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lfaino / LoReAn

Long Reads Annotation pipeline
MIT License
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running time of LoReAn #42

Closed simoncchu closed 3 years ago

simoncchu commented 3 years ago

I am running LoReAn with singularity, and log show it is running at braker step with content:

### RUNNING IN STRAND MODE AND FINDING ADAPTER AUTOMATICALLY ###
### LOREAN IS CHECKING THAT GMAP IS CORRECTLY BUILD ###

###GMAP MAPPING  STARTED AT:    02:02:43 08-03  ###
###BUILD INDEX###
###MAP###
 ### GMAP IS CORRECTLY BUILD ###

###STAR MAPPING  STARTED AT:    02:03:29 08-03  ###
###BUILD INDEX###
###MAP###
###SAM to BAM###
###SORTING BAM###
###TRINITY STARTS AT:   04:06:35 08-03  ###
###GMAP MAPPING  STARTED AT:    15:17:13 08-03  ###
###BUILD INDEX###
###MAP###
###PASA STARTS AT:      16:42:28 08-03  ###
###BRAKER1 (USING SHORT READS) AND EXONERATE STARTED AT:        23:29:15 08-03  ###
###RUNNING BRAKER1 ###

Go into the temporary folder, and under the braker folder it shows braker has finished running. But after that, the program seems quite and has been there for more than 2 days. I wonder which steps are following the braker step, and are these expected or something wrong with my running? Thank you!

simoncchu commented 3 years ago

It's because of a missing file. Problem solved.