Issue with bam2chicago.sh

[Shashank Tiwari]

On running bam2chicago.sh as suggested in the readme files, the .chinput file generated is empty for some reason, even after providing all the required inputs.
The error is possibly in the step
bedtools pairtobed -abam $bam -bedpe -b $baitfendsid -f 0.6 > ${samplename}/${bamname}_mappedToBaits.bedpe
When I tried to run this command in terminal separatley the out

I get the following output:
Checking rmap and baitmap files...
Rmap and baitmap files checked successfully
Processing sample final...
Using bam file /home/shashank/Project/Data/NiGa/13.bam
Using baitmap file /home/shashank/Project/Data/Des/D13.baitmap
Using digest map (rmap) file /home/shashank/Project/Data/Des/D13.rmap
Baitmap file contains >4 columns. Checking if /home/shashank/Project/Data/Des/D13.baitmap_4col.txt exists...
It doesn't. So trimming the extra columns and saving the result in /home/shashank/Project/Data/Des/D13.baitmap_4col.txt...
Intersecting with bait fragments (using min overhang of 0.6)...
Flipping all reads that overlap with the bait on to the right-hand side...
Intersecting with bait fragments again to produce a list of bait-to-bait interactions that can be used separately; note they will also be retained in the main output...
Intersecting with restriction fragments (using min overhang of 0.6)...
Removing reads that failed the min overhang filter...
Adding frag length and signed distance from bait; removing self-ligation fragments (if any; not expected with HiCUP input)...
Pooling read pairs...
Done! The file to be used for Chicago R package input is final/final.chinput