I am trying to use CLIPper (https://github.com/YeoLab/clipper) to identify peaks on eCLIP data generated from Drosophila tissues. When I am running the program using following command it gives me the error that is shown in the attached image saying "ValueError: invalid contig
python peakfinder.py -b /N/dc2/scratch/jbuddika/ikckt_eclip/umi_dedup/FMR1_UV1_X1A_alignedsorted_dupRm.bam -s dm3 --processors=1 --FDR=0.05 -v -o /N/dc2/scratch/jbuddika/ikckt_eclip/umi_dedup/FMR1_UV1_X1A_alignedsorted.bed
Based on the instructions given in here: https://github.com/YeoLab/clipper/issues/74, I have uploaded required dm3.AS.STRUCTURE.COMPILED.gff and dm3_exons.bed in the data/ and data/regions/ directories as shown in the image. So I think all the files must be in place properly and in correct organization (see attached images).
Format of the dm3.AS.STRUCTURE.COMPILED.gff file:
Format of the dm3_exons.bed file:
Has anyone used CLIPper peak calling tool on Drosophila datasets? If so can someone please give me some instructions on how to fix this issue? I had been struggling on this for days now.