Что такое 160 seq id no value
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Что такое 160 seq id no value

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org.postgresql.util.PSQLException: ERROR: column user0_.id does not exist — Hibernate

database

My database from bash shell looks like: How does hibernate map class attributes to table columns? Does it match based on the @Column(name=»username») only or does it also try to match based on datatypes and constraints such as unique/auto-increment?

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asked Aug 20, 2017 at 12:49
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what is the name of your shcema you are using?
Aug 20, 2017 at 12:53
schema name is myapp .
Aug 20, 2017 at 12:54

9 Answers 9

Solution

In PostgreSQL you have to specify the name of schema like so :

@Table(name="table_name", schema = "myapp") ^^^^^^^^^^^^^^^^ 

Long Story

you got this error :

org.postgresql.util.PSQLException: ERROR: column user0_.id does not exist 

because when you create a database in PostgreSQL, it create a default schema named public, so when you don’t specify the name in the Entity then Hibernate will check automatically in the public schema.

Good practices

  1. Don’t use Upper letters in the name of database , schema , tables or columns in PostgreSQL. Else you should to escape this names with quotes, and this can cause Syntax errors, so instead you can use :
@Table(name="table_name", schema = "schema_name") ^^^^^^^^^^ ^^^^^^^^^^^ 
+----------+-----------+----------+-----------+---------+ | Key Word |PostgreSQL |SQL:2003 | SQL:1999 | SQL-92 | +----------+-----------+----------+-----------+---------+ | . . . . . | +----------+-----------+----------+-----------+---------+ | USER | reserved |reserved | reserved | reserved| +----------+-----------+----------+-----------+---------+ 
  1. to difference between Dto and Entity its good practice to use Entity in the end of the name of your Entity for example UserEntity

answered Aug 20, 2017 at 12:55
Youcef LAIDANI Youcef LAIDANI
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Thanks for updating the answer. I can’t put the actual schema as it contains some business information. But your advice fixed the issue 🙂

Aug 20, 2017 at 14:28

No, I followed your original answer and now there is no issue. Everything is working as expected. We can close the thread. Thanks very much for your help!

Aug 20, 2017 at 14:33
Thanks bro, using capital letters in column name was my issue
Feb 23, 2021 at 18:30
I’m falling for this sneaky USER keyword every time��
Apr 24, 2021 at 10:26
@OmGupta take a look here postgresql.org/docs/8.1/sql-keywords-appendix.html
Aug 7, 2023 at 15:39

For people getting this exception ,In postgres Whenever you write an Entity Class try to associate it with the correct schema (where your table is present), like this:

@Entity @Table(name = "user", schema = "users_details") public class User implements Serializable < @Column(name = "id") Long id; //long is not recommended // Other data >

As @YCF_L has said Don’t use Upper_case letters in a table name or column name otherwise you will get this exception.

This convention becomes more important when their is a scenario where you have to auto generate the tables from entity classes or vice-versa.

answered Aug 5, 2019 at 9:47
Vikash Kumar Vikash Kumar
1,176 12 12 silver badges 10 10 bronze badges

Should add schema name on the Entity class. For this example, when the schema name is public

@Table(name = "user", schema = "public") 

See the PostgreSQL Admin view below

enter image description here

answered Apr 25, 2020 at 1:58
Cebu CM Solutions Cebu CM Solutions
111 1 1 silver badge 5 5 bronze badges

I did this, but still facing the issue: [select u1_0.id from public.user u1_0 where u1_0.email=? fetch first ? rows only] [ERROR: relation «public.user» does not exist

Aug 7, 2023 at 15:11

I obtained using general names like user are making troubles in the app.

I got the same issue as reported here with the following simple entity.

import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.SequenceGenerator; @Entity public class User implements Serializable < private static final long serialVersionUID = 6843302791607583447L; @Id @SequenceGenerator(name = "user_id_seq", sequenceName = "user_id_seq", allocationSize = 1) @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "user_id_seq") private Long id; @Column private String name; @Column private String password; @Override public String toString() < return name; >public Long getId() < return id; >public String getName() < return name; >public void setName(final String name) < this.name = name; >public String getPassword() < return password; >public void setPassword(final String password) < this.password = password; >> 

All i did was renaming the entity from User to Sessionxuser (and renaming the datatable from user to sessionxuser to fix this issue.

