error occur in KINgaroo

[xiaomiyang36]

Hi ! I have tried to use the software KIN to estimate the kinship cofficient 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:

multiprocessing.pool.RemoteTraceback:

""" `Traceback (most recent call last): File "/home/administrator/miniconda3/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 154, in get_merged_chrm diffs_list = findDiff(inds=probs_list, posall=pos_list) File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/KINgaroo_scripts/input_preparation_functions.py", line 124, in findDiff diff0=(np.vstack(inds[:,0]) (1-inds)) + ((1-np.vstack(inds[:,0])) * inds) File "<__array_function__ internals>", line 180, in vstack File "/home/administrator/miniconda3/lib/python3.9/site-packages/numpy/core/shape_base.py", line 282, in vstack return _nx.concatenate(arrs, 0) File "<__array_function__ internals>", line 180, in concatenate ValueError: need at least one array to concatenate """

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

Traceback (most recent call last): File "/home/administrator/miniconda3/bin/KINgaroo", line 8, in sys.exit(main.main()) File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/main.py", line 120, in main libraries, listf, dwins, twins, id_dwins, id_twins, chrmlist = hel.pipeline1(targetsfile = args.target_location, File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 354, in pipeline1 dwins,twins,id_dwins,id_twins, chrmlist = parallel_mergedchrm(libraries=libraries, totalch=chrmf, interval=interval, cores=cores) File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 174, in parallel_mergedchrm allf = [p.get() for p in res] File "/home/administrator/miniconda3/lib/python3.9/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 174, in allf = [p.get() for p in res] File "/home/administrator/miniconda3/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value ValueError: Can not process input data. Please check all input files. In particular, bedfile and bamfiles should have chromosomes listed as 1,2,... and the bedfile should be tab-separated. Please check the README.md for example input files`

Is there any way to address this issue? Thanks! Yang

[DivyaratanPopli]

Hi, the error suggests there is some issue with the input files: "Can not process input data. Please check all input files. In particular, bedfile and bamfiles should have chromosomes listed as 1,2,... and the bedfile should be tab-separated. Please check the README.md for example input files"

[xiaomiyang36]

We mapped the rawdata-fastaq to hs37d5 and generated bamfiles with chromosomes listed as 1,2,3,....，and the bedfile we used as follows:

The same error still reports~

[DivyaratanPopli]

Can you check if the bedfile is tab-separated?

[xiaomiyang36]

Thanks! This problem has been sovled already.