cat: /volumes/easystore/HiChIP_CTCF/Matrix_BinSize5000/sample.interactions.initial.bed: No such file or directory - FitHiChIP is quiting #107
Description
Hi Here,
I was trying to do use FitHiChIP to analyze both the text data or the public available data from (https://hichip.readthedocs.io/en/latest/loops.html). I am using macOS with ARM64 chip. But I got the same errors as following:
Installed python version: 3.9.19
*** 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 - line
Installed R version: 4.1.0
Installed samtools version: 1.20
*** bgzip utility is installed in the system
*** tabix utility is installed in the system
Installed bedtools version: 2.31.1
Warning message:
package ‘data.table’ was built under R version 4.1.2
Warning message:
In data.table::fread(MatrixFile, header = F, sep = "\t", stringsAsFactors = F) :
File '/volumes/easystore/HiChIP_CTCF/Matrix_BinSize5000/Matrix.matrix' has size 0. Returning a NULL data.frame.
Error in names(x) <- value :
'names' attribute [3] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
======= Generated interaction file : /volumes/easystore/HiChIP_CTCF/Matrix_BinSize5000/sample.interactions.initial.bed
cat: /volumes/easystore/HiChIP_CTCF/Matrix_BinSize5000/sample.interactions.initial.bed: No such file or directory
==>>> Number of locus pairs with nonzero contact count (without any distance thresholding): 0
********** Number of locus pairs with nonzero contact count is zero - FitHiChIP is quiting !!!
It seems that the program can't produce the matrix.matrix file nor the initial.bed file. I changed the bin size but I got the same error. The absolute paths of these files were used. My config is:
ValidPairs=/volumes/easystore/Sample_ValidPairs.gz
ChrSizeFile=/volumes/easystore/chrom_hg19.sizes
PeakFile=/volumes/easystore/Sample.Peaks.gz
CircularGenome=0
BINSIZE=5000
LowDistThr=20000
UppDistThr=2000000
UseP2PBackgrnd=0
BiasType=2
MergeInt=1
QVALUE=0.01
Thanks very much for any suggestions or advices!!!