Help! submit jobs about Corona Lite

[skblazer]

There were some errors when I submit the matching jobs.

Here is the error message:

[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.

[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

[skblazer]

tracking queue and secondary queue have been created

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

How can I do ...

[Xi Wang]

Check whether the name of your job exceeds 15 characters or not.

[skblazer]

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.

[Xi Wang]

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.

[skblazer]

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.

[Xi Wang]

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.

[luckyjin]

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) ?

[Xi Wang]

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 .

[skblazer]

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.

[sarwar]

what is exact solution

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

[Xi Wang]

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.

[sarwar]

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

[Xi Wang]

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.

[sarwar]

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 ..