Running error

[JhinAir]

Hi, I got a such error when running fithic with command: python /home/user/liu/Software/fithic/fithic/fithic.py -f fithic.fragmentMappability.gz -i fithic.interactionCounts.gz -o ./Inter -r 40000 -t fithic.biases.gz -x interOnly Btw, the test running is working successfully.

####################################################### Reading fragments file from: fithic.fragmentMappability.gz Reading interactions file from: fithic.interactionCounts.gz Output path created ./Inter Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: fithic.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be Emu Upper Distance threshold is inf Lower Distance threshold is 0 Only inter-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now...

Reading the contact counts file to generate bins... Interactions file read. Time took 154.33874917030334 Traceback (most recent call last): File "/home/user/liu/Software/fithic/fithic/fithic.py", line 1317, in main() File "/home/user/liu/Software/fithic/fithic/fithic.py", line 323, in main (binStats,noOfFrags, maxPossibleGenomicDist, possibleIntraInRangeCount, possibleInterAllCount, interChrProb, baselineIntraChrProb) = generate_FragPairs(observedInterAllCount, observedInterAllSum, binStats, fragsFile, resolution) File "/home/user/liu/Software/fithic/fithic/fithic.py", line 597, in generate_FragPairs maxFrags[ch]=max([int(i)-resolution/2 for i in allFragsDic[ch]]) ValueError: max() arg is an empty sequence #######################################################

Could you please help with it?

Best~ Jing

[ay-lab]

Hi, seems like there may be a problem with the format of your input files. The dictionary structure supposed to have a list of fragments in it per each chromosome seems to be empty. This may be a problem with your fragment mappability file

[JhinAir]

Hi, thanks for the reply. The fragment file seems to be ok, as following: ######################## 1 0 20000 621 1 1 40000 60000 1073 1 1 80000 100000 837 1 1 120000 140000 976 1 1 160000 180000 1793 1 1 200000 220000 846 1 ######################## The inputs were produced by HiCPro2FitHiC.py.

Best, Jing

[ay-lab]

what I can guess is that you have a chromosome (maybe chr Y if human) in your input file that has no fragments above mappability threshold so hence the error. Try removing chrs that are unmappable. If it doesn't work please share your input files. thanks

[JhinAir]

Hi,

I've checked that all chromosomes have the mappability threshold. The inputs are too big (about 50Mb), so I put them on the google drive. https://drive.google.com/drive/folders/1_wm-CAsXY2oDzRGPLEuPtIIIT5UPIhqA. Please let me know if they are not available. Thanks a lot!

Jing

[ay-lab]

as I have suspected, there are scaffolds in your fragment list and bias file that do not have any valid/mappable fragment. See the examples below. if you don't remove them fithic won't work. Scaffold_274 20000 -1 Scaffold_275 20000 -1 Scaffold_275 60000 -1 Scaffold_275 100000 -1 Scaffold_275 140000 -1 Scaffold_275 180000 -1

[JhinAir]

It's working! Thanks very much! I thought fithic would deal with those -1 value. I have another question that how the ExpCC is calculated for inter-chr interaction, as I found some ExpCC values are equal to zero?

[ay-lab]

It is in the below piece of code. If bias values are outside the desired range then it gets set to zero.

        if allReg or interOnly:
            prior_p=interChrProb*(bias1*bias2)
            p_val=scsp.bdtrc(interxn.getCount()-1,observedInterAllSum,prior_p)
            interCount += 1
            # computing expected contact count
            if ((bias1 >= biasLowerBound) and (bias1 <= biasUpperBound) and (bias2 >= biasLowerBound) and (bias2 <= biasUpperBound)):
                expected_CC = (observedInterAllSum * prior_p)
            else:
                expected_CC = 0