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
Not sure if it is related with copy/paste, but the file `target.interval_list` does not have any file extension. 

Is this file a GFF/GTF or BED file?

Regarding the file `bam_file.txt`, the first column, I think it is the sample name that you want to give, not necessarily the same as the file name. In the second column you need to specify the bam file (this is my understanding from reading the docs - I never run this specific command), something like this: 

    sample_1   /media/molmed/Data/PJRCT1/bam/001X1.sorted.deduped.bqsr.bam 

If you do not have `BAM QC result` you might need to specify the `-r` option: 

> Raw BAM files are provided as input. If this option is activated BAM QC process first will be run for each sample, then multi-sample analysis will be performed.

[Source](http://qualimap.conesalab.org/doc_html/command_line.html#multi-sample-bam-qc) of this information. 
 
I hope this helps, 

António