invalid contig error when running clipper on dm3

[Kasun Buddika]

Hello,

I am trying to use clipper to identify peaks on eCLIP data generated from Dorosophila 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 `chrX`". 

Command: 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.

Can please someone give me any advice how to fix this issue? I had been struggling on this for two days now.

Thanks,

Kasun