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google-code-export / yabi

Automatically exported from code.google.com/p/yabi
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Status Errors on SSH+SGE #254

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Running jobs on and ssh_sge backend. Jobs report an error in Yabi but still 
seem to have completed fine according to qaact and they return expected output 
files.

$ qacct -j yabi-65563
==============================================================
qname        all.q               
hostname     master              
group        ubuntu              
owner        ubuntu              
project      NONE                
department   defaultdepartment   
jobname      yabi-65563          
jobnumber    18                  
taskid       undefined
account      sge                 
priority     0                   
qsub_time    Thu Aug  9 12:46:08 2012
start_time   Thu Aug  9 12:46:16 2012
end_time     Thu Aug  9 12:47:15 2012
granted_pe   NONE                
slots        1                   
failed       0    
exit_status  0                   
ru_wallclock 59           
ru_utime     54.363       
ru_stime     1.436        
ru_maxrss    217668              
ru_ixrss     0                   
ru_ismrss    0                   
ru_idrss     0                   
ru_isrss     0                   
ru_minflt    81557               
ru_majflt    0                   
ru_nswap     0                   
ru_inblock   0                   
ru_oublock   2352                
ru_msgsnd    0                   
ru_msgrcv    0                   
ru_nsignals  0                   
ru_nvcsw     1723                
ru_nivcsw    2236                
cpu          55.799       
mem          68.274            
io           0.058             
iow          0.000             
maxvmem      1.410G
arid         undefined

$ qstat -j yabi-65563
Following jobs do not exist: 
yabi-65563

Yabi Syslog page

Task failed task    65563   Aug. 9, 2012, 12:48 p.m.
Deleting containing folder 
<snip>2769b250-17cc-4ea1-a375-661499289086...   task    65563   Aug. 9, 2012, 12:48 
p.m.
Deleting 
<snip>2769b250-17cc-4ea1-a375-661499289086/input/seqs_otus_reps.fna...  task    6556
3   Aug. 9, 2012, 12:48 p.m.
Cleaning up job...  task    65563   Aug. 9, 2012, 12:48 p.m.
Files successfuly staged out    task    65563   Aug. 9, 2012, 12:48 p.m.
4 files 1 folders copied successfuly    task    65563   Aug. 9, 2012, 12:48 p.m.
making stageout directory <snip>assign_taxonomy/2 - 
assign_taxonomy/    task    65563   Aug. 9, 2012, 12:47 p.m.
Staging out remote <snip>2769b250-17cc-4ea1-a375-661499289086/output/ to 
<snip>assign_taxonomy/2 - assign_taxonomy/...   task    65563   Aug. 9, 2012, 12:47 
p.m.
Staging out results task    65563   Aug. 9, 2012, 12:47 p.m.
Task has failed. Staging out any job remnants...    task    65563   Aug. 9, 2012, 12:47 
p.m.
Execution of assign_taxonomy.py --assignment_method "rdp" -i 
"<snip>2769b250-17cc-4ea1-a375-661499289086/input/seqs_otus_reps.fna" 
--output_dir "." on <snip>/ failed with status unsubmitted  task    65563   Aug. 9, 
2012, 12:47 p.m.
Remote execution backend sent status message: Error task    65563   Aug. 9, 2012, 
12:47 p.m.
Remote execution backend sent status message: Unsubmitted   task    65563   Aug. 9, 
2012, 12:46 p.m.
Remote execution backend sent status message: id=yabi-65563 task    65563   Aug. 9, 
2012, 12:46 p.m.
Submitting to <snip>/ command: assign_taxonomy.py --assignment_method "rdp" -i 
"<snip>2769b250-17cc-4ea1-a375-661499289086/input/seqs_otus_reps.fna" 
--output_dir "."    task    65563   Aug. 9, 2012, 12:46 p.m.
Copying <snip>assign_taxonomy/1 - select file/seqs_otus_reps.fna to 
<snip>2769b250-17cc-4ea1-a375-661499289086/input/seqs_otus_reps.fna 
Success task    65563   Aug. 9, 2012, 12:46 p.m.
Copying <snip>assign_taxonomy/1 - select file/seqs_otus_reps.fna to 
<snip>2769b250-17cc-4ea1-a375-661499289086/input/seqs_otus_reps.fna using 
method copy...

Original issue reported on code.google.com by amacgregor on 9 Aug 2012 at 7:21