error about KINgaroo

[triangbyam]

Hi! I have tried to use the software KIN to estimate the relationship of ancient individual, and prepared the bedfile and bamfiles as require, but I have met some troubles in running KINgaroo, the reported error as follow:

Finished indexing, sorting and splitting bamfiles... Merging all chromosomes.. Creating input files from chromosome 1... Creating input files from chromosome 2... Creating input files from chromosome 3... Creating input files from chromosome 4... Creating input files from chromosome 5... Creating input files from chromosome 6... Creating input files from chromosome 7... Creating input files from chromosome 8... Creating input files from chromosome 9... Creating input files from chromosome 10... Creating input files from chromosome 11... Creating input files from chromosome 12... Creating input files from chromosome 13... Creating input files from chromosome 14... Creating input files from chromosome 15... Creating input files from chromosome 16... Creating input files from chromosome 17... Creating input files from chromosome 18... Creating input files from chromosome 19... Creating input files from chromosome 20... Creating input files from chromosome 21... Creating input files from chromosome 22... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/Users/fanzhang/anaconda3/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 139, in get_merged_chrm diffs_list = findDiff(inds=probs_list, posall=pos_list) File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/input_preparation_functions.py", line 121, in findDiff inds[inds==-9]=np.nan ValueError: cannot convert float NaN to integer """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/Users/fanzhang/anaconda3/bin/KINgaroo", line 8, in sys.exit(main.main()) File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/main.py", line 104, in main libraries, listf, dwins, twins, id_dwins, id_twins, chrmlist = hel.pipeline1(targetsfile = args.target_location, File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 330, in pipeline1 dwins,twins,id_dwins,id_twins, chrmlist = parallel_mergedchrm(libraries=libraries, totalch=chrmf, interval=interval, cores=cores) File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 154, in parallel_mergedchrm allf = [p.get() for p in res] File "/Users/fanzhang/anaconda3/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 154, in allf = [p.get() for p in res] File "/Users/fanzhang/anaconda3/lib/python3.10/multiprocessing/pool.py", line 774, in get raise self._value ValueError: cannot convert float NaN to integer

Is there any way to address this issue? Thanks!

[DivyaratanPopli]

Hi, I think you are using an old version. Also, you can use the test function to see if there is an issue with the format of input files.