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Attempt at fixing markdup memory issues #179

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merged 5 commits into from
Mar 25, 2019
Merged

Attempt at fixing markdup memory issues #179

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c98b0ed
Attempt at fixing markdup memory issues
apeltzer Mar 25, 2019
ff48684
Add changelog
apeltzer Mar 25, 2019
93ac1fa
Splicesites was shifted :-(
apeltzer Mar 25, 2019
5c279f8
Adjusted memory command for <8GB systems
apeltzer Mar 25, 2019
1f020c9
Use defaults for markDuplicates
apeltzer Mar 25, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
#### Bug fixes
* Fixing HISAT2 Index Building for large reference genomes [#153](https://github.com/nf-core/rnaseq/issues/153)
* Fixing HISAT2 BAM sorting using more memory than available on the system
* Fixing MarkDuplicates memory consumption issues following [#179](https://github.com/nf-core/rnaseq/pull/179)


#### Dependency Updates
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6 changes: 6 additions & 0 deletions conf/base.config
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Expand Up @@ -23,6 +23,12 @@ process {
withName: trim_galore {
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withName:markDuplicates {
// Actually the -Xmx value should be kept lower,
// and is set through the markdup_java_options
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
}
withName: makeHISATindex {
cpus = { check_max( 10, 'cpus' ) }
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
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11 changes: 3 additions & 8 deletions main.nf
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Expand Up @@ -852,7 +852,6 @@ process preseq {
* STEP 6 Mark duplicates
*/
process markDuplicates {
label 'low_memory'
tag "${bam.baseName - '.sorted'}"
publishDir "${params.outdir}/markDuplicates", mode: 'copy',
saveAs: {filename -> filename.indexOf("_metrics.txt") > 0 ? "metrics/$filename" : "$filename"}
Expand All @@ -869,14 +868,10 @@ process markDuplicates {
file "${bam.baseName}.markDups.bam.bai"

script:
if( !task.memory ){
log.info "[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this."
avail_mem = 3
} else {
avail_mem = task.memory.toGiga()
}
markdup_java_options = (task.memory.toGiga() > 8) ? ${params.markdup_java_options} : "\"-Xms" + (task.memory.toGiga() / 2 )+"g "+ "-Xmx" + (task.memory.toGiga() - 1)+ "g\""

"""
picard -Xmx${avail_mem}g MarkDuplicates \\
picard ${markdup_java_options} MarkDuplicates \\
INPUT=$bam \\
OUTPUT=${bam.baseName}.markDups.bam \\
METRICS_FILE=${bam.baseName}.markDups_metrics.txt \\
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -18,6 +18,7 @@ params {
fcExtraAttributes = 'gene_name'
fcGroupFeatures = 'gene_id'
fcGroupFeaturesType = 'gene_biotype'
markdup_java_options = '"-Xms4000m -Xmx7g"' //Established values for markDuplicate memory consumption, see issue PR #689 (in Sarek) for details
splicesites = false
saveReference = false
saveTrimmed = false
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