Qualimap multi-bamqc input file

Question

[DanielEB_fisk]

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,

[DBScan]

I remember I also had this error once with relative paths, with absolute paths the error disappeared.

[DanielEB_fisk]

Worth a try, thank you.

Ok, it did not work. It is an error no matter what. If the first column is the samples and the second is the directory, the error is actually that the directory is a directory. If I do the reverse, then is the same error that I indicated before. This is odd.

Answer 1

[DanielEB_fisk]

I found out what was wrong:

In the examples above, in the input file, the path did not include the sample name at the end:

sample1.bam ../path/to/sample

So one line in the input must be:

sample1.bam ../path/to/sample/sample1.bam

This is, the sample name and the path (relative or absolute) including the sample, separated by tabulation.

[DBScan]

Indeed, you also don't need the .bam extension for your sample name.