Schema was still public .

Since pre- or postfix some names like mycoolappuser or usermycoolapp to avoid troubles like this.

Find below a list with reserved keywords and literals preventing using as table, column, and further customized names.

In this case user is preserved for PostgreSQL , SQL:2003 , SQL:1999 and SQL-92 .

Что такое 160 seq id no value

This view lists session information for each current session.

Column Datatype Description
SADDR RAW(4 | 8) Session address
SID NUMBER Session identifier
SERIAL# NUMBER Session serial number. Used to uniquely identify a session’s objects. Guarantees that session-level commands are applied to the correct session objects if the session ends and another session begins with the same session ID.
AUDSID NUMBER Auditing session ID
PADDR RAW(4 | 8) Address of the process that owns the session
USER# NUMBER Oracle user identifier
USERNAME VARCHAR2(30) Oracle username
COMMAND NUMBER Command in progress (last statement parsed); for a list of values, see Table 5-5. These values also appear in the AUDIT_ACTIONS table.
OWNERID NUMBER The column contents are invalid if the value is 2147483644 . Otherwise, this column contains the identifier of the user who owns the migratable session.

For operations using Parallel Slaves, interpret this value as a 4-byte value. The low-order 2 bytes of which represent the session number, and the high-order bytes the instance ID of the query coordinator.

See Also:

