Negative complete jobs in qstat output

[s-andrews]

trafficstars

======================================================================
 Cluster Flow Pipeline: samtools_sort_index
 Submitted:             20 minutes, 5 seconds ago
 Working Directory:     /bi/group/bioinf/Rachael_Huntly/Cufflinks_Analysis/Rachel_0_vs_8_hour
 Cluster Flow ID:       samtools_sort_index_1485260139
 Submitted Jobs:        17
 Running Jobs:          8
 Queued Jobs:           11 (resources)
 Completed Jobs:        -2 (-11%)
======================================================================

 - samtools_sort_index                             [4 cores]
      - email_run_complete
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete
           - email_pipeline_complete

 - samtools_sort_index                             [4 cores]
      - email_run_complete
      - email_run_complete

[ewels]

Is this always the case? Or only occasionally?

The code that does this parses how many jobs were submitted from the initial log file, then subtracts the number of running / pending jobs etc. I guess I could easily add a check that this number is ≥ 0 (and make it 0 if not), but it would be better to figure out why it's able to get a negative number..

Phil

[ewels]

@s-andrews / @FelixKrueger - if one of you could send me the CF submission log for a run where this is happened I'll take a look. I think it must be a case that the number of jobs submitted aren't being counted properly.

[FelixKrueger]

here is one, cheers. cf_bismark_singlecell_1488545447_submissionlog.txt

[ewels]

submission log:

Cluster Flow Pipeline: bismark_singlecell
Submitted:             7 minutes, 2 seconds ago
Working Directory:     /path/to/dir
Cluster Flow ID:       bismark_singlecell_1488545447
Submitted Jobs:        902
Running Jobs:          75
Queued Jobs:           1102 (resources)
Completed Jobs:        -275 (-30%)

Hmm, strange. I agree that it looks like there were 902 jobs submitted there. So it must be over-counting the queued jobs somehow.

Ok, next up - could you do a cf --qstat to get the above log followed by a normal qstat so that I can try to figure out why it thinks that there are so many pipeline jobs queued please..

[ewels]

Also - I didn't actually explicitly say this myself, but it works fine for me 😁 That's why I'm asking you guys to do stuff.

Two more questions:

1. Does it always do this, or only sometimes?
2. Why are you running v0.4_dev? v0.4 is the latest released version and v0.5_dev is the most recent development version 😉

Phil

[FelixKrueger]

Are you sure you want this? ^^ CF_qstat.txt qstat.txt

[ewels]

Ah, no good - everything is fine in CF_qstat.txt, looks like the correct number of running and queued jobs, no negative Completed Jobs number..

[ewels]

..spoke to soon, there are a lot of different pipeline runs in this file it would seem...!!!

[FelixKrueger]

I see this:

 Cluster Flow ID:       bismark_singlecell_1488545447
 Submitted Jobs:        902
 Running Jobs:          77
 Queued Jobs:           1095 (resources)
 Completed Jobs:        -270 (-29%)
======================================================================

 - bismark_align                                   [4 cores]  [queued, priority 0]
      - bismark_deduplicate
           - bismark_methXtract
                - bismark_report

[FelixKrueger]

yes sorry, it's not like I have nothing to do... :)

[ewels]

Ah, I need longer qstat output though. The default trims the full job name, I forgot that. Can you instead do qstat -pri -r -xml please?

[FelixKrueger]

Here you go: qstat.txt

[ewels]

Yay, 75114 lines of xml for me to read through. Such a lucky boy! 🥇