Bio-Grid-Run-SGE v0.066 Perl 5 v5.41.2 x86_64-linux-thread-multi
- Status
- Pass
- From
- Andreas J. König (ANDK)
- Dist
-
Bio-Grid-Run-SGE v0.066
- Platform
- Perl 5 v5.41.2 x86_64-linux-thread-multi
- Date
- 2024-08-16 11:41:02
- ID
- 6a0b1d5c-5bc4-11ef-ac46-bb5cb2a0091c
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Joachim Bargsten,
This is a computer-generated report for Bio-Grid-Run-SGE-0.066
on perl 5.41.2, created by CPAN-Reporter-1.2019.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
# USAGE
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_env.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_env.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# --help (or -h) print help message and exit
# --stage STR run post task with job id of previous task
# --range STR (or -r) run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
# 1st test
[16 Aug 11:36:10] [INFO]: INDEXING ....
[16 Aug 11:36:10] [INFO]: CONFIGURATION:
(/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/test_env.job.conf.json)
{
args => [],
idx_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/idx/test_env.0.idx",
},
],
job_name => "test_env",
log_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/r",
stderr_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/err",
stdout_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/out",
submit_bin => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/qfake.pl",
submit_params => [],
tmp_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp",
working_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX",
}
[16 Aug 11:36:10] [INFO]: Running: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/qfake.pl -t 1-6 -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N test_env -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/out /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/env.test_env.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_env.pl --stage worker /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/test_env.job.conf.json
[16 Aug 11:36:18] [INFO]: >>job_id:1723808170
[16 Aug 11:36:18] [INFO]: post processing: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/qfake.pl -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N p1723808170_test_env -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/out -hold_jid 1723808170 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/env.test_env.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_env.pl --stage post_task --job_id 1723808170 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/f2n4CXGBAX/test_env.tmp/test_env.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfake.t ................................ ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_fail_on_purpose.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_fail_on_purpose.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# --help (or -h) print help message and exit
# --stage STR run post task with job id of previous task
# --range STR (or -r) run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[16 Aug 11:36:22] [INFO]: INDEXING ....
[16 Aug 11:36:22] [INFO]: CONFIGURATION:
(/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/test_all_fail.job.conf.json)
{
args => [],
idx_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/idx/test_all_fail.0.idx",
},
],
job_name => "test_all_fail",
log_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/r",
stderr_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/err",
stdout_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/out",
submit_bin => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/qfake.pl",
submit_params => [],
tmp_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp",
working_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE",
}
[16 Aug 11:36:22] [INFO]: Running: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/qfake.pl -t 1-6 -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N test_all_fail -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/out /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/env.test_all_fail.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_fail_on_purpose.pl --stage worker /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/test_all_fail.job.conf.json
[16 Aug 11:36:31] [INFO]: >>job_id:1723808183
[16 Aug 11:36:31] [INFO]: post processing: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/qfake.pl -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N p1723808183_test_all_fail -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/out -hold_jid 1723808183 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/env.test_all_fail.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_fail_on_purpose.pl --stage post_task --job_id 1723808183 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/6WedAfyWsE/test_all_fail.tmp/test_all_fail.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfake_err.t ............................ ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_syntax_error.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_syntax_error.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# --help (or -h) print help message and exit
# --stage STR run post task with job id of previous task
# --range STR (or -r) run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[16 Aug 11:36:35] [INFO]: INDEXING ....
[16 Aug 11:36:35] [INFO]: CONFIGURATION:
(/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/test_all_fail.job.conf.json)
{
args => [],
idx_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/idx/test_all_fail.0.idx",
},
],
job_name => "test_all_fail",
log_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/r",
stderr_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/err",
stdout_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/out",
submit_bin => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/qfake.pl",
submit_params => [],
tmp_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp",
working_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs",
}
[16 Aug 11:36:35] [INFO]: Running: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/qfake.pl -t 1-6 -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N test_all_fail -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/out /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/env.test_all_fail.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_syntax_error.pl --stage worker /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/test_all_fail.job.conf.json
[16 Aug 11:36:44] [INFO]: >>job_id:1723808196
[16 Aug 11:36:44] [INFO]: post processing: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/qfake.pl -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N p1723808196_test_all_fail -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/out -hold_jid 1723808196 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/env.test_all_fail.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_syntax_error.pl --stage post_task --job_id 1723808196 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/YmqmtxFJvs/test_all_fail.tmp/test_all_fail.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfake_syntax_error.t ................... ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_env.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_env.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# --help (or -h) print help message and exit
