The format of input file for multi-bamqc

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clinbio wang

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Mar 30, 2016, 3:06:48 PM3/30/16
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Hi,

QualiMap is a really good tool in my research, I put all bam file and output directory in on folder. it give me below error, please help:

My input.txt looks like:

1406940 1406940.bam
1406956 1406956.bam

Thanks

QualiMap v.2.2
Built on 2016-01-29 12:10

Selected tool: multi-bamqc
Wed Mar 30 15:00:04 EDT 2016            WARNING Output folder already exists, the results will be saved there

Running multi-sample BAM QC

Checking input paths
Failed to run multi-bamqc
java.lang.NullPointerException
        at java.io.File.<init>(File.java:277)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.findRawDataPath(MultisampleBamQcAnalysis.java:714)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.checkInputPaths(MultisampleBamQcAnalysis.java:741)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run(MultisampleBamQcAnalysis.java:85)
        at org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool.execute(MultisampleBamQcTool.java:159)
        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)
        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

Konstantin Okonechnikov

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Apr 1, 2016, 9:21:36 AM4/1/16
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Hi!

The problem was that the raw BAM files were not detected. 

Was the configuration file located in the same folder as the BAM files? What was the command to launch? From which folder was it launched?


--
  Konstantin





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clinbio wang

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Apr 1, 2016, 10:15:56 AM4/1/16
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Yes.

They are in the same folder with BAM files.  for bam in *.bam; do echo $bam; do echo $bam; /sc/NTC/qualimap_v2.2/qualimap bamqc -bam $bam -outdir qulimap.results/  --java-mem-size=9G;done

/sc/NTC/ is where the qualimap installed.

Thank you

在 2016年4月1日星期五 UTC-4上午9:21:36,Konstantin Okonechnikov写道:

Konstantin Okonechnikov

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Apr 8, 2016, 6:52:14 AM4/8/16
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By default multi-bamqc mode requires the results of Qualimap BAM QC.

Basically, configuration should be something like this:
1406940 1406940_stats
1406956 1406956_stats

This will work if the default BAM QC outdirs are located in the same directory, where the script was launched. However in your script:
echo $bam; /sc/NTC/qualimap_v2.2/qualimap bamqc -bam $bam -outdir qulimap.results/  --java-mem-size=9G;done

is only a launch of BAM QC analysis for each BAM file Moreover, the same output dir is always used.

I would suggest to launch analysis of multi-bamqc mode using special option "-r". In this case BAM QC analysis will be performed initially for each BAM file and then multi bamqc mode will perform the final analysis. Your initial configuration should work for this.

--
  Konstantin


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