NO error with NO results

[ELMMA-FUNNY]

hello,when I run with overlap_peakfi_with_bam_PE.pl

perl overlap_peakfi_with_bam_PE.pl
/home/lulu/chenhui_project/eclip/changxin_lab/IP_1/collapse_samtools/EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam
/home/lulu/chenhui_project/eclip/changxin_lab/input_1/collapse_samtools/INPUT_PE.rep2_clip.NIL.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam
/home/lulu/chenhui_project/eclip/changxin_lab/IP_1/clipper/EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.bed
/home/lulu/chenhui_project/eclip/changxin_lab/IP_1/clipper/ip_mapped_readnum.txt
/home/lulu/chenhui_project/eclip/changxin_lab/input_1/clipper/input_mapped_readnum.txt
/home/lulu/chenhui_project/perl-test/EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.normed.bed

it runs without error,but also without results.
Here is my nohup.out:

reading peak file /home/lulu/chenhui_project/eclip/changxin_lab/IP_1/clipper/EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.bed
now doing expt /home/lulu/chenhui_project/eclip/changxin_lab/IP_1/collapse_samtools/EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam
now doing input /home/lulu/chenhui_project/eclip/changxin_lab/input_1/collapse_samtools/INPUT_PE.rep2_clip.NIL.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam

[byee4]

Hi,

It looks like you're trying to run the input normalization script, which now lives here:

https://github.com/YeoLab/eclip/blob/master/bin/overlap_peakfi_with_bam.pl

It also looks like the script did run, so I'd want to check how many reads and peaks are in your bam and peak files, respectively?

[ELMMA-FUNNY]

Thanks ,I solve the problem from reopened my server.
but when I run it again ,it turns out new problems.

reading peak file EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.bed
now doing expt EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam
now doing input INPUT_PE.rep2_clip.NIL.r1.fq.genome-mappedSo.rmDupSo.merged.r2.bam
Use of uninitialized value in division (/) at overlap_peakfi_with_bam_PE.pl line 67.
Illegal division by zero at overlap_peakfi_with_bam_PE.pl line 67.

How to solve it? Could you help me?

[ELMMA-FUNNY]

and here is the reads in bam files :
cat input_mapped_readnum.txt 1326495
cat ip_mapped_readnum.txt 2608493

[ELMMA-FUNNY]

Here is the peaks in peak files :
45369 EXAMPLE_PE.rep2_clip.A03.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.bed
23652 INPUT_PE.rep2_clip.NIL.r1.fq.genome-mappedSo.rmDupSo.merged.r2.peakClusters.bed