# --stage STR run post task with job id of previous task
# --range STR (or -r) run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[16 Aug 11:36:48] [INFO]: INDEXING ....
[16 Aug 11:36:48] [INFO]: CONFIGURATION:
(/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/test_env.job.conf.json)
{
args => [],
idx_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/idx",
input => [
{
elements => ["a" .. "e", "...", "v" .. "z"],
format => "List",
idx_file => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/idx/test_env.0.idx",
},
],
job_name => "test_env",
log_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 26,
prefix_output_dirs => 1,
result_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/r",
stderr_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/err",
stdout_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/out",
submit_bin => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/qfork.pl",
submit_params => [],
tmp_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp",
working_dir => "/tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X",
}
[16 Aug 11:36:48] [INFO]: Running: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/qfork.pl -t 1-26 -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N test_env -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/out /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/env.test_env.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_env.pl --stage worker /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/test_env.job.conf.json
[16 Aug 11:37:03] [INFO]: >>job_id:1723808209
[16 Aug 11:37:03] [INFO]: post processing: /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/qfork.pl -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N p1723808209_test_env -e /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/err -o /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/out -hold_jid 1723808209 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/env.test_env.pl /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/scripts/cl_env.pl --stage post_task --job_id 1723808209 /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0/tmp_test/cSNPKZQ_9X/test_env.tmp/test_env.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfork.t ................................ ok
# Testing Bio::Grid::Run::SGE 0.066, Perl 5.041002, /tmp/basesmoker-reloperl-LuaR/bin/perl
t/00-load.t ....................................... ok
t/Bio-Grid-Run-SGE-Index-Dummy.t .................. ok
[16 Aug 11:37:06] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-FileList.t ............... ok
[16 Aug 11:37:06] [INFO]: INDEXING ....
# 4303
# $VAR1 = {
# 'key' => 'eins',
# 'data' => [
# 'SL2.40ch00 21805821 12 80 81',
# 'SL2.40ch01 90304244 22078418 80 81',
# 'SL2.40ch02 49918294 113511478 80 81',
# 'SL2.40ch03 64840714 164053763 80 81',
# 'SL2.40ch04 64064312 229704998 80 81',
# 'SL2.40ch05 65021438 294570126 80 81',
# 'SL2.40ch06 46041636 360404344 80 81'
# ],
# 'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai'
# };
# $VAR1 = {
# 'key' => 'eins',
# 'data' => [
# 'SL2.40ch07 65268621 407021513 80 81',
# 'SL2.40ch08 63032657 473106004 80 81',
# 'SL2.40ch09 67662091 536926582 80 81',
# 'SL2.40ch10 64834305 605434462 80 81',
# 'SL2.40ch11 53386025 671079208 80 81',
# 'SL2.40ch12 65486253 725132571 80 81'
# ],
# 'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai'
# };
# $VAR1 = {
# 'key' => 'zwei',
# 'data' => [
# 'SL2.40ct00001 1652 15 80 81',
# 'SL2.40ct00002 2066 1703 80 81',
# 'SL2.40ct00003 4871 3810 80 81',
# 'SL2.40ct00004 2086 8757 80 81',
# 'SL2.40ct00005 1622 10885 80 81',
# 'SL2.40ct00006 1679 12543 80 81',
# 'SL2.40ct00007 1166 14258 80 81'
# ],
# 'file' => 't/data/S_lycopersicum_contigs.2.40.fa.bg.gz.fai'
# };
t/Bio-Grid-Run-SGE-Index-FileRecordsFromNDJSON.t .. ok
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [INFO]: SKIPPING INDEXING STEP, THE INDEX IS UP TO DATE
t/Bio-Grid-Run-SGE-Index-General.t ................ ok
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[16 Aug 11:37:07] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-List.t ................... ok
[16 Aug 11:37:07] [INFO]: INDEXING ....
