MACS2 Set pValue to -1 and terrifies IDR

[amirshams84]

Hi It seems MACS2 Set pValue for some peaks to -1 and IDR cannot accept that and crashed have to convert all -1 to 0 and it worked

[amirshams84]

AB2955-L1_R1.trim.PE2SE.nodup.pr1.tn5.pf.500K.pval0.01.narrowPeak.gz chr16 67192014 67192579 Peak_102120 34 . 3.17360 3.48800 1.21916 319 chr16 89923548 89923621 Peak_102121 34 . 3.17360 3.48800 1.21916 -1 chr16 2223989 2224074 Peak_102119 34 . 3.17360 3.48800 1.21916 8 chr14 102140051 102140159 Peak_102118 34 . 3.17360 3.48800 1.21916 66 chr14 100110943 100111138 Peak_102117 34 . 3.17360 3.48800 1.21916 17 chr13 82549279 82549524 Peak_102116 34 . 3.17360 3.48800 1.21916 101

[amirshams84]

usr/local/envs/bds_atac_py3/bin/idr --samples /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/pseudo_reps/rep1/pr1/AB2955-L1_R1.trim.PE2SE.nodup.pr1.tn5.pf.500K.pval0.01.narrowPeak.gz /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/pseudo_reps/rep1/pr2/AB2955-L1_R1.trim.PE2SE.nodup.pr2.tn5.pf.500K.pval0.01.narrowPeak.gz --peak-list /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/rep1/AB2955-L1_R1.trim.PE2SE.nodup.tn5.pf.500K.pval0.01.narrowPeak.gz --input-file-type narrowPeak --output-file /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/idr/pseudo_reps/rep1/VA2.7+CCR6+CCR2+_rep1-pr.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --log-output-file /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/idr/pseudo_reps/rep1/VA2.7+CCR6+CCR2+_rep1-pr.IDR0.05.log.txt

Traceback (most recent call last): File "/usr/local/envs/bds_atac_py3/bin/idr", line 4, in import('pkg_resources').run_script('idr==2.0.3', 'idr') File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/pkg_resources/init.py", line 748, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/pkg_resources/init.py", line 1517, in run_script exec(code, namespace, namespace) File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in idr.idr.main() File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 840, in main merged_peaks, signal_type = load_samples(args) File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 760, in load_samples oracle_pks, args.use_nonoverlapping_peaks) File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 281, in merge_peaks use_nonoverlapping_peaks=use_nonoverlapping_peaks) File "/usr/local/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 223, in merge_peaks_in_contig all_intervals.sort() TypeError: unorderable types: NoneType() < int()

[amirshams84]

ARGUMENTS LIST: name = /gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/peak/macs2/pooled_pseudo_reps/ppr2/AB2955-L1_R1.trim.PE2SE.nodup.pr2.tn5_AB2959-L1_R1.trim.PE2SE.nodup.pr2.tn5.pf format = BED ChIP-seq file = ['/gs6/users/shamsaddinisha/jfarber-20160119-E1/VA2.7+CCR6+CCR2+/hg38/align/pooled_pseudo_reps/ppr2/AB2955-L1_R1.trim.PE2SE.nodup.pr2.tn5_AB2959-L1_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz'] control file = None effective genome size = 2.70e+09 band width = 300 model fold = [5, 50] pvalue cutoff = 1.00e-02

qvalue will not be calculated and reported as -1 in the final output.

Larger dataset will be scaled towards smaller dataset. Range for calculating regional lambda is: 10000 bps Broad region calling is off Searching for subpeak summits is on MACS will save fragment pileup signal per million reads