Open aguilar-gomez opened 5 months ago
I have a lot of warnings of long ROHS, but why is this giving an error? python3.8
This is the command I am running: smc++ estimate -o KOR 1.25e-8 --cores 6 -p 0.5 KOR.*.smc.gz
1096 smcpp.analysis.base INFO theta: 0.000100 1097 smcpp.analysis.base INFO rho: 0.000100 1097 smcpp.data_filter INFO Loading data... 1691 smcpp.data_filter INFO 2.88 Gb of data 1698 smcpp.data_filter INFO 1 population 1701 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr17.smc.gz: [ 141925 212496 81384 3883555 70531 285514 361626 74390 56123 442623 697586 50913 53032] (base pairs) 1705 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr11.smc.gz: [ 192356 97412 79478 3716844 100065 68881 103867 174302] (base pairs) 1708 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr9.smc.gz: [ 57888 192180 297238 67504 235196 349697 561834 55085 58006 60110 132425 82160 54385 247643 286950 112772 17250289 966857 245950 881607 393259 296625 94958 204129 114513 348612 85647 104802 304466 1308385 99832 531422 707868 177147] (base pairs) 1711 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr10.smc.gz: [ 50943 84459 2139844 245327 68197 60557 85892 79745 76838 62619 67699 239731 120891 133143] (base pairs) 1712 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr21.smc.gz: [5066103 234296 697308 1677101 752008 158999 1078044 132225 440601 96456 2374083 214094 121521 143962 50384 195090 103745 52906] (base pairs) 1715 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr19.smc.gz: [ 246963 2822458 56274] (base pairs) 1723 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr1.smc.gz: [ 55319 541941 149480 125536 164856 74249 67301 106310 80872 156061 95297 84360 84326 76930 211613 211353 173683 101088 3193325 138891 18378680 77601 517688 58090 378103 239255 126184 313451 70821 82178 387268 281244 171388 69631 90386 66176] (base pairs) 1725 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr13.smc.gz: [16056768 2117859 101241 71516 68077 112196 50021 50665] (base pairs) 1730 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr12.smc.gz: [ 61392 114103 1478458 312027 627050] (base pairs) 1732 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr15.smc.gz: [17010073 2711216 199277 81704 227738 329527 67055 466540 687802 81922 189326 181797 56640 138742 263649 403058 129814 63811 255329 126948 53774 108644 219160 113409 60962 66055] (base p airs) 1737 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr3.smc.gz: [ 566339 2173843 75567 126017] (base pairs) 1743 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr2.smc.gz: [ 105166 64444 59368 102019 76060 51503 312830 57106 75243 1180728 77540 83900 165587 51176 54535 2087057 226735 122832 78201 51664 76240 278224 51552 329820 70327 51438 104378 104162 50093 67290] (base pairs) 1748 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr4.smc.gz: [ 68828 214248 97143 123117 183727 2308624 149480] (base pairs) 1750 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr18.smc.gz: [ 380485 4787162 168395 109420 69251 110821] (base pairs) 1751 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr22.smc.gz: [10661594 262956 249316 63303 120679 128078 156412 101716 56717 3319884 74758 241256 232363 87284 110527 773007 331707 86465] (base pairs) 1756 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr7.smc.gz: [ 125963 2794730 148828 462957 191186 61408 77551 75582 71727 65832 54501 277624 59545 81656 80793 259945 51181 57847 217237 206339 105032 173258] (base pairs) 1759 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr14.smc.gz: [16092940 2322344 61838 147894 488228 117196 115920 182134 108162 58880 160157] (base pairs) 1763 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr8.smc.gz: [ 205802 107605 96993 94036 57914 531482 283097 78525 139504 219969 1992151 183438 62692] (base pairs) 1764 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr20.smc.gz: [ 60187 65725 73586 216531 1969827 93706 77914 97996 230668 78373 163207 110517] (base pairs) 1767 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr16.smc.gz: [ 142540 155889 72252 335341 50086 101205 285553 120073 85996 106357 143844 134501 171023 119473 122159 59094 258572 125368 245410 662671 66111 60171 56701 324269 56406 112776 76667 767891 9298063 231515] (base pairs) 1772 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr5.smc.gz: [ 82199 138112 528707 3044307 82167 327068 1418989 75119 52387 93422 249590] (base pairs) 1776 smcpp.estimation_tools WARNING Long runs of homozygosity in contig KOR.KOREA1K-348.chr6.smc.gz: [ 148084 68897 72092 82609 1782765 50771 50288 194609] (base pairs) Traceback (most recent call last): File "/home/diana/anaconda3/bin/smc++", line 8, in <module> sys.exit(main()) File "/home/diana/anaconda3/lib/python3.8/site-packages/smcpp/frontend/console.py", line 28, in main cmds[args.command].main(args) File "/home/diana/anaconda3/lib/python3.8/site-packages/smcpp/commands/estimate.py", line 47, in main analysis = Analysis(args.data, args) File "/home/diana/anaconda3/lib/python3.8/site-packages/smcpp/analysis/analysis.py", line 30, in __init__ m[:] = np.log(NeN0)
I have a lot of warnings of long ROHS, but why is this giving an error? python3.8
This is the command I am running: smc++ estimate -o KOR 1.25e-8 --cores 6 -p 0.5 KOR.*.smc.gz