Database Error Gi
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faq • rss Community Log In Sign Up Add New Post Question: Blastdb_Aliastool Error 1 2.9 years ago by holyrapan • 20 holyrapan • 20 wrote: Hi
Blastdb_aliastool
everyone, I would like to build a human+bacteria+archaea subset of the nr database. blast database error: blastdb alias file creation failed. some referenced files may be missing So what I did is: Get the nr database Get the GI list of human+bacteria+archaea from Entrez Protein database
Blast Alias Database
Use this GI list with blastdb_aliastool to build an aliased database of the subset proteins. I used the following command and get the error blastdb_aliastool -db nr -gilist sequence_human_bacteria_archaea_26112013.gi -dbtype prot -out makeblastdb human_bacteria_archaea_nov2013 -title "Human plus bacteria and archaea entries" Converted 74595073 GIs from sequence_human_bacteria_archaea_26112013.gi to binary format in human_bacteria_archaea_nov2013.p.gil BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing Does anyone have any idea what the problem is? Thanks! database blast+ • 2.3k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.9 ncbi blast years ago • written 2.9 years ago by holyrapan • 20 What's the output of: blastdbcmd -info -db nr ? ADD REPLY • link written 2.9 years ago by Michael Dondrup ♦ 38k I get BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/Users/holy/blastdatabase/db::/Users/holy/blastdatabase/db:] But I have the nr.pal file there, or does it need something else? ADD REPLY • link written 2.9 years ago by holyrapan • 20 It might be a path problem, try: blastdbcmd -info -db /Users/holy/blastdatabase/nr and blastdbcmd -info -db /Users/holy/blastdatabase/db/nr. Most likely, your setting should be BLASTDB=/Users/holy/blastdatabase/ It might be a blast db download problem, run update_blastdb.pl nr to check if it is up to date and get the database. Extract the tar.gz file it downloads. ADD REPLY • link written 2.9 years ago by Michael Dondrup ♦ 38k 1 2.9 years ago by holyrapan • 20 holyrapan • 20 wrote: It's working now. A database volume was missing. Thanks guys for your help! ADD COMMENT • link written 2.9 years ago by holyrapan • 20 0 2.9 years ago by 5heikki ♦ 5.6k Finland 5heikki ♦ 5
faq • rss Community Log In Sign Up Add New Post Question: Option Negative_Gilist With Blastp Version 2.2.25. No Isam File? 1 3.7 years ago by Angele • 40 Norway Angele • 40 wrote: Hi everyone, I want to use the option negative_gilist from blastp with the version blast 2.2.25. I need to search a query against the swissprot database but I want to remove a set of sequences in my swissprot database. I saw that negative_gilist can restrict search of database to everything except the listed GIs . Here is my command line that I used: /blast-2.2.25/bin/blastp -num_alignments 100 -evalue 1 -db /db/uniprot/uniprot/uniprot_sprot.fasta -query seq.fasta -out https://www.biostars.org/p/87510/ seq.out -negative_gilist sequence.gi.txt *sequence.gi.txt is a GI list of the sequence that blastp doesn't have to take into account during the search. I obtain this error message: BLAST Database error: GI list specified but no ISAM file found for GI I searched what was the ISAM file and I found it was additional file with different information for the database as db.phr db.pin db.psq.... My swissprot database is formatted with formatdb with https://www.biostars.org/p/61085/ the option -o T, so it should give all the ISAM file. I noticed that I don't have the file with extensions: .pni and .pnd which seems to contain GI information. I can't figure it out why (I tried to reformat the database with formatdb andmakeblast_db, I can't obtain this file) but I don't know if it is why negative_gilist does not work. Thanks for any help! • 1.7k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.7 years ago by Adrian Pelin • 1.9k • written 3.7 years ago by Angele • 40 On this note, how come we can't search with Entrez queries when we do local searches? For instance, I would be more interested in excluding a whole phylum from my search rather than just a few GIs. ADD REPLY • link written 2.7 years ago by Adrian Pelin • 1.9k 2 3.7 years ago by Michael Dondrup ♦ 38k Bergen, Norway Michael Dondrup ♦ 38k wrote: Using formatdb without the "-o T" indexing option results in three BLAST database files (.nhr, .nin, ,nsq). Using the "-o T" option will result in additional files. If gi's are present in the FASTA definition lines of the source file, there will be f
