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# enable extended apache server status, which is sometimes useful for debugging | |
ExtendedStatus On | |
<VirtualHost *:80> | |
ServerName sgn.localhost.localdomain | |
PerlWarn On | |
PerlTaintCheck On |
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(datura)(~/git/sgn master$ )$ git rebase git-svn | |
First, rewinding head to replay your work on top of it... | |
Applying: Add more tests to t/bulk.t | |
Applying: Add more tests for downloading bulk data to t/bulk.t | |
Applying: Add tests for microarray and clone_search modes on /bulk/input.pl | |
Applying: Add test for bulk bac_end | |
Applying: added markup_string.mas, which displays an arbitrary string formatted with Text.Markup | |
Using index info to reconstruct a base tree... | |
Falling back to patching base and 3-way merge... | |
Auto-merging mason/util/markup_string.mas |
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#!/usr/bin/env perl | |
use strict; | |
use warnings; | |
use CGI; | |
use JSON::Any; | |
use Mail::Sendmail; | |
use Tie::Function; | |
use DateTime::Format::ISO8601; |
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running sgn_unigenes in batch 7 | |
CXGN::Tools::Run: cluster job id: 392852.eggplant.cluster.sgn | |
CXGN::Tools::Run: date: 2010-05-15 04:11:44 EDT | |
CXGN::Tools::Run: command failed: 'itag_wrapper perl -MCXGN::ITAG::Pipeline::Analysis::sgn_unigenes -e CXGN::ITA | |
G::Pipeline::Analysis::sgn_unigenes->run_gth('scaffold174','/data/shared/tomato_genome/itagpipeline/itag/pipe001 | |
/batch007/seq/scaffold174.seq.vecscreened.itag001.batch007.v1.fasta','/data/prod/tmp/itag-analysis-sgn_unigenes- | |
2JsDQD/scaffold174/xml','/data/prod/tmp/itag-analysis-sgn_unigenes-2JsDQD/scaffold174/gff3')' | |
CXGN::Tools::Run: Command failed on host 'shiv4', user 'itagpipeline', with $?=9, exit value 0, signal KILL (9), $r=5677, $!='' (string could be spurious) | |
CXGN::Tools::Run: last few lines of stdout: | |
CXGN::Tools::Run: last few lines of stderr: |
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rob@banana cxgn-corelibs (master$)$ sudo parted /dev/sda | |
GNU Parted 1.8.8 | |
Using /dev/sda | |
Welcome to GNU Parted! Type 'help' to view a list of commands. | |
(parted) p | |
Model: ATA INTEL SSDSA2MH08 (scsi) | |
Disk /dev/sda: 80.0GB | |
Sector size (logical/physical): 512B/512B | |
Partition Table: msdos |
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rob@banana sgn (master$)$ a2restart; prove `perl -E 'print join " ", map "-I $_", @ARGV' ../*/lib` -lrv t/bulk.t | |
* Restarting web server apache2 apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName | |
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName | |
[ OK ] | |
t/bulk.t .. | |
ok 1 - GET http://sgn.localhost.localdomain/bulk/input.pl?mode=unigene | |
ok 2 - Content contains "Download unigene information" | |
ok 3 - Form submit test | |
ok 4 - Result page title check | |
ok 5 - Result check 1 |
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rob@blade2:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unigenes | |
Password: | |
running sgn_unigenes in batch 7 | |
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions | |
at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838 | |
CXGN::Tools::Run error running `qsub`: qsub: Invalid credential | |
CXGN::Tools::Run retrying cluster job submission. | |
CXGN::Tools::Run: cluster job id: 406351.eggplant.cluster.sgn | |
CXGN::Tools::Run: start time: 2010-05-19 00:05:27 EDT | |
CXGN::Tools::Run: error time: 2010-05-19 00:08:06 EDT |
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rob@blade2:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unigenes | |
running sgn_unigenes in batch 7 | |
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions | |
at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838 | |
CXGN::Tools::Run: cluster job id: 409069.eggplant.cluster.sgn | |
CXGN::Tools::Run: start time: 2010-05-20 00:18:19 EDT | |
CXGN::Tools::Run: error time: 2010-05-20 00:26:27 EDT | |
CXGN::Tools::Run: command failed: 'itag_wrapper perl -MCXGN::ITAG::Pipeline::Analysis::sgn_unigenes -e CXGN::ITAG::Pipeline::An | |
alysis::sgn_unigenes->run_gth('scaffold760','/data/shared/tomato_genome/itagpipeline/itag/pipe001/batch007/seq/scaffold760.seq. | |
vecscreened.itag001.batch007.v1.fasta','/data/prod/tmp/itag-analysis-sgn_unigenes-DlPM9v/scaffold760/xml','/data/prod/tmp/itag- |
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rob@eggplant:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unige\ | |
n | |
es | |
running sgn_unigenes in batch 7 | |
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions | |
at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838 | |
qstat: Unknown Job Id 417939.eggplant.cluster.sgn | |
CXGN::Tools::Run: cluster job id: 417939.eggplant.cluster.sgn | |
CXGN::Tools::Run: start time: 2010-05-27 06:22:39 EDT | |
CXGN::Tools::Run: error time: 2010-05-27 06:25:53 EDT |
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psql -AX -f t/sql/plperl6.sql | |
1..9 | |
ok 1 - Return an integer from PL/Perl6 | |
ok 2 - Return nothing from PL/Perl6 | |
ok 3 - Return a float from PL/Perl6 | |
ok 4 - Return a varchar from PL/Perl6 | |
ok 5 - Use a single quote in a PL/Perl6 procedure | |
ok 6 - Calculate the sum of all Fibonacci numbers <= 100 | |
not ok 7 - We can return an argument unchanged | |
# Failed test 7: "We can return an argument unchanged" |