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:
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.
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Konstantin