From 397d6b079b2c415df35338fe6b1115203d5199a9 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 18 Nov 2013 09:39:36 +0000
Subject: [PATCH] updated README stable id lookup now also contains an
archive_id_lookup table, which stores retired stable ids also reduced the
required memory for release 74 and 66 species, it ran with less than 600Mb,
no need to request 1.5G
---
misc-scripts/stable_id_lookup/README | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/stable_id_lookup/README b/misc-scripts/stable_id_lookup/README
index e013ab9fdd..479d339354 100644
--- a/misc-scripts/stable_id_lookup/README
+++ b/misc-scripts/stable_id_lookup/README
@@ -16,6 +16,8 @@ core Exon
compara GeneTree
Family
+For Gene, Transcript and Translation, an archive_id_lookup is also created, containing all previously used ids
+
Command to create the stable_id database on ens-staging1 and copy stable ids from databases on ens-staging1 and 2:
@@ -26,8 +28,8 @@ USR=''
PASS=''
cd $DIR
-bsub -q normal -M 1500000 -R'select[mem>1500] rusage[mem=1500]' -o ./stable_ids_${RELEASE}.out -e ./stable_ids_${RELEASE}.err perl populate_stable_id_lookup.pl \
+bsub -q normal -M 700000 -R'select[mem>700] rusage[mem=700]' -o ./stable_ids_${RELEASE}.out -e ./stable_ids_${RELEASE}.err perl populate_stable_id_lookup.pl \
-lhost ens-staging1 -luser $USR -lpass $PASS -create -host ens-staging1 -host ens-staging2 -user ensro
-For release 70 the job consumed 1Gb of memory and took 1hr 40 minutes to run
+For release 74, the job consumed 584Mb of memory and took 1hr 53 minutes to run
--
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