Table 5-5 COMMAND Column of V$SESSION and Corresponding Commands

Number Command Number Command
1 CREATE TABLE 2 INSERT
3 SELECT 4 CREATE CLUSTER
5 ALTER CLUSTER 6 UPDATE
7 DELETE 8 DROP CLUSTER
9 CREATE INDEX 10 DROP INDEX
11 ALTER INDEX 12 DROP TABLE
13 CREATE SEQUENCE 14 ALTER SEQUENCE
15 ALTER TABLE 16 DROP SEQUENCE
17 GRANT OBJECT 18 REVOKE OBJECT
19 CREATE SYNONYM 20 DROP SYNONYM
21 CREATE VIEW 22 DROP VIEW
23 VALIDATE INDEX 24 CREATE PROCEDURE
25 ALTER PROCEDURE 26 LOCK
27 NO-OP 28 RENAME
29 COMMENT 30 AUDIT OBJECT
31 NOAUDIT OBJECT 32 CREATE DATABASE LINK
33 DROP DATABASE LINK 34 CREATE DATABASE
35 ALTER DATABASE 36 CREATE ROLLBACK SEG
37 ALTER ROLLBACK SEG 38 DROP ROLLBACK SEG
39 CREATE TABLESPACE 40 ALTER TABLESPACE
41 DROP TABLESPACE 42 ALTER SESSION
43 ALTER USER 44 COMMIT
45 ROLLBACK 46 SAVEPOINT
47 PL/SQL EXECUTE 48 SET TRANSACTION
49 ALTER SYSTEM 50 EXPLAIN
51 CREATE USER 52 CREATE ROLE
53 DROP USER 54 DROP ROLE
55 SET ROLE 56 CREATE SCHEMA
57 CREATE CONTROL FILE 59 CREATE TRIGGER
60 ALTER TRIGGER 61 DROP TRIGGER
62 ANALYZE TABLE 63 ANALYZE INDEX
64 ANALYZE CLUSTER 65 CREATE PROFILE
66 DROP PROFILE 67 ALTER PROFILE
68 DROP PROCEDURE 70 ALTER RESOURCE COST
71 CREATE MATERIALIZED VIEW LOG 72 ALTER MATERIALIZED VIEW LOG
73 DROP MATERIALIZED VIEW LOG 74 CREATE MATERIALIZED VIEW
75 ALTER MATERIALIZED VIEW 76 DROP MATERIALIZED VIEW
77 CREATE TYPE 78 DROP TYPE
79 ALTER ROLE 80 ALTER TYPE
81 CREATE TYPE BODY 82 ALTER TYPE BODY
83 DROP TYPE BODY 84 DROP LIBRARY
85 TRUNCATE TABLE 86 TRUNCATE CLUSTER
91 CREATE FUNCTION 92 ALTER FUNCTION
93 DROP FUNCTION 94 CREATE PACKAGE
95 ALTER PACKAGE 96 DROP PACKAGE
97 CREATE PACKAGE BODY 98 ALTER PACKAGE BODY
99 DROP PACKAGE BODY 100 LOGON
101 LOGOFF 102 LOGOFF BY CLEANUP
103 SESSION REC 104 SYSTEM AUDIT
105 SYSTEM NOAUDIT 106 AUDIT DEFAULT
107 NOAUDIT DEFAULT 108 SYSTEM GRANT
109 SYSTEM REVOKE 110 CREATE PUBLIC SYNONYM
111 DROP PUBLIC SYNONYM 112 CREATE PUBLIC DATABASE LINK
113 DROP PUBLIC DATABASE LINK 114 GRANT ROLE
115 REVOKE ROLE 116 EXECUTE PROCEDURE
117 USER COMMENT 118 ENABLE TRIGGER
119 DISABLE TRIGGER 120 ENABLE ALL TRIGGERS
121 DISABLE ALL TRIGGERS 122 NETWORK ERROR
123 EXECUTE TYPE 157 CREATE DIRECTORY
158 DROP DIRECTORY 159 CREATE LIBRARY
160 CREATE JAVA 161 ALTER JAVA
162 DROP JAVA 163 CREATE OPERATOR
164 CREATE INDEXTYPE 165 DROP INDEXTYPE
167 DROP OPERATOR 168 ASSOCIATE STATISTICS
169 DISASSOCIATE STATISTICS 170 CALL METHOD
171 CREATE SUMMARY 172 ALTER SUMMARY
173 DROP SUMMARY 174 CREATE DIMENSION
175 ALTER DIMENSION 176 DROP DIMENSION
177 CREATE CONTEXT 178 DROP CONTEXT
179 ALTER OUTLINE 180 CREATE OUTLINE
181 DROP OUTLINE 182 UPDATE INDEXES
183 ALTER OPERATOR

Patent Biological Sequence Listings Data Dictionary

1.0 Overview of Canadian Biological Sequence Listings Data

Patents apply to newly developed technology as well as to improvements on products or processes. A full description of what constitutes a Patent is described in the Patent Act. A patent is a right, granted by government, to exclude others from making, using, or selling your invention in Canada.

Canadian Biological Sequence Listings data contain information on nucleotide and amino acid sequences. This section will give an overview of what information is supplied and a description of the file structures.

1.1 Biological Sequence Listings Data

A patent’s biological sequence listing is presented as a separate part of the description of a patent application/granted patent and as a separate collection of data. The file structure is governed by World Intellectual Property Organization (WIPO) standard ST.25 for the presentation of nucleotide and amino acid sequence listings in patent applications.

Biological Sequence Listings (BSL) data consists of the applicant submitted file (often a text file) and two additional file types (.PEP and .SEQ) generated by the Office. The official documentation for a Biological Sequence Listing patent application/granted patent is the file supplied by the applicant. The Office generated files are created as working files and may be incomplete if the file submitted by the client is incomplete. The Office will request a new sequence listing from the client when it is deemed incomplete.

It should also be noted that applications entering the national phase import the sequence listing from the international application at the World Intellectual Property Organization (WIPO) and at times these downloaded sequence listings are incomplete.

1.2 Weekly Data File

BSL in patent applications and granted patents are included in a weekly update file. Patent data is open to public inspection after a confidentiality period of up to 18 months after the filing date of an application, or the earliest filing date of any previously regularly filed application on which a request for priority has been made.

