Test-drive the GATK tools and Best Practices pipelines on Terra
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QScript/scala jobreport.txt format
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.