[16 Aug 11:37:07] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[16 Aug 11:37:07] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-ListFromFile.t ........... ok
[16 Aug 11:37:07] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-NDJSON.t ................. ok
[16 Aug 11:37:08] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-Range.t .................. ok
t/Bio-Grid-Run-SGE-Index.t ........................ ok
t/Bio-Grid-Run-SGE-Iterator-AllvsAllNoRep.t ....... ok
[16 Aug 11:37:08] [INFO]: INDEXING ....
[16 Aug 11:37:08] [INFO]: INDEXING ....
[16 Aug 11:37:08] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-AvsB.t ................ ok
[16 Aug 11:37:09] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-Consecutive.t ......... ok
t/Bio-Grid-Run-SGE-Log-Analysis.t ................. ok
# [
# "env",
# "config",
# "log",
# "iterator"
# ]
[16 Aug 11:37:09] [INFO]: INDEXING ....
[16 Aug 11:37:09] [INFO]: Running: /tmp/ykIjs2ad29/Bio-Grid-Run-SGE-Master.qsub.pl -t 1-45 -S /tmp/basesmoker-reloperl-LuaR/bin/perl -N cluster_job -e /tmp/ykIjs2ad29/cluster_job.tmp/err -o /tmp/ykIjs2ad29/cluster_job.tmp/out /tmp/ykIjs2ad29/cluster_job.tmp/env.cluster_job.pl t/Bio-Grid-Run-SGE-Master.script.pl --stage worker /tmp/ykIjs2ad29/cluster_job.tmp/cluster_job.job.conf.json
[SUBMIT_WARNING] could not parse job id, using -1 as job id.
STDOUT:
STDERR:
t/Bio-Grid-Run-SGE-Master.t ....................... ok
t/Bio-Grid-Run-SGE-Role-Iterable.t ................ ok
t/Bio-Grid-Run-SGE-Util-Blast.t ................... ok
# /tmp/loop_over_bdir-2922500-lBBYGM/Bio-Grid-Run-SGE-0.066-0
t/Bio-Grid-Run-SGE-Util.t ......................... ok
t/Bio-Grid-Run-SGE-Worker.t ....................... skipped: 1
t/Bio-Grid-Run-SGE.t .............................. ok
t/boilerplate.t ................................... ok
t/manifest.t ...................................... skipped: Author tests not required for installation
t/pod-coverage.t .................................. skipped: no pod coverage checks
t/pod.t ........................................... ok
t/zz-00-basic_qsub_live.t ......................... skipped: This test requires qsub
All tests successful.
Files=29, Tests=2701, 63 wallclock secs ( 0.18 usr 0.08 sys + 28.37 cusr 6.06 csys = 34.69 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------- ----- --------
AnyEvent 0 7.17
AnyEvent::XMPP 0 0.55
Bio::Gonzales 0.068 0.083
Capture::Tiny 0 0.48
Clone 0 0.46
Config::Auto 0 0.44
Config::IniFiles 0 3.000003
Data::Dump 0 1.25
Email::Sender::Simple 0 2.601
Email::Simple 0 2.218
Email::Simple::Creator 0 2.218
Error 0 0.17029
File::Copy 0 2.41
File::HomeDir 0 1.006
File::Next 0 1.18
File::Spec 0 3.92
File::Which 0 1.27
Getopt::Long::Descriptive 0 0.114
HTTP::Date 0 6.06
IO::Prompt::Tiny 0 0.003
JSON::XS 0 4.03
List::MoreUtils 0 0.430
List::Util 0 1.65
Mouse 0 v2.5.11
Parallel::ForkManager 0 2.02
Params::Util 0 1.102
parent 0 0.241
Path::Tiny 0 0.146
perl 5.010 5.041002
Proc::Daemon 0 0.23
Storable 0 3.33
String::ShellQuote 0 1.04
Try::Tiny 0 0.31
URI 0 5.28
XML::LibXML 0 2.0210
build_requires:
Module Need Have
------------------------- ----- --------
Module::Build 0.28 0.4234
Test2::V0 0 1.302200
Test::More 0 1.302200
configure_requires:
Module Need Have
------------------------- ----- --------
Module::Build 0.28 0.4234
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LC_ADDRESS = de_DE.UTF-8
LC_IDENTIFICATION = de_DE.UTF-8
LC_MEASUREMENT = de_DE.UTF-8
LC_MONETARY = de_DE.UTF-8
LC_NAME = de_DE.UTF-8
LC_NUMERIC = de_DE.UTF-8
LC_PAPER = de_DE.UTF-8
LC_TELEPHONE = de_DE.UTF-8
LC_TIME = de_DE.UTF-8
PATH = /home/sand/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/perl/bin:/usr/X11/bin
PERL = /tmp/basesmoker-reloperl-LuaR/bin/perl
PERL5LIB = /tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 2922508
PERL5_CPAN_IS_RUNNING = 2922508