A weekly collection contains TXT, PEP, and SEQ files. This collection contains updated and new files for the current week. The weekly data file ranges in size from 1 to 350 Mb depending on the volume of activity. The weekly collection includes a report that lists all the files included in that week’s extract.

Mandatory data elements in the applicant-provided file include:

  • Bibliographical Information (applicant name, title of invention)
  • Sequence Listing Information (number of sequence ID numbers, SEQ ID number, Length, Type, Organism, Sequence).

1.3 Description of ST.25 Structure

The file structure is governed by the World Intellectual Property Organization (WIPO) standard ST.25 for the presentation of nucleotide and amino acid sequence listings in patent applications. All information regarding this standard as it relates to the file structure and technical specification can be found on the WIPO website at: https://www.wipo.int/export/sites/www/standards/en/pdf/03-25-01.pdf (PDF Version)

Weekly update files are structured as follows:

BSL Weekly Zip File:
BSLYYYYWW.zip (ie. BSL201825.zip) contains a folder for the week of the extract and a report file where YYYY represents the year and WW represents the week number (01 to 52 weeks)

  • Weekly Extract Folder:
    • YYYY-MM-DD (i.e. 2018-06-23 ) contains folders named XXXXXXXX (i.e. 02836299) where X represents the patent application number.
      • Patent numbered folders contain PEP, SEQ and or TXT files:
        • These filenames contain a prefix (CA), the patent application number, the production date, the file type and version CAXXXXXXXXYYYYMMDD-DNAvXX.PEP (or .SEQ or .TXT)
        • Examples:
          • CA0278203320180618-DNAv03.PEP;
          • CA0278203320180618-DNAv04.SEQ;
          • CA0278203320180618-DNAv03.TXT)
          • Report.txt contains the extract range for the week, the number of patent applications processed, the number of files output and a complete list of all patents along with their PEP, SEQ and TXT filenames included in the weekly extract. Some basic information regarding laid open dates, national entry and PCT are also included in the report.txt file for each patent application in the weekly extract.

          2.0 Canadian Patent Biological Sequence Listings

          This numeric identifier is followed by the applicant name. This may include an individual and/or a company.

          Note: If the applicant name is written in characters other than those of the Latin alphabet, the value will be a translation or transliteration.

          This numeric identifier is followed by the title of the invention.

          This numeric identifier is followed by the physical file reference to the application.

          Note: This numeric identifier appears if the sequence listing was furnished at any time prior to the assignment of an application number.

          This numeric identifier is followed by the patent application’s number.

          Note: This numeric identifier appears if the sequence listing was furnished following the assignment of an application number.

          This numeric identifier is followed by the filing date of the application.

          Note: This numeric identifier appears if the sequence listing was furnished following the assignment of an application number.

          This numeric identifier is followed by the application number of an earlier application when a sequence listing is filed relating to an application which claims the priority of an earlier application.

          This numeric identifier is followed by the date of filing of an earlier application when a sequence listing is filed relating to an application which claims the priority of an earlier application.

          This numeric identifier is followed by the number of sequences () found in the document.

          This numeric identifier is followed by the software used in the creation of sequence listings for inclusions in patent applications.

          This numeric identifier is followed by the sequence identification number related to the following sequence ().

          This numeric identifier is followed by the length of the sequence (i.e. number of base pairs or amino acids).

          This numeric identifier is followed by the type of molecule sequenced. The type can be DNA, RNA or PRT.

          Note: If a nucleotide sequence contains both DNA and RNA fragments, the value following this numeric identifier will be DNA.

          This numeric identifier is followed by the Genus Species/scientific name of the molecule sequenced. This value may also be «Artificial Sequence» or «Unknown».

          This numeric identifier is always blank, but is followed by other numeric identifiers having a description of points of biological significance in the sequence.

          Note: This numeric identifier is used when «n» or «Xaa» or a modified base or modified/unusual L-amino acid is used in the sequence or if the organism (numeric identifier ) is «Artificial Sequence» or «Unknown».

          This numeric identifier is followed by the feature key representing points of biological significance in the sequence. These feature keys and their definition can be found in Appendix E and Appendix F.

