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Old 10-31-2009, 12:39 AM   #1
skblazer
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Default Help! submit jobs about Corona Lite

There were some errors when I submit the matching jobs.

Here is the error message:
Code:
[zhan@head mapping_F_25_2]$ submit_scripts_to_PBS.pl -j JOB_LIST.txt &
[1] 17307
[zhan@head mapping_F_25_2]$
Parse a job list file containing script names and run them on PBS.

SUBMIT: output_ALIGN_1_1: /home/zhan/solid/bifxTrainingData_10panels_auto/mappin                                                                                      g_F_25_2/scripts/output_ALIGN_1_1.sh
qsub: illegal -N value
Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/                                                                                      lib/perl/PBSJob.pm line 102.
[ERROR] qsub: (17308):

 --
Sleeping 5 seconds and retrying
[zhan@head mapping_F_25_2]$ qsub: illegal -N value
Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/lib/perl/PBSJob.pm line 102.
[ERROR] qsub: (17336):

 --
Sleeping 10 seconds and retrying
qsub: illegal -N value
Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/lib/perl/PBSJob.pm line 102.
[ERROR] qsub: (17385):

 --
[FATAL]: Submission of job failed after 3 retries
Job submission output_ALIGN_1_1 failed.
There was openPBS patched on my cluster.

Code:
[zhan@head mapping_F_25_2]$ qmgr
Max open servers: 4
Qmgr: p s
#
# Create queues and set their attributes.
#
#
# Create and define queue workq
#
create queue workq
set queue workq queue_type = Execution
set queue workq enabled = True
set queue workq started = True
#
# Create and define queue tracking
#
create queue tracking
set queue tracking queue_type = Execution
set queue tracking enabled = True
set queue tracking started = True
#
# Create and define queue secondary
#
create queue secondary
set queue secondary queue_type = Execution
set queue secondary enabled = True
set queue secondary started = True
#
# Set server attributes.
#
set server scheduling = True
set server default_queue = workq
set server log_events = 511
set server mail_from = adm
set server query_other_jobs = True
set server resources_default.nodect = 1
set server resources_default.nodes = 1
set server scheduler_iteration = 600
set server node_pack = False
Want some helps, thanks
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Old 10-31-2009, 12:41 AM   #2
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tracking queue and secondary queue have been created

the other tasks could be completed by PBS (such as Iprscan)

How can I do ...
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Old 10-31-2009, 08:02 AM   #3
Xi Wang
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Check whether the name of your job exceeds 15 characters or not.
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Old 10-31-2009, 09:48 AM   #4
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Quote:
Originally Posted by Xi Wang View Post
Check whether the name of your job exceeds 15 characters or not.
Thank you.

However, this is the standard submitting procedure according to the instructions in Documents.

I think Job name is set by default.
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Old 10-31-2009, 06:26 PM   #5
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Quote:
Originally Posted by skblazer View Post
Thank you.

However, this is the standard submitting procedure according to the instructions in Documents.

I think Job name is set by default.
Yes, I thinks so. I dont know if it is a bug of Corona. I also encountered this problem days ago, and I solved this problem by replacing the names of job to shorter ones. I edited the perl script.
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Old 11-01-2009, 05:42 AM   #6
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Quote:
Originally Posted by Xi Wang View Post
Yes, I thinks so. I dont know if it is a bug of Corona. I also encountered this problem days ago, and I solved this problem by replacing the names of job to shorter ones. I edited the perl script.
Ah...

So can you tell me which perl script should be edited?

The version I used is 4.2.2

Thank you.
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Old 11-01-2009, 06:35 AM   #7
Xi Wang
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Quote:
Originally Posted by skblazer View Post
Ah...

So can you tell me which perl script should be edited?

The version I used is 4.2.2

Thank you.
My version is 4.0r2.0.

In the file "matching_large_genomes_cmap_save_script.pl", search "$jobname", make sure all the "$jobname"s are of length less than 15.
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Old 11-01-2009, 11:24 PM   #8
luckyjin
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Hi.. Xi Wang
I have a question.

some error when I submit the matching jobs on SGE
-----------------------------------------------------------
[ngs@bio matching_F3]$ submit_scripts_to_SGE.pl -j JOB_LIST.txt

Parse a job list file containing script names and run them on SGE.

Submitting job ALIGN_1_1
WARNING: No job number. This message was received:

Failed to submit job ALIGN_1_1
[ngs@bio matching_F3]$

[ngs@bio matching_F3]$ cat JOB_LIST.txt
1 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_1_1.sh
2 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_2_1.sh
3 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_3_1.sh
4 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_4_1.sh
5 echo "wait for matching jobs to finish" 1,2,3,4
6 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_SETS_1.sh
7 echo "wait for post_matching_by_sets jobs to finish" 6
8 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_1.sh
9 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_2.sh
10 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_3.sh
11 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_4.sh
12 echo "wait for post_matching_by_sets jobs to finish" 8,9,10,11
13 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_CONCAT_MATCH_FILES.sh
13 echo "wait for post_matching_concat_match_files jobs to finish" 13
14 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_FINAL.sh
15 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_MAKING_INDEX.sh
-----------------------------------------------------------

Do I need to modify a script(submit_scripts_to_SGE.pl or matching_large_genomes_cmap_save_script.pl) ?

