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uniprot: Updates Cycles

bank: uniprot

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Release

Release 12.6
BankSize 61,210G
Downloaded files size
Elapsed time 10:51:20
Online Directory /db/uniprot/uniprot_12.6

Sessions infos

Start End Elapsed Time Nb Files Status
session 09-01-2008 13:36:53 09-01-2008 17:26:31 03:49:38 download=0/ Extract=0/ Local=0 Update Cycle crashed
warning
No parallel process defined! (db.pre.process not set)
error
Biomaj stopped. See the logs to obtain more information.
session 09-01-2008 17:29:57 11-01-2008 00:28:13 06:58:16 download=0/ Extract=0/ Local=0 Update Cycle crashed
session 10-01-2008 16:01:53 11-01-2008 00:28:13 08:26:20 download=0/ Extract=0/ Local=0 Update Cycle crashed
error
A biomaj process running for bank:uniprot
session 10-01-2008 16:02:09 11-01-2008 00:28:13 08:26:03 download=0/ Extract=0/ Local=0 Update Cycle Completed
warning
Number of processes defined inside metaprocess [GENERATIONFASTA] has changed. old[1] new [2] All process from [FASTA:GENERATIONFASTA] have to be launch!
warning
The dependence file [/db/uniprot/uniprot_12.6/emboss/uniprot_swissprot.ent] is not find ! Process [emboss] need to be launched.
warning
[emboss] is not ok...Process need to be launched.

(Local => files from preview release)

METAPROCESS :


Session:09-01-2008 13:36:53

Meta Process : ORGANIZATION (duration : 00:00:00)
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_sprot.fasta fasta/Swiss-Prot/uniprot_sprot.fasta El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_sprot_varsplic.fasta fasta/Swiss-Prot_Annotated_Splice_Variants/uniprot_sprot_varsplic.fasta El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_trembl.fasta fasta/TrEMBL/uniprot_trembl.fasta El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_sprot.dat swissprot/Swiss-Prot/uniprot_sprot.dat El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_trembl.dat swissprot/TrEMBL/uniprot_trembl.dat El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_sprot.xml xml/Swiss-Prot/uniprot_sprot.xml El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot_trembl.xml xml/TrEMBL/uniprot_trembl.xml El.Time.: 00:00:00 Process completed
PP Name description cmd Elabs. Time Status
linkfile Section organisation linkfile.sh flat/uniprot.xsd xsd/all/uniprot.xsd El.Time.: 00:00:00 Process completed

Session:09-01-2008 13:36:53

Meta Process : GENERATIONFASTA (duration : 00:01:03)
PP Name description cmd Elabs. Time Status
concatUniprot concat fasta files concat.sh "flat/*.fasta" "" "fasta/UniProtKB/all.fasta" El.Time.: 00:01:03 Process completed

Session:09-01-2008 13:36:53

Meta Process : BLAST_ALL (duration : 00:16:27)
PP Name description cmd Elabs. Time Status
formatdb Index blast formatdb.sh "fasta/UniProtKB/all.fasta" "blast/All/" "-p T -o F" "uniprot" El.Time.: 00:16:27 Process completed

Session:09-01-2008 13:36:53

Meta Process : BLAST_SWISS (duration : 00:01:21)
PP Name description cmd Elabs. Time Status
formatdb Index blast formatdb.sh "fasta/Swiss-Prot/uniprot_sprot.fasta" "blast/Swiss-Prot/" "-p T -o F" "uniprot_sprot" El.Time.: 00:01:21 Process completed

Session:09-01-2008 13:36:53

Meta Process : BLAST_TREMBL (duration : 00:15:31)
PP Name description cmd Elabs. Time Status
formatdb Index blast formatdb.sh "fasta/TrEMBL/uniprot_trembl.fasta" "blast/TrEMBL/" "-p T -o F" "uniprot_trembl" El.Time.: 00:15:31 Process completed

Session:09-01-2008 13:36:53

Meta Process : EMBOSS_SWISS (duration : 03:48:07)
PP Name description cmd Elabs. Time Status
emboss Indexation format EMBOSS migale/build_emboss.pl -biomaj -outinput uniprot_swissprot=uniprot_sprot.dat -program dbxflat -informat swiss El.Time.: 03:48:07 Process completed

Session:09-01-2008 13:36:53

Meta Process : EMBOSS_TREMBL (duration : 00:00:00)
PP Name description cmd Elabs. Time Status
emboss Indexation format EMBOSS migale/build_emboss.pl -biomaj -outinput uniprot_trembl=uniprot_trembl.dat -program dbxflat -informat trembl El.Time.: 00:00:00 Process crashed
Warning
mkdir /db/uniprot/future_release/emboss
Errors
Error: 'trembl' is not a valid menu option
Accepted short codes are: EMBL,SWISS,GB,REFSEQ
Error: Bad menu option 'trembl'
Died: dbxflat terminated: Bad value for '-idformat' with -auto defined
Uncaught exception from user code:
Error - /local/emboss/EMBOSS-5.0.0/bin//dbxflat returned non-zero exit code : 256
No such file or directory at /db/biomaj/Bin/conf/process/migale/MigaleBiomaj.pm line 589.
at /db/biomaj/Bin/conf/process/migale/MigaleBiomaj.pm line 589
MigaleBiomaj::execution_factory('HASH(0x645238)') called at /db/biomaj/Bin/conf/process/migale/build_emboss.pl line 205
"Process emboss_trembl (with executable emboss_trembl.exe) generate an error." See the logs to obtain more information.

Session:09-01-2008 17:29:57

Meta Process : EMBOSS_TREMBL (duration : 00:00:00)
PP Name description cmd Elabs. Time Status
emboss Indexation format EMBOSS migale/build_emboss.pl -biomaj -outinput uniprot_trembl=uniprot_trembl.dat -program dbxflat -informat swiss El.Time.: 00:00:00 Process completed

Session:10-01-2008 16:02:09

Meta Process : GENERATIONFASTA (duration : 00:00:00)
PP Name description cmd Elabs. Time Status
concatUniprot concat fasta files concat.sh "flat/*.fasta" "" "fasta/UniProtKB/all.fasta" El.Time.: 00:00:51 Process completed
PP Name description cmd Elabs. Time Status
emboss_prep Link un repertoire pour la generation sur le /local (pour palier au bug de panfs) pre_emboss.sh El.Time.: 00:00:00 Process completed

Session:10-01-2008 16:02:09

Meta Process : EMBOSS_SWISS (duration : 00:27:08)
PP Name description cmd Elabs. Time Status
emboss Indexation format EMBOSS migale/build_emboss.pl -biomaj -outinput uniprot_swissprot=uniprot_sprot.dat -program dbxflat -informat swiss El.Time.: 00:27:08 Process completed

Session:10-01-2008 16:02:09

Meta Process : EMBOSS_TREMBL (duration : 08:14:09)
PP Name description cmd Elabs. Time Status
emboss Indexation format EMBOSS migale/build_emboss.pl -biomaj -outinput uniprot_trembl=uniprot_trembl.dat -program dbxflat -informat swiss El.Time.: 08:14:09 Process completed

Session:10-01-2008 16:02:09

Meta Process : EMBOSSPOST (duration : 00:10:54)
PP Name description cmd Elabs. Time Status
emboss_post copy du repertoire d'index post_emboss.sh El.Time.: 00:10:54 Process completed