Database Provisioning Issues Troubleshooting Linux Provisioning Issues Troubleshooting Patching Issues Troubleshooting Linux Patching Issues Frequently Asked Questions on Linux Provisioning Refreshing Configurations https://docs.oracle.com/cd/E24628_01/em.121/e27046/troubleshooting.htm Reviewing Log Files F.1 Troubleshooting Database Provisioning Issues This section provides https://docs.oracle.com/database/121/CWLIN/trouble.htm troubleshooting tips for common database provisioning issues. F.1.1 Grid Infrastructure Root Script Failure See the details below. F.1.1.1 Issue Grid Infrastructure root script fails. F.1.1.2 Description After Grid Infrastructure bits are laid down, the next essential step is Grid Infrastructure root script execution. database error This is the most process intensive phase of your deployment procedure. During this process, the GI stack configures itself and ensures all subsystems are alive and active. The root script may fail to run. F.1.1.3 Solution Visit each node that reported error and run the following command on n-1 nodes: $GI_ORACLE_HOME/crs/install/rootcrs.pl -deconfig -force If the database error gi root script did not run successfully on any of the nodes, pass the -lastNode switch on nth node (conditionally) to the final invocation as shown below. $GI_ORACLE_HOME/crs/install/rootcrs.pl -deconfig -force -lastNode Now, retry the failed step from the Procedure Activity page. F.1.2 SUDO Error During Deployment Procedure Execution See the details below. F.1.2.1 Issue A SUDO error occurs while performing a deployment. F.1.2.2 Description While performing a deployment, all root-related operations are performed over sudo. To improve security, production environments tend to fortify sudo. Therefore, you may encounter errors related to sudo. F.1.2.3 Solution Make the following changes in your sudoer's file: Remove entry Default requiretty, if it exists in your sudoer's file. If sudoers file contains entry Default env_reset, add the following entries after this parameter: Defaults env_keep="JRE_HOME PERL5LIB EMDROOT" F.1.3 Prerequisites Checks Failure See the details below. F.1.3.1 Issue Prerequisites checks fail when submitting a deployment procedure F.1.3.2 Cause Perform a meticulous analysis of output from prerequisite checks. While mo
(12.1) Oracle RAC documentation set in the Documentation directory: Oracle Clusterware Administration and Deployment Guide Oracle Real Application Clusters Administration and Deployment Guide This appendix contains the following topics: Best Practices for Contacting Oracle Support General Installation Issues Interpreting CVU "Unknown" Output Messages Using Verbose Mode Interpreting CVU Messages About Oracle Grid Infrastructure Setup About the Oracle Clusterware Alert Log Missing Operating System Packages On Linux Performing Cluster Diagnostics During Oracle Grid Infrastructure Installations About Using CVU Cluster Healthchecks After Installation Interconnect Configuration Issues SCAN VIP and SCAN Listener Issues Storage Configuration Issues Failed or Incomplete Installations and Upgrades A.1 Best Practices for Contacting Oracle Support If you find that it is necessary for you to contact Oracle Support to report an issue, then Oracle recommends that you follow these guidelines when you enter your service request: Provide a clear explanation of the problem, including exact error messages. Provide an explanation of any steps you have taken to troubleshoot issues, and the results of these steps. Provide exact versions (major release and patch release) of the affected software. Provide a step-by-step procedure of what actions you carried out when you encountered the problem, so that Oracle Support can reproduce the problem. Provide an evaluation of the effect of the issue, including affected deadlines and costs. Provide screen shots, logs, Remote Diagnostic Agent (RDA) output, or other relevant information. A.2 General Installation Issues The following is a list of examples of types of errors that can occur during installation. It contains the following issues: root.sh failed to complete with error messages such as: Start of resource "ora.cluster_interconnect.haip" failed... During installation of Oracle Clusterware, check for Oracle ASM disks failed with the error: PRVF-5150 : Path /dev/mapper/