Last edited by luckyjin; 11-01-2009 at 11:27 PM.
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Old 11-02-2009, 04:12 AM   #9
Xi Wang
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Quote:
Originally Posted by luckyjin View Post
Hi.. Xi Wang
I have a question.

some error when I submit the matching jobs on SGE
-----------------------------------------------------------
[ngs@bio matching_F3]$ submit_scripts_to_SGE.pl -j JOB_LIST.txt

Parse a job list file containing script names and run them on SGE.

Submitting job ALIGN_1_1
WARNING: No job number. This message was received:

Failed to submit job ALIGN_1_1
[ngs@bio matching_F3]$

[ngs@bio matching_F3]$ cat JOB_LIST.txt
1 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_1_1.sh
2 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_2_1.sh
3 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_3_1.sh
4 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_4_1.sh
5 echo "wait for matching jobs to finish" 1,2,3,4
6 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_SETS_1.sh
7 echo "wait for post_matching_by_sets jobs to finish" 6
8 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_1.sh
9 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_2.sh
10 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_3.sh
11 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_4.sh
12 echo "wait for post_matching_by_sets jobs to finish" 8,9,10,11
13 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_CONCAT_MATCH_FILES.sh
13 echo "wait for post_matching_concat_match_files jobs to finish" 13
14 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_FINAL.sh
15 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_MAKING_INDEX.sh
-----------------------------------------------------------

Do I need to modify a script(submit_scripts_to_SGE.pl or matching_large_genomes_cmap_save_script.pl) ?
Sorry, I've never used SGE before. Does anybody else know it?

I think you should check the job number manually when you submit a job to SGE. And it would be a problem in the script submit_scripts_to_SGE.pl .
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Old 11-02-2009, 09:31 AM   #10
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Quote:
Originally Posted by Xi Wang View Post
My version is 4.0r2.0.

In the file "matching_large_genomes_cmap_save_script.pl", search "$jobname", make sure all the "$jobname"s are of length less than 15.
Thank you very much.

I have solved it according to your suggestion.
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Old 05-10-2010, 01:39 AM   #11
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Default what is exact solution

Quote:
Originally Posted by skblazer View Post
Thank you very much.

I have solved it according to your suggestion.
I have the same problem but i dont know how to solve exactly . so please tell me where to change
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Old 05-10-2010, 01:59 AM   #12
Xi Wang
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Quote:
Originally Posted by sarwar View Post
I have the same problem but i dont know how to solve exactly . so please tell me where to change
Do you have a file named: matching_large_genomes_cmap_save_script.pl?
If yes, please edit this file. You can search for "$jobname", and delete some letters of its value.
If you can give me some more detailed info, I may help you with more details.
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Old 05-10-2010, 03:24 AM   #13
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Quote:
Originally Posted by Xi Wang View Post
Do you have a file named: matching_large_genomes_cmap_save_script.pl?
If yes, please edit this file. You can search for "$jobname", and delete some letters of its value.
If you can give me some more detailed info, I may help you with more details.
when we submit the job through submit_script_SGE.pl then it says like following in terminal:
###############################################
warning : no job number .this message was received:
qsub: illigal -c value
failed to submit job ALIGN_1_1
####################################

ofcourse i have file matching_large_genome..._cmap_save_script.pl
so please help me out .
thanks in advance

Last edited by sarwar; 05-10-2010 at 03:43 AM. Reason: adding more information
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Old 05-10-2010, 03:46 AM   #14
Xi Wang
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Quote:
Originally Posted by sarwar View Post
when we submit the job through submit_script_SGE.pl then it says like following in terminal:
###############################################
warning : no job number .this message was received:
qsub: illigal -c value
failed to submit job ALIGN_1_1
####################################

so please help me out .
thanks in advance
Sorry, I've no idea about the problem regarding SGE. Hope others can help you.
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Old 05-10-2010, 03:58 AM   #15
sarwar
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Quote:
Originally Posted by Xi Wang View Post
Sorry, I've never used SGE before. Does anybody else know it?

I think you should check the job number manually when you submit a job to SGE. And it would be a problem in the script submit_scripts_to_SGE.pl .

is this problem solved?

i have the same problem
please help me out ..
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Old 05-12-2010, 06:36 AM   #16
skblazer
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Quote:
Originally Posted by sarwar View Post
I have the same problem but i dont know how to solve exactly . so please tell me where to change
I change it by:

$jobname = substr($jobname,-15);
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Old 05-12-2010, 06:43 AM   #17
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Quote:
Originally Posted by skblazer View Post
I change it by:

$jobname = substr($jobname,-15);
i have proble in SGE
my problem is :
[ngs@bio matching_F3]$ submit_scripts_to_SGE.pl -j JOB_LIST.txt

Parse a job list file containing script names and run them on SGE.

Submitting job ALIGN_1_1
WARNING: No job number. This message was received:

Failed to submit job ALIGN_1_1
[ngs@bio matching_F3]$



anybody who has solved this
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