Closed alexiswl closed 1 month ago
Not sure if this is the reason but this is the error we're seeing
From
icav2 projectanalyses get-analysis-step-logs 5c05e45b-f301-4256-a96e-2b344bbd9978 --step-name cwltool --stderr
We see the following error
Java memory size is set to 20G Launching application... detected environment java options -Djava.io.tmpdir=/scratch QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: rnaseq Initializing regions from /ces/docker-stagedir/stg304b29c9-a8cf-44ec-94a5-e1013416999b/gencode.v39.annotation.gtf... Initialized 100000 regions... Initialized 200000 regions... Initialized 300000 regions... Initialized 400000 regions... Initialized 500000 regions... Initialized 600000 regions... Initialized 700000 regions... Initialized 800000 regions... Initialized 900000 regions... Initialized 1000000 regions... Initialized 1100000 regions... Initialized 1200000 regions... Initialized 1300000 regions... Initialized 1400000 regions... Initialized 1500000 regions... Initialized 1600000 regions... Initialized 1700000 regions... Initialized 1800000 regions... Initialized 1900000 regions... Initialized 2000000 regions... Initialized 2100000 regions... Initialized 2200000 regions... Initialized 2300000 regions... Initialized 2400000 regions... Initialized 2500000 regions... Initialized 2600000 regions... Initialized 2700000 regions... Initialized 2800000 regions... Initialized 2900000 regions... Initialized 3000000 regions... Initialized 3100000 regions... Initialized 3200000 regions... Initialized 3241002 regions it total Starting constructing transcripts for RNA-seq stats... Finished constructing transcripts Starting BAM file analysis Sorting BAM file by name... Thu Jul 25 13:12:42 GMT 2024 WARNING Cleanup output dir Failed to run rnaseq java.io.IOException: No such file or directory at java.base/java.io.UnixFileSystem.createFileExclusively(Native Method) at java.base/java.io.File.createTempFile(File.java:2092) at java.base/java.io.File.createTempFile(File.java:2138) at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.sortSamByName(ComputeCountsTask.java:144) at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:488) at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68) at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:221) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
It is possible for the qualimap tool we need to add in the tmpDirMin requirement.
From the java error above it looks like it is trying sort a bam file inside /tmp so it is possible it has run out of space.
Previous successful workflows of the transcriptome pipeline may have occurred since specifying tmpDirMin has only been a recent requirement.
Not sure if this is the reason but this is the error we're seeing
From
We see the following error
It is possible for the qualimap tool we need to add in the tmpDirMin requirement.
From the java error above it looks like it is trying sort a bam file inside /tmp so it is possible it has run out of space.
Previous successful workflows of the transcriptome pipeline may have occurred since specifying tmpDirMin has only been a recent requirement.