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /tmp/basesmoker-reloperl-LuaR/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.36
CPAN::Meta 2.150010
Cwd 3.92
ExtUtils::CBuilder 0.280240
ExtUtils::Command 7.70
ExtUtils::Install 2.22
ExtUtils::MakeMaker 7.70
ExtUtils::Manifest 1.75
ExtUtils::ParseXS 3.52
File::Spec 3.92
JSON 4.10
JSON::PP 4.16
Module::Build 0.4234
Module::Signature 0.88
Parse::CPAN::Meta 2.150010
Test2 1.302200
Test::Harness 3.48
Test::More 1.302200
YAML 1.31
YAML::Syck 1.34
version 0.9932
--
Summary of my perl5 (revision 5 version 41 subversion 2) configuration:
Commit id: bcb5884b9b0ae1345ac74420bacb865ba11baab3
Platform:
osname=linux
osvers=6.5.0-41-generic
archname=x86_64-linux-thread-multi
uname='linux k93jammy 6.5.0-41-generic #41~22.04.2-ubuntu smp preempt_dynamic mon jun 3 11:32:55 utc 2 x86_64 x86_64 x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93jammy/v5.41.2/b4f3 -Dmyhostname=k93jammy -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dlibswanted=cl pthread socket inet nsl gdbm dbm malloc dl ld sun m crypt sec util c cposix posix ucb BSD gdbm_compat -Duseithreads -Uuselongdouble -DEBUGGING=-g'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
Compiler:
cc='cc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
optimize='-O2 -g'
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='11.4.0'
gccosandvers=''
intsize=4
longsize=8
ptrsize=8
doublesize=8
byteorder=12345678
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=16
longdblkind=3
ivtype='long'
ivsize=8
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='cc'
ldflags =' -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib/x86_64-linux-gnu /usr/lib /usr/lib64
libs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=/lib/x86_64-linux-gnu/libc.so.6
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.35'
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags='-Wl,-E'
cccdlflags='-fPIC'
lddlflags='-shared -O2 -g -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_LONG_DOUBLE
HAS_STRTOLD
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_SIPHASH13
PERL_HASH_USE_SBOX32
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_DEVEL
PERL_USE_SAFE_PUTENV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
USE_THREAD_SAFE_LOCALE
Built under linux
Compiled at Jul 21 2024 16:53:05
%ENV:
PERL="/tmp/basesmoker-reloperl-LuaR/bin/perl"
PERL5LIB="/tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/lib:/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/arch:/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="2922508"
PERL5_CPAN_IS_RUNNING="2922508"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/Courier-Filter-v0.200-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/AllKnowingDNS-1.7-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/Linux-InitFS-0.2-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/dta-tokwrap-0.98-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/Device-Kiln-0.03-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/ProjectBuilder-0.14.1-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/makepp-1.19-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/Lingua-YaTeA-0.626-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/NoZone-1.3-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/mmds-1.902-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/MP3-PodcastFetch-1.05-0/blib/lib
/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/arch
/tmp/loop_over_bdir-2922500-lBBYGM/Devel-Required-0.16-0/blib/lib
/home/sand/src/perl/repoperls/installed-perls/host/k93jammy/v5.41.2/b4f3/lib/site_perl/5.41.2/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93jammy/v5.41.2/b4f3/lib/site_perl/5.41.2
/home/sand/src/perl/repoperls/installed-perls/host/k93jammy/v5.41.2/b4f3/lib/5.41.2/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93jammy/v5.41.2/b4f3/lib/5.41.2
.