QScript/scala jobreport.txt format

SophiaSophia Member
edited October 2012 in Ask the GATK team

Dear all,

I was looking at the jobreport that is output with the Queue hoping to extract some numbers for runtimes etc. and encountered some difficulties in assigning the headers to the fields for each job. In particular, the header seems to have 10 fields (after replacing spaces with tabs)...

                jobName exechosts   startTime   formattedStartTime  analysisName    iteration   intermediate    formattedDoneTime   runtime doneTime

...while the lines for each job seem to have 12:

                DataProcessingPipeline_121016-8-86  cn64.bullx  1350651114021   12-10-19    14:51:54:021    .qlog_bamprocess_and_ug.27090198-01.post_recal.table.covariates 1   true    12-10-19    14:53:39:290    105269  1350651219290

... the columns for startTime and formattedStartTime seem to be switched

... and there are two extra fields indicating the date that are not labeled in the header.

Nothing really to worry about but maybe you would like to correct this.


Best Answer


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