          Note: This numeric identifier is used when «n» or «Xaa» or a modified base or modified/unusual L-amino acid is used in the sequence.

          This numeric identifier is followed by the location of the points of biological significance in the sequence as per the length of the sequence.

          Note: This numeric identifier is used when «n» or «Xaa» or a modified base or modified/unusual L-amino acid is used in the sequence.

          This numeric identifier is followed by the description of points of biological significance in the sequence.

          Note: This numeric identifier is used when «n» or «Xaa» or a modified base or modified/unusual L-amino acid is used in the sequence or if the organism (numeric identifier ) is «Artificial Sequence» or «Unknown».

          This numeric identifier is always blank but is followed by publication information.

          This numeric identifier is followed by the name of the author of the publication in which the sequence listing can be found.

          This numeric identifier is followed by the title of publication in the journal in which the sequence listing can be found.

          This numeric identifier is followed by the title of the journal in which the sequence listing can be found.

          This numeric identifier is followed by the volume of the journal in which the sequence listing can be found.

          This numeric identifier is followed by the issue of the journal in which the sequence listing can be found.

          This numeric identifier is followed by the range of pages of the journal in which the sequence listing can be found.

          This numeric identifier is followed by the date of publication of the journal in which the sequence listing can be found.

          Accession number assigned by database including database name.

          Date of entry in database

          Document number, for patent-type citations only.

          Document filing date, for patent-type citations only.

          Document publication date; for patent-type citations only.

          Sequence ID numbers (SEQ ID NOS) referred to in the cited publication.

          Met Ser Arg Asp Arg Phe Arg Ser Arg Gly Gly Gly Gly Gly Gly Phe

          His Arg Arg Gly Gly Gly Gly Gly Arg Gly Gly Leu His Asp Phe Arg

          Ser Pro Pro Pro Gly Met Gly Leu Asn Gln Asn Arg Gly Pro Met Gly

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          createdb max number of sequences #303

          altaetran opened this issue Apr 26, 2020 · 9 comments

          createdb max number of sequences #303

          altaetran opened this issue Apr 26, 2020 · 9 comments

          Comments

          altaetran commented Apr 26, 2020

          Expected Behavior

          createdb creates a database with no error

          Current Behavior

          createdb stalls and stops reporting once 10962815327 sequences have been added and fails to make progress. Is there a limit to the number of sequences that can be in a database?

          Steps to Reproduce (for bugs)

          /custom_install/installations/mmseqs-nonmpi/MMseqs2/build/bin/mmseqs createdb ../2020-04-19-in.fa/part-* inDB —createdb-mode 1

          MMseqs Output (for bugs)

          MMseqs Version: 3863af9ac6d30f3b17620254f3a4a05b7f6b7010 Database type 0 Shuffle input database true Createdb mode 1 Offset of numeric ids 0 Compressed 0 Verbosity 3 Shuffle database can not be combined with --createdb-mode 0. We recompute with --shuffle 0. Converting sequences [10962815327] 2h 14m 39s 271ms 

          The text was updated successfully, but these errors were encountered:

          altaetran commented May 6, 2020

          Linclust seemed to fail still with 3.6B sequences. Is the max 2^31-1?

          milot-mirdita commented May 6, 2020

          Could you post the log and the machine specs? It should work up to UINT_MAX without issue, however RAM overhead just for holding the entries also increases linearly and might become an issue at this point.

          altaetran commented May 6, 2020

          96238089_662789574576457_5579459952579182592_n

          There should be enough RAM, since the usage never tops 40% or so. It is a 2TB memory machine with 160 cores. Usually I get something like this, which happens after the cluster calculation step.

          martin-steinegger commented May 8, 2020

          @altaetran this is indeed not right. Could you please provide the whole log and command call?

