_seq.97
-rw-r--r-- 1 root     root     376M Oct 27 03:12 uniref30_2202_db_seq.98
-rw-r--r-- 1 root     root     222M Oct 27 03:12 uniref30_2202_db_seq.99
-rw-r--r-- 1 root     root        4 Oct 27 03:13 uniref30_2202_db_seq.dbtype
lrwxrwxrwx 1 root     root       18 Oct 27 03:14 uniref30_2202_db_seq_h -> uniref30_2202_db_h
lrwxrwxrwx 1 root     root       25 Oct 27 03:14 uniref30_2202_db_seq_h.dbtype -> uniref30_2202_db_h.dbtype
lrwxrwxrwx 1 root     root       24 Oct 27 03:14 uniref30_2202_db_seq_h.index -> uniref30_2202_db_h.index
-rw-r--r-- 1 root     root     7.3G Oct 27 03:13 uniref30_2202_db_seq.index
-rw-r--r-- 1 ec2-user ec2-user 620M Apr  1  2022 uniref30_2202_db_taxonomy
-rw------- 1   528745     9100 6.2G Jun  1 12:06 uniref30_2202_h.tsv
-rw------- 1   528745     9100 4.8G Jun  1 22:39 uniref30_2202_mapping.tsv
-rw------- 1   528745     9100  397 Jul 17 03:22 uniref30_2202.md5sum
-rw------- 1   528745     9100 112G Jun  1 13:28 uniref30_2202_seq.tsv
-rw-r--r-- 1 root     root      78G Oct 27 01:27 uniref30_2202.tar.gz
-rw------- 1   528745     9100 7.5G Jun  1 13:29 uniref30_2202.tsv
-rw-r--r-- 1 root     root        0 Oct 27 03:18 UNIREF30_READY
xieqihui commented 1 year ago

Have you found out any solution to this? I'm encoutering exactly the same issue. I'm using the latest release of mmseqs - MMseqs2 Release 14-7e284. I tried both uniref30_2202 and uniref30_2103, all have the same issue.

Attached is the output of ls -lha <databases>

colabfold_db_folder-2.txt

milot-mirdita commented 1 year ago

I figured out what's going wrong here. We don't create the correct symlink for the taxonomic support files with precomputed index.

You should create these two symlinks (and also the same two for the colabfolddb).

ln -s uniref30_2202_db_mapping uniref30_2202_db.idx_mapping
ln -s uniref30_2202_db_taxonomy uniref30_2202_db.idx_taxonomy
xieqihui commented 1 year ago

I figured out what's going wrong here. We don't create the correct symlink for the taxonomic support files with precomputed index.

You should create these two symlinks (and also the same two for the colabfolddb).

ln -s uniref30_2202_db_mapping uniref30_2202_db.idx_mapping
ln -s uniref30_2202_db_taxonomy uniref30_2202_db.idx_taxonomy

Great, this works. Thanks a lot!