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DivyaratanPopli / Kinship_Inference

This is a tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias.
GNU General Public License v3.0
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problems about KINgaroo installation #2

Closed zhangjsyeah closed 1 year ago

zhangjsyeah commented 1 year ago

Dear professor： The KINgaroo was installed successfully, but When I run the "KINgaroo -bam /trimBam -bed /bed -T /Bam_list.txt -cnt 0" command it gives the following error : what should i do with it？Thank you very much ` File "/.conda/envs/aDNA/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/.conda/envs/aDNA/bin/KINgaroo", line 8, in sys.exit(main.main()) File "/.conda/envs/aDNA/lib/python3.10/site-packages/KINgaroo/main.py", line 91, in main libraries, listf, dwins, twins, id_dwins, id_twins, chrmlist = hel.pipeline1(targetsfile = args.target_location, File "/.conda/envs/aDNA/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 315, in pipeline1 dwins,twins,id_dwins,id_twins, chrmlist = parallel_mergedchrm(libraries=libraries, totalch=chrmf, interval=interval, cores=cores) File "/.conda/envs/aDNA/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 139, in parallel_mergedchrm allf = [p.get() for p in res] File "/.conda/envs/aDNA/lib/python3.10/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 139, in allf = [p.get() for p in res] File "/.conda/envs/aDNA/lib/python3.10/multiprocessing/pool.py", line 771, in get raise self._value FileNotFoundError: [Errno 2] No such file or directory: 'hapProbs/hapProbs_chrm1_probs.csv'`

DivyaratanPopli commented 1 year ago

Hi, it looks like the input files may not be in the right format. You can check this in the README.md (https://github.com/DivyaratanPopli/Kinship_Inference/blob/main/README.md), and compare to the example files.