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Illumina / pyflow

A lightweight parallel task engine
http://Illumina.github.io/pyflow/
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Notification mail received but the pyflow process still running #16

Closed kcshashidhar closed 8 years ago

kcshashidhar commented 8 years ago

Hi,

I sometimes have the situation that I get a pyflow notification mail that workflow is successfully completed, but when I check the screen session, the pyflow process is still running. I'm appending below a tail snippet of what I see on the terminal. Any idea what could be causing this?

I'm using pyflow 1.1.12 and the run is in SGE mode.

Thanks!

===== AnnotateVariantFlow StatusUpdate ===== [2016-01-21T17:05:15.762396] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False [2016-01-21T17:05:15.763486] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 1/0/1/4/0 [2016-01-21T17:05:15.764365] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000 [2016-01-21T17:05:15.765316] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: '' [2016-01-21T17:05:15.766058] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 7.5733 [2016-01-21T17:05:15.766792] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'vcfcv_dedupdb_MSK61+vcfcv' [2016-01-21T18:05:15.901648] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] ===== AnnotateVariantFlow StatusUpdate ===== [2016-01-21T18:05:15.937098] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False [2016-01-21T18:05:15.937865] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 1/0/1/4/0 [2016-01-21T18:05:15.938674] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000 [2016-01-21T18:05:15.939514] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: '' [2016-01-21T18:05:15.940162] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 8.5733 [2016-01-21T18:05:15.940787] [ussf-prd-lndt-b-4-2.local] [25530_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'vcfcv_dedupdb_MSK61+vcfcv'

kcshashidhar commented 8 years ago

I was misled by notifications generated by other simultaneous runs.