          altaetran commented May 8, 2020

          the whole log overwhelms my system, but I captured most of the information that occurs before this bug:

          clusterer:/mnt/cluster/filt_80_2020-04-19/combined12$ time /custom_install/installations/mmseqs-nonmpi/MMseqs2/build/bin/mmseqs linclust inDB linClu90DB tmp --min-seq-id 0.90 --kme r-per-seq 40 -c 0.9 Tmp tmp folder does not exist or is not a directory. Create dir tmp linclust inDB linClu90DB tmp --min-seq-id 0.90 --kmer-per-seq 40 -c 0.9 MMseqs Version: 290668474611312a94a868bf041b38c8618f5ef6 Cluster mode 0 Max connected component depth 1000 Similarity type 2 Threads 160 Compressed 0 Verbosity 3 Substitution matrix nucl:nucleotide.out,aa:blosum62.out Add backtrace false Alignment mode 2 Allow wrapped scoring false E-value threshold 0.001 Seq. id. threshold 0.9 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Coverage threshold 0.9 Coverage mode 0 Max sequence length 65535 Compositional bias 1 Realign hits false Max reject 2147483647 Max accept 2147483647 Include identical seq. id. false Preload mode 0 Pseudo count a 1 Pseudo count b 1.5 Score bias 0 Gap open cost 11 Gap extension cost 1 Zdrop 40 Alphabet size nucl:5,aa:21 k-mers per sequence 40 Spaced k-mers 0 Spaced k-mer pattern Scale k-mers per sequence nucl:0.200,aa:0.000 Adjust k-mer length false Mask residues 0 Mask lower case residues 0 k-mer length 0 Shift hash 67 Split memory limit 0 Include only extendable false Skip repeating k-mers false Rescore mode 0 Remove hits by seq. id. and coverage false Sort results 0 Remove temporary files false Force restart with latest tmp false MPI runner Set cluster mode SET COVER. kmermatcher inDB tmp/18375844090983922724/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size nucl:5,aa:13 --min-seq-id 0.9 --kmer-per-seq 40 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 0 -c 0.9 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-mul ti-kmer 0 --threads 160 --compressed 0 -v 3 kmermatcher inDB tmp/18375844090983922724/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size nucl:5,aa:13 --min-seq-id 0.9 --kmer-per-seq 40 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 0 -c 0.9 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-mul ti-kmer 0 --threads 160 --compressed 0 -v 3 Database size: 2830651961 type: Aminoacid Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) Generate k-mers list for 1 split [=================================================================] 100.00% 2.83B 2h 28m 50s 478ms Sort kmer 1h 11m 10s 680ms Time for fill: 0h 14m 35s 645ms Time for merging to pref: 0h 31m 17s 620ms Time for processing: 5h 43m 57s 88ms rescorediagonal inDB inDB tmp/18375844090983922724/pref tmp/18375844090983922724/pref_rescore1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 0 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 0.9 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 160 --compressed 0 -v 3 [=================================================================] 100.00% 2.83B 1h 11m 50s 841ms [=================================================================] . . . 100.00% 1.00M 0s 440ms [=================================================================] 100.00% 1.00M 0s 541ms [=================================================================] 100.00% 1.00M 0s 501ms [=================================================================] 100.00% 1.00M 0s 455ms [=================================================================] 100.00% 1.00M 0s 609ms [=================================================================] 100.00% 1.00M 0s 536ms [=================================================================] 100.00% 1.00M 0s 626ms [=================================================================] 100.00% 1.00M 0s 591ms [=================================================================] 100.00% 1.00M 0s 572ms [=================================================================] 100.00% 651.96K 0s 344ms Sort entries Find missing connections 

          altaetran commented Nov 2, 2020

          I saw there was a potential fix regarding the database size limit on the github. Was anyone able to take a look at this issue? I’m excited to try MMseqs2 out on very large databases! Thanks!

          milot-mirdita commented Dec 16, 2020

          Sorry, your issue fell through the cracks. Did you try again? We clustered things that were just under the INT_MAX limit before without issues. If you can give us any more details to investigate what might have gone wrong we can look into it, right now I have no idea where to start.

          durrantmm commented Aug 4, 2021

          Following up on this, running into the same issue. Any plans to increase the limit?

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