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YeoLab / clipper

A tool to identify CLIP-seq peaks
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Clipper does not output anything #117

Open ramirobarrantes opened 3 months ago

ramirobarrantes commented 3 months ago

I am trying to run Clipper, I am just using a small test bam (attached: test.zip ) but when I run it clipper just ends with no bed file as output. Do you understand why that could be? I just do: 

(env_nf) bash-4.2$ singularity exec docker://brianyee/clipper:5d865bb  clipper --species=hg19 --bam=test1_signal.bam --outfile=test1_signal.clip.peakClusters.bed -v
singularity exec docker://brianyee/clipper:5d865bb  clipper --species=hg19 --bam=test1_signal.bam --outfile=test1_signal.clip.peakClusters.bed -v
INFO:    Using cached SIF image
{'bam': 'test1_signal.bam', 'species': 'hg19', 'outfileF': 'test1_signal.clip.peakClusters.bed', 'gene': None, 'minreads': 3, 'poisson_cutoff': 0.05, 'use_global_cutoff': True, 'FDR_alpha': 0.05, 'binom': 0.05, 'threshold': None, 'maxgenes': None, 'np': 'autodetect', 'plotit': False, 'verbose': True, 'quiet': False, 'save_pickle': False, 'debug': False, 'max_gap': 15, 'timeout': None, 'premRNA': True, 'gtfFile': None, 'method': 'binomial', 'SloP': True, 'bonferroni_correct': True, 'algorithm': 'spline', 'reverse_strand': False, 'max_width': 75, 'min_width': 50}
(env_nf) bash-4.2$

It just runs for more than 2hours and then stops. I have run it successfully in the past, not sure if this dataset is too small? How can I figure out the problem?