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Qscript of Picard tools
dklevebring
Member ✭
Hi,
So I've finally taken the plunge and migrated our analysis pipeline to Queue. With some great feedback from @johandahlberg, I have gotten to a state where most of the stuff is running smoothly on the cluster.
I'm trying to add Picard's CalculateHSMetrics to the pipeline, but am having some issues. This code:
case class hsmetrics(inBam: File, baitIntervals: File, targetIntervals: File, outMetrics: File) extends CalculateHsMetrics with ExternalCommonArgs with SingleCoreJob with OneDayJob {
@Input(doc="Input BAM file") val bam: File = inBam
@Output(doc="Metrics file") val metrics: File = outMetrics
this.input :+= bam
this.targets = targetIntervals
this.baits = baitIntervals
this.output = metrics
this.reference = refGenome
this.isIntermediate = false
}
Gives the following error message:
ERROR 06:56:25,047 QGraph - Missing 2 values for function: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/Users/dankle/IdeaProjects/eclipse/AutoSeq/.queue/tmp' null 'INPUT=/Users/dankle/tmp/autoseqscala/exampleIND2/exampleIND2.panel.bam' 'TMP_DIR=/Users/dankle/IdeaProjects/eclipse/AutoSeq/.queue/tmp' 'VALIDATION_STRINGENCY=SILENT' 'OUTPUT=/Users/dankle/tmp/autoseqscala/exampleIND2/exampleIND2.panel.preMarkDupsHsMetrics.metrics' 'BAIT_INTERVALS=/Users/dankle/IdeaProjects/eclipse/AutoSeq/resources/exampleINTERVAL.intervals' 'TARGET_INTERVALS=/Users/dankle/IdeaProjects/eclipse/AutoSeq/resources/exampleINTERVAL.intervals' 'REFERENCE_SEQUENCE=/Users/dankle/IdeaProjects/eclipse/AutoSeq/resources/bwaindex0.6/exampleFASTA.fasta' 'METRIC_ACCUMULATION_LEVEL=SAMPLE'
ERROR 06:56:25,048 QGraph - @Argument: jarFile - jar
ERROR 06:56:25,049 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath
And yeah, is seems that the jar file is currently set to null in the command line. However, MarkDuplicates runs fine without setting the jar:
case class dedup(inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs with SingleCoreJob with OneDayJob {
@Input(doc = "Input bam file") var inbam = inBam
@Output(doc = "Output BAM file with dups removed") var outbam = outBam
this.REMOVE_DUPLICATES = true
this.input :+= inBam
this.output = outBam
this.metrics = metricsFile
this.memoryLimit = 3
this.isIntermediate = false
}
Why does CalculateHSMetrics need the jar, but not MarkDuplicates? Both are imported with import org.broadinstitute.sting.queue.extensions.picard._.
Best Answer
-
pdexheimer
✭✭✭✭
Hmm, that's interesting. It looks like the Queue extension for CalculateHsMetrics is missing a line. Try adding
this.javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"into your hsmetrics case class
Answers
Hmm, that's interesting. It looks like the Queue extension for CalculateHsMetrics is missing a line. Try adding
this.javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"into your hsmetrics case classHuh, so it is indeed missing the class line. I'll patch that in the codebase; in the meantime @pdexheimer's suggestion should work to get your script up and working. (thanks Phil!)
Hmm… I'm now getting this:
Any ideas?
Can you try running the Picard command (using the same inputs, parameters etc) directly from command line? This to check whether it's the Picard tool bugging out or Queue is misbehaving.
Got the same error. sigh It seems this is on picard. Thanks.
For future reference: The latter error happens when
METRIC_ACCUMULATION_LEVEL=SAMPLEis set but no read groups are present in the BAM file. If the metric accumulation level is unset, or read groups are added, it runs fine. Sorry about the non-GATK-related part of this post, and thanks for the help identifying the initial issue.Ah, thanks for reporting your solution. Feel free to tell the Picard devs they need to add more graceful handling for that error case.
Update: we reported the issue to the Picard team, and they have developed a fix to handle this error case. Now, for any reads that are missing read group, there will be a row at whatever level of accumulation is requested with "unknown" in the appropriate columns.
Great work, both teams!