Website:WormMine Builds
Contents
WS244
Build
AceDB Dump
Host: dev.wormbase.org
User: intermine
Path: /home/intermine
Command: ./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws244
Note: DO NOT add a trailing backslash after the path
Output
./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws244
Did not specify AceDB dir in $ACEDB. Searching for tace...
ACEDB set to: /usr/local/wormbase/acedb/wormbase
Transcript
... done.
Variation
... done.
Phenotype
... done.
Expr_pattern
... done.
Expression_cluster
... done.
Anatomy_term
... done.
Expr_cluster
... done.
Life_stage
... done.
RNAi
... done.
**** Program tace, compiled on: May 14 2010 09:21:02 ****
**** Using ACEDB 4.9.52, compiled on: May 14 2010 09:20:07 ****
Code by: Jean Thierry-Mieg (CNRS, France) mieg@crbm.cnrs-mop.fr
Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk
Ed Griffiths (Sanger Centre, UK) edgrif@sanger.ac.uk
You may redistribute this program and database subject to the
conditions in the accompanying copyright file. Anyone interested in
maintaining an up-to-date version should contact one of the authors
at the above email addresses.
// Database directory: /usr/local/wormbase/acedb/wormbase
// Session 594 is readlocked by acabunoc since 2014-08-11_18:29:04 using tace (process 31767 on machine dev.wormbase.org)
// Session 594 is readlocked by getLoginFailed since 2014-08-11_19:28:09 using tace (process 672 on machine dev.wormbase.org)
acedb>
// Found 223435 objects
// 223435 Active Objects
acedb> // 223435 objects dumped
// 223435 Active Objects
acedb>
// Found 199169 objects
// 199169 Active Objects
acedb> // 199169 objects dumped
// 199169 Active Objects
acedb>
// Found 201722 objects
// 201722 Active Objects
acedb> // 201722 objects dumped
// 201722 Active Objects
acedb>
// Found 239936 objects
// 239936 Active Objects
acedb> // 239936 objects dumped
// 239936 Active Objects
acedb> // ERROR - Failed to open for reading: /home/intermine/website-intermine/acedb-dev/acedb/species.ace (system error 2 - No such file or directory)
// Sorry, I could not open file /home/intermine/website-intermine/acedb-dev/acedb/species.ace
// 239936 Active Objects
acedb> // 239936 objects dumped
// 239936 Active Objects
acedb> // 239936 Active Objects
acedb>
// A bientot
Pre-Processing
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /nfs/wormbase/data/acedmp
Commands:
mkdir WS244 cd WS244 scp acabunoc@dev.wormbase.org:/mnt/ephemeral0/acedb_dump_ws244/* . cd /home/intermine/website-intermine/acedb-dev/intermine/redeployment # Set "release = WS244" in update.properties ant
Build failed with error:
/nfs/wormbase/data/intermine/redeployment/build.xml:68: Property 'bpid-c_sp11' is not defined.
Fixed by changing c_sp11 to c_tropicalis in genomic-fasta-species.txt, protein-fasta-species.txt and gff3-species.txt
InterMine Build
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /home/intermine/website-intermine
Command: ./scripts/build_intermine.sh WS240
Output (stdout, stderr not shown):
USING RELEASE: WS244
DATABASE NAME: wormmine_ws244
Updating ~/.intermine/wormmine.properties...
Updating project.xml...
Building the InterMine database...
=== WS240 ===
==== Build ====
===== ACeDB Dump =====
Host: Website dev server
User: intermine
Path: <code>/home/intermine</code>
Command: <code>./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws240</code>
Output:
<pre>
Did not specify AceDB dir in $ACEDB. Searching for tace...
ACEDB set to: /usr/local/wormbase/acedb/wormbase
Transcript
... done.
Variation
... done.
Phenotype
... done.
Expr_pattern
... done.
Expression_cluster
... done.
Anatomy_term
... done.
Expr_cluster
... done.
Life_stage
... done.
RNAi
... done.
**** Program tace, compiled on: May 14 2010 09:21:02 ****
**** Using ACEDB 4.9.52, compiled on: May 14 2010 09:20:07 ****
Code by: Jean Thierry-Mieg (CNRS, France) mieg@crbm.cnrs-mop.fr
Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk
Ed Griffiths (Sanger Centre, UK) edgrif@sanger.ac.uk
You may redistribute this program and database subject to the
conditions in the accompanying copyright file. Anyone interested in
maintaining an up-to-date version should contact one of the authors
at the above email addresses.
// Database directory: /usr/local/wormbase/acedb/wormbase
acedb>
// Found 204526 objects
// 204526 Active Objects
acedb> // 204526 objects dumped
// 204526 Active Objects
acedb>
// Found 186343 objects
// 186343 Active Objects
acedb> // 186343 objects dumped
// 186343 Active Objects
acedb>
// Found 188862 objects
// 188862 Active Objects
acedb> // 188862 objects dumped
// 188862 Active Objects
acedb>
// Found 221196 objects
// 221196 Active Objects
acedb> // 221196 objects dumped
// 221196 Active Objects
acedb> // ERROR - Failed to open for reading: /home/jbaran/src/website-intermine/acedb-dev/acedb/species.ace (system error 2 - No such file or directory)
// Sorry, I could not open file /home/jbaran/src/website-intermine/acedb-dev/acedb/species.ace
// 221196 Active Objects
acedb> // 221196 objects dumped
// 221196 Active Objects
acedb> // 221196 Active Objects
acedb>
// A bientot
Pre-Processing
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /nfs/wormbase/data/acedmp
Commands:
mkdir WS240 cd WS240 scp jbaran@dev.wormbase.org:/mnt/ephemeral0/acedb_dump_ws240/* . cd /home/intermine/website-intermine/acedb-dev/intermine/redeployment # Set "release = WS240" in update.properties ant
Output: too long to show here
InterMine Build
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /home/intermine/website-intermine
Command: ./scripts/build_intermine.sh WS240
Output (stdout, stderr not shown):
USING RELEASE: WS240 DATABASE NAME: wormmine_ws240 Updating ~/.intermine/wormmine.properties... Updating project.xml... Building the InterMine database... action name time in seconds ------------------------------------------------------------- entrez-organism 130 create-chromosome-locations-and-lengths 1075 do-sources 51 create-search-index 3747 summarise-objectstore 740 create-autocomplete-index 41 create-attribute-indexes 191 transfer-sequences 209663 final-dump 1246 total 216884
Quick fix for resolving missing organisms.xml file:
cd /nfs/wormbase/data/intermine/datadir mkdir entrez-organism cp /home/intermine/organisms.xml entrez-organism
Deployment
TBD
WS239
Build
Host: WormMine dev server (206.108.125.174)
Path: /home/jbaran/src/website-intermine/acedb-dev/intermine/wormmine
Command: ../bio/scripts/project_build -l -v localhost joachim_ws239_2
Summary:
action name time in seconds ------------------------------------------------------------- entrez-organism 95 create-chromosome-locations-and-lengths 708 do-sources 25 create-search-index 983 summarise-objectstore 245 create-autocomplete-index 28 create-attribute-indexes 95 transfer-sequences 248429 final-dump 697 total 251305
Deployment
Host: WormMine production server (206.108.125.166)
Path: /nfs/wormbase/archive/jbaran/WS239-2
Commands:
dropdb -U intermine joachim-ws239-2 createdb -U intermine -E SQL_ASCII joachim-ws239-2 pg_restore -U intermine_admin -d joachim-ws239-2 joachim_ws239_2.final
Required Disk Space:
1.3G joachim_ws239_2.final + 17G PostgreSQL DB
