I am trying to run qualimap on multiple bam file via command.

    qualimap multi-bamqc -d bam_file.txt -gff target.interval_list

But it gives an error as follows:

    qualimap multi-bamqc -d bam_file.txt -gff target.interval_list 
    Java memory size is set to 120000M
    Launching application...
    
    OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0
    QualiMap v.2.2.1
    Built on 2016-10-03 18:14
    
    Selected tool: multi-bamqc
    Running multi-sample BAM QC
    
    Checking input paths
    Failed to run multi-bamqc
    java.lang.RuntimeException: The raw data doesn't exist for sample: 001X1.sorted.deduped.bqsr.bam
    Folder path:/media/molmed/Data/PJRCT1/bam
    Please check raw data directory is present.

bam_file.txt conatins

`head bam_file.txt`

    001X1.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam
    001X2.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam
    001M1.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam
    001M2.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam
    003X3.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam
    003M1.sorted.deduped.bqsr.bam	/media/molmed/Data/PJRCT1/bam

I also tried by giving the complete path to the file as `/media/molmed/Data/PJRCT1/bam/001X1.sorted.deduped.bqsr.bam`

and also by adding `/` to the folder ends as `/media/molmed/Data/PJRCT1/bam/`. But all gives the same error
Summary:

To run `multi-bamqc` in `qualimap`, you should have a `bed` file containg six columns: You can see the comments [here][1]

    cat bed3.bed | perl -lane 'print "$F[0]\t$F[1]\t$F[2]\t.\t0\t."' > target.bed #this will contain 6 columns

The file containing name of the sample and paths should be as:

    sample_1    /media/User/Data//bam/sample_1.bam #file name with extension `.bam`
and run the following command

    qualimap multi-bamqc -r -d bam_file.txt -gff target.bed


  [1]: https://www.biostars.org/p/14889/