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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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KINgaroo input #15

Closed h-pawar closed 1 year ago

h-pawar commented 1 year ago

Hello, I am experiencing issues running KINgaroo.

From running KINgaroo -bam /scratch/devel/hpawar/exome_gor/kin/test.in/ \ -bed /scratch/devel/hpawar/exome_gor/kin/varpos.bed \ -T /scratch/devel/hpawar/exome_gor/kin/test.in/test_crg_mbe.txt -cnt 0 -test 1 I establish that the installation worked fine.

The problem arises from incompatibility of 'chr1' vs '1' in the input files. I tried to amend this as suggested by converting ‘chr’ to numeric entries in the bed file and bams, but am still getting the same error message.

Would it be possible to add a line of code permitting bam files with ‘chr’ to be read in and then convert this column to integers if the rest of the code requires integer format?

Many thanks,

tail /scratch/devel/hpawar/exome_gor/log/kingatest_10459998_1.err libraries, listf, dwins, twins, id_dwins, id_twins, chrmlist = hel.pipeline1(targetsfile = args.target_location, File "/home/groups/compgen/hpawar/.conda/envs/kin-3.1.3/lib/python3.8/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 362, in pipeline1 dwins,twins,id_dwins,id_twins, chrmlist = parallel_mergedchrm(libraries=libraries, totalch=chrmf, interval=interval, cores=cores) File "/home/groups/compgen/hpawar/.conda/envs/kin-3.1.3/lib/python3.8/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 174, in parallel_mergedchrm allf = [p.get() for p in res] File "/home/groups/compgen/hpawar/.conda/envs/kin-3.1.3/lib/python3.8/site-packages/KINgaroo/KINgaroo_scripts/helpers.py", line 174, in allf = [p.get() for p in res] File "/home/groups/compgen/hpawar/.conda/envs/kin-3.1.3/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value IndexError: 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.

DivyaratanPopli commented 1 year ago

Hi, have you changed the format from 'chr1' to'1' in all bamfiles and the bed file? It should solve your problem.