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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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NO error with NO results #96

Open ELMMA-FUNNY opened 2 years ago

ELMMA-FUNNY commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

ELMMA-FUNNY commented 2 years ago

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