Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff <

[FarmOmics]

Rscript /home/dguan/bin/FunctionalAnnotation/Scripts/run_spp.R -c=Temp/CTCF_Follicle_F05.tagAlign.gz -rf -out=Metrics/CTCF_Follicle_F05.spp_stats.txt -p=24 -s=0:2:400 -savp=Metrics/CTCF_Follicle_F05_Cross_Correlation.pdf -tmpdir=Temp Activating conda environment: /group/zhougrp3/dguan/BovineFAANG/RunApril21/.snakemake/conda/f4792041 ################ ChIP data: Temp/CTCF_Follicle_F05.tagAlign.gz Control data: NA strandshift(min): 0 strandshift(step): 2 strandshift(max) 400 user-defined peak shift NA exclusion(min): 10 exclusion(max): NaN num parallel nodes: 24 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: Temp narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: NA plot pdf filename: Metrics/CTCF_Follicle_F05_Cross_Correlation.pdf result filename: Metrics/CTCF_Follicle_F05.spp_stats.txt Overwrite files?: TRUE

Decompressing ChIP file Loading required package: Rcpp Reading ChIP tagAlign/BAM file Temp/CTCF_Follicle_F05.tagAlign.gz opened Temp/CTCF_Follicle_F05.tagAlignaf3a5b0e3d32 done. read 80521935 fragments ChIP data read length 105 [1] TRUE Calculating peak characteristics Minimum cross-correlation value 0.04338113 Minimum cross-correlation shift 400 Top 3 cross-correlation values NA Top 3 estimates for fragment length NA Window half size NA Phantom peak location 102 Phantom peak Correlation 0.06972427 Normalized Strand cross-correlation coefficient (NSC) NA Relative Strand cross-correlation Coefficient (RSC) NA Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < : missing value where TRUE/FALSE needed Execution halted

[Nitin123-4]

Same error I am also facing.

[Nitin123-4]

I am getting the below error:

Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < : missing value where TRUE/FALSE needed

Command I ran:

Rscript -e "library(caTools); source("run_spp.R")" -c=S4T1NC2.sorted.rmD.bam -savp=S4T1NC2.spp.pdf -savd=S4T1NC2.spp.Rdata -out=S4T1NC2.spp.out -p=10

Output:

ChIP data: S4T1NC2.sorted.rmD.bam Control data: NA strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift NA exclusion(min): 10 exclusion(max): NaN num parallel nodes: 10 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: . narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: S4T1NC2.spp.Rdata plot pdf filename: S4T1NC2.spp.pdf result filename: S4T1NC2.spp.out Overwrite files?: FALSE

Reading ChIP tagAlign/BAM file S4T1NC2.sorted.rmD.bam opened /tmp/RtmpsQAYaB/S4T1NC2.sorted.rmD.tagAlign6dda181a32aa done. read 44795285 fragments ChIP data read length 100 Calculating peak characteristics Minimum cross-correlation value 0.2325768 Minimum cross-correlation shift 1500 Top 3 cross-correlation values NA Top 3 estimates for fragment length NA Window half size NA Phantom peak location 100 Phantom peak Correlation 0.56152 Normalized Strand cross-correlation coefficient (NSC) NA Relative Strand cross-correlation Coefficient (RSC) NA

Command error: Loading required package: Rcpp Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < : missing value where TRUE/FALSE needed Calls: source -> withVisible -> eval -> eval Execution halted

I tried it with run_spp_nodups.R also, I am getting the same issue.

Please help with this. Read length here for the fastq file was 100 BP paired end.

Thanks