Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Hi,
I am trying to run fithic downstream of HiC-pro.
I managed to convert the Hicpro output and the iced base using the HiCPro2FitHiC utility function.
Nevertheless when running FitHiC with the produced files I get the following error which is hard for me to grasp.
Any insight is appreciated
Thanks
Francesco
Reading the contact counts file to generate bins...
Interactions file read. Time took 535.2248961925507
Traceback (most recent call last):
File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/bin/fithic", line 10, in
sys.exit(main())
File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/lib/python3.6/site-packages/fithic/fithic.py", line 310, in main
(binStats,noOfFrags, maxPossibleGenomicDist, possibleIntraInRangeCount, possibleInterAllCount, interChrProb, baselineIntraChrProb)= generate_FragPairs(binStats, fragsFile, resolution)
File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/lib/python3.6/site-packages/fithic/fithic.py", line 542, in generate_FragPairs
maxFrags[ch]=max([int(i)-resolution/2 for i in allFragsDic[ch]])
ValueError: max() arg is an empty sequence
ay-lab
commented
3 years ago
Hi, I am trying to run fithic downstream of HiC-pro. I managed to convert the Hicpro output and the iced base using the HiCPro2FitHiC utility function. Nevertheless when running FitHiC with the produced files I get the following error which is hard for me to grasp. Any insight is appreciated Thanks Francesco
Reading the contact counts file to generate bins... Interactions file read. Time took 535.2248961925507 Traceback (most recent call last): File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/bin/fithic", line 10, in
sys.exit(main())
File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/lib/python3.6/site-packages/fithic/fithic.py", line 310, in main
(binStats,noOfFrags, maxPossibleGenomicDist, possibleIntraInRangeCount, possibleInterAllCount, interChrProb, baselineIntraChrProb)= generate_FragPairs(binStats, fragsFile, resolution)
File "/hpcnfs/data/GN2/fgualdrini/tools/anaconda3/envs/EnvFITHIC2/lib/python3.6/site-packages/fithic/fithic.py", line 542, in generate_FragPairs
maxFrags[ch]=max([int(i)-resolution/2 for i in allFragsDic[ch]])
ValueError: max() arg is an empty sequence