Hello all,

I recently discovered the tools bamqc and qualimap, which seem to be extremely useful. However, I have been trying to do the following call

qualimap multi-bamqc -d bam-files-list.txt -outfile ../bam/reports/report.pdf -outformat PDF -r

Notice that my intention is to have bamqc run before producing a multi-samples comparison (flag -r). I have tried with two different kinds of input for it, following the instructions in the manual (note that I did not manage to write it in table format here, thus the spaces between lines):

../relative/path/to/samples  sample1.bam

../relative/path/to/samples  sample2.bam

../relative/path/to/samples  sample3.bam

or

sample1.bam  ../relative/path/to/samples  

sample2.bam  ../relative/path/to/samples  

sample3.bam  ../relative/path/to/samples  

Also, note that the lists are tabulated files (\t separation).

I get this error in return:

Failed to run multi-bamqc
net.sf.samtools.util.RuntimeIOException: java.io.FileNotFoundException: null/sample1.bam (No such file or directory)

I have also got other errors, all of them indicating the file not to exist. I am running the program from the location of the list (bam-files-list.txt) and in the manual it says that it can contain relative paths to this location. I am not understanding the error, nor why it is creating a directory called "null" where I have the list. Is someone familiar with qualimap and/or this error?

Thank you,