run.log

 ================ Parsing input configuration file =================
Content of ValidPairs is /media/hd2/hichip/results/hic_results/data/FT282-A_S3_001.allValidPairs
Content of Interval is /media/hd2/hichip/results/hic_results/matrix/raw/FT282-A_S3_001_5000_abs.bed
Content of Matrix is /media/hd2/hichip/results/hic_results/matrix/raw/FT282-A_S3_001_5000.matrix
Content of PeakFile is /media/hd2/hichip/FT282-rep1-rep2.overlap.narrowPeak.gz
Content of OutDir is FT282-A_S3
Content of ChrSizeFile is /media/hd2/hichip/data_aux/chrom.size
Content of RefFasta is /media/hd2/hichip/data_aux/genome.fa
Content of REFragFile is /media/hd2/hichip/data_aux/restriction_fragments.bed
Content of LowDistThr is 5000
Content of UppDistThr is 3000000
Content of PREFIX is FitHiChIP
Content of DrawFig is 1
Content of TimeProf is 1
Content of OverWrite is 1

 ================ Verifying input configuration parameters =================
***** Specified output directory : FT282-A_S3
HiC-pro is installed in the system
Installed HiC-pro version: 2.11.1
*** Valid python version is detected - installed version: 2.7.16
*** Python library gzip is installed
*** Python module OptionParser (from the package optparse) is installed
*** Python package networkx is installed
*** Found MACS2 package (for peak calling) installed in the system -  2.1.2
*** Valid R version is detected - installed R version: 3.6.1
*** Valid samtools version is detected - installed version: 1.9
*** bgzip utility is installed in the system
*** tabix utility is installed in the system
*** Valid bedtools version is detected - installed version: 2.28.0

 ================ Changing relative pathnames of the input files to their absolute path names =================
Absolute converted path: OutDir: /media/hd2/hichip/FitHiChIP/FT282-A_S3
/
Executable of python (2): /root/miniconda2/bin//python
Executable of R : /usr/bin/Rscript

 ================ Processing HiC-pro contact matrices =================

 ================ Creating input interactions =================
Number of locus pairs with nonzero contact count (without any distance thresholding): 3121029

 ================ Limiting input interactions to the specified distance ranges 5000 to 3000000 =================
Number of locus pairs with nonzero contact count (after distance thresholding): 1783673

 ================ Generating coverage statistics for individual bins =================
======== Computed initial coverage information for individual genomic bins

 ================ Merging coverage with bias statistics =================
======== Appended coverage bias information for individual genomic bins

 ================ Merging coverage + bias with mappability, GC content, and number of cut sites - creating all feature file =================

 ================ Generating interactions + features =================
Input interaction file: /media/hd2/hichip/FitHiChIP/FT282-A_S3/HiCPro_Matrix_BinSize5000/L_5000_U3000000/FitHiChIP.cis.interactions.DistThr.bed 
Output file: /media/hd2/hichip/FitHiChIP/FT282-A_S3/FitHiChIP_ALL2ALL_b5000_L5000_U3000000/Coverage_Bias/Interactions.bed 
File storing the normalization features for individual genomic intervals: /media/hd2/hichip/FitHiChIP/FT282-A_S3/NormFeatures/Coverage_Bias/FitHiChIP.AllBin_CompleteFeat.bed 

 Output directory: /media/hd2/hichip/FitHiChIP/FT282-A_S3/FitHiChIP_ALL2ALL_b5000_L5000_U3000000/Coverage_Bias 
Contact count col: 7
Total number of columns for the complete feature interactions: 19
Specified IntType: 3
Derived IntLow: 3
Derived IntHigh: 3


 **** Start of while Loop ----- current interaction type: 3  ****** 



 ============ Calling significant interactions =============== 

Created sorted genomic distance based interaction file
============== ************* Current directory for FitHiChIP significant interaction calling: /media/hd2/hichip/FitHiChIP/FT282-A_S3/FitHiChIP_Peak2ALL_b5000_L5000_U3000000/P2PBckgr_1/Coverage_Bias/FitHiC_BiasCorr

 Peak to peak background usage for spline fit: 1 
 Number of cores in the system: 12 
 Total Number of interactions: 0 
 No of interactions : 0 - exit !!!******** FINISHED calling significant interactions
ERROR !!!!!!!! FitHiChIP could not compute the statistical significance of input interactions
Check the input parameters, or check if the number of input nonzero contact locus pairs are too few !!!
If you are using peak to peak background only (UseP2PBackgrnd=1 or stringent background), check the number of nonzero peak-to-peak locus pairs (peak-to-peak) !!! In such a case, you should go for loose background (UseP2PBackgrnd=0) for modeling interaction significance!!! Specially, if the sequencing depth of your data is very low....
----- Extracted significant interactions ---- FDR threshold lower than: 0.01
SORRY !!!!!!!! FitHiChIP could not find any statistically significant interactions
Check the input parameters, or check if the number of input nonzero contact locus pairs are too few !!!
If you are using peak to peak background only (UseP2PBackgrnd=1 or stringent background), check the number of nonzero peak-to-peak locus pairs (peak-to-peak) !!! In such a case, you should go for loose background (UseP2PBackgrnd=0) for modeling interaction significance!!! Specially, if the sequencing depth of your data is very low....
There is no significant interaction - so no WashU specific session file is created !!
Updated CurrIntType: 4

 **** Now summarizing FitHiChIP results in the HTML file *** 

***** There are one or more errors / notifications (such as zero interaction count) associated with this execution !!!
***** Please check the console to know about them !!