Commit f60f00bb authored by Holger Brandl's avatar Holger Brandl
Browse files

readjusted chunk settings

parent 41510ef3
......@@ -16,6 +16,7 @@ if(!exists("reportName")){
reportName=".jobs"
# reportName=".ipsjobs"
# reportName=".trinjob"
# reportName=".blastn"
# reportName=".failchunksblastx"
# stop("Usage: RemoveContaminants.R <assemblyBaseName>")
}else{
......@@ -34,16 +35,20 @@ jobData <- read.table(paste0(reportName, ".cluster_snapshots.txt"), header=F, fi
transform(jobid=factor(jobid)) %>%
arrange(jobid) %>%
subset(stat=="RUN") %>%
transform(num_cores=str_match(exec_host, "([0-9]+)[*]n")[,2])
transform(num_cores=str_match(exec_host, "([0-9]+)[*]n")[,2]) %>% mutate(num_cores=ifelse(is.na(num_cores), 1, num_cores))
jobData %>% select(submit_time, start_time, finish_time) %>% head
# filter(finish_time!="-") %>% head
#parse_date_time(ac("00:00:00.00"), c("%d:%H:%M.%S"))
#parse_date_time(ac("00:04:55.18"), c("%d:%H%M%S"))
## parse the submission time
curYear=str_match(ac(jobData$snapshot_time[1]), "-([0-9]*)_")[,2]
convertTimes <- function(someDate) parse_date_time(paste0(curYear, ac(someDate)), c("%Y/%m/%d-%H%M%S"))
convertedTimes <- colwise(convertTimes, .(submit_time, start_time, finish_time))(jobData)
jobData <- cbind(subset(jobData, select=!(names(jobData) %in% names(convertedTimes))), convertedTimes)
#convertedTimes <- colwise(convertTimes, .(submit_time, start_time, finish_time))(jobData)
#jobData <- cbind(subset(jobData, select=!(names(jobData) %in% names(convertedTimes))), convertedTimes)
jobData %<>% mutate_each(funs(convertTimes), submit_time, start_time, finish_time)
jobData <- transform(jobData, snapshot_time=parse_date_time(ac(snapshot_time), c("%d-%m-%y_%H%M%S")))
......
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