Commit ee236d89 authored by Holger Brandl's avatar Holger Brandl

fixed madmax config

parent 87cd7170
...@@ -8,7 +8,6 @@ ...@@ -8,7 +8,6 @@
import joblist.JobConfiguration import joblist.JobConfiguration
import joblist.JobList import joblist.JobList
import joblist.ResubmitStrategy
import kutils.evalBash import kutils.evalBash
import org.docopt.Docopt import org.docopt.Docopt
import java.io.File import java.io.File
...@@ -76,7 +75,7 @@ fastqFiles.filter { !it.isFile }.let { ...@@ -76,7 +75,7 @@ fastqFiles.filter { !it.isFile }.let {
println("Running STAR using igenome '${igenome}' for the following files:\n ${fastqFiles.joinToString("\n")}") println("Running STAR using igenome '${igenome}' for the following files:\n ${fastqFiles.joinToString("\n")}")
val jl = JobList(".starjobs") val jl = JobList(".starjobs").apply { reset() }
for (fastqFile in fastqFiles) { for (fastqFile in fastqFiles) {
println("submitting STAR job for $fastqFile") println("submitting STAR job for $fastqFile")
...@@ -101,7 +100,7 @@ for (fastqFile in fastqFiles) { ...@@ -101,7 +100,7 @@ for (fastqFile in fastqFiles) {
// or use process substiutation in case of zipped reads (see https://github.com/alexdobin/STAR/issues/143#issuecomment-216597465) // or use process substiutation in case of zipped reads (see https://github.com/alexdobin/STAR/issues/143#issuecomment-216597465)
// detect if paired end reads are supplied // detect if paired end reads are supplied
val revReads = if (isPE) fastqFile.parentFile.resolve(fastqFile.name.replace("_1.fastq", "_2.fastq")).path else "" val revReads = if (isPE) fastqFile.absoluteFile.parentFile.resolve(fastqFile.name.replace("_1.fastq", "_2.fastq")).path else ""
val cmd = """ val cmd = """
STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3 STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
...@@ -113,7 +112,8 @@ for (fastqFile in fastqFiles) { ...@@ -113,7 +112,8 @@ for (fastqFile in fastqFiles) {
// todo provide proper walltime here // todo provide proper walltime here
// slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/ // slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
// sacct -o MaxRSS -j JOBID // sacct -o MaxRSS -j JOBID
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000, "", better.files.File(File(".").toPath()))) // jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000, "", better.files.File(File(".").toPath())))
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, 0, "", better.files.File(File(".").toPath())))
} }
......
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