Question: Invalid contig error when running CLIPper with dm3
gravatar for jkkbuddika
8 weeks ago by
Bloomington, USA
jkkbuddika150 wrote:


I am trying to use 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 chrX".


python -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

enter image description here

Based on the instructions given in here:, 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).

enter image description here

Format of the dm3.AS.STRUCTURE.COMPILED.gff file:

Format of the dm3_exons.bed file:

enter image description here

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.

Thank you,


software error • 158 views
ADD COMMENTlink modified 3 days ago by Biostar ♦♦ 20 • written 8 weeks ago by jkkbuddika150
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