bamqc not generating raw_data_qualimapReport subfolder

[seth musker]

Hi, I'm using qualimap v2.2.1 on several samples. I've run bamqc on each of them and specified an output directory for each, but inside each directory I only have the pdf report and the 'genome_results.txt' file, no  raw_data_qualimapReport. This means I can't run multi-bamqc (I get the error message: "java.lang.RuntimeException: The raw data doesn't exist for sample"). 

My commands:

mkdir -p qualimap

cd qualimap

while read i;do

~/qualimap_v2.2.1/qualimap bamqc \

    -bam ../bams/${i}_to_RR_spades_k24.bam \

    -outdir qualimap_${i}_to_RR_spades_k24 \

    -outfile qualimap_${i}_to_RR_spades_k24.pdf  \

    --java-mem-size=8G \

    -nt ${SLURM_CPUS_PER_TASK} --collect-overlap-pairs

done < samplenames

(above is repeated for different k values, which I use as the group below)

ls -d qualimap_*_RR_spades* | awk -F'_' '{print $2"_"$3,$0,$7}' \

OFS='\t' > ../qualimap_multi_bamqc_input.txt

~/qualimap_v2.2.1/qualimap multi-bamqc \

    -d ../qualimap_multi_bamqc_input.txt \

    -outdir ../qualimap_multi_bamqc_bwa \

    -outfile qualimap_multi_bamqc_bwa.pdf