Baumwelch iteration not working

[Meer9234]

Hi my run errors at the Baumwelch iteration step. Any ideas on how to fix this? I have given the run 750GB of memory so that cannot be the issue. Is it with my input files or my p? I used whole genome data (1.3 GB) and the chromosomes are actually scaffolds. I did all the steps in the tutorial. And it does seem to read my input files normally.

I used this command:
NAMES=cat names.txt

msmc2 -t 32 -p 12+251+12+13 -i 100 -o /Msmc/OUTPUT -I 0,1 $NAMES
Thanks in advance!

read 181 SNPs from file msmc_input.IND.chromosome1.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome10.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome100.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome104.txt, using indices [[0, 1]]
read 1249 SNPs from file msmc_input.IND.chromosome105.txt, using indices [[0, 1]]
read 69 SNPs from file msmc_input.IND.chromosome106.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome107.txt, using indices [[0, 1]]
read 102 SNPs from file msmc_input.IND.chromosome108.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome109.txt, using indices [[0, 1]]
read 13 SNPs from file msmc_input.IND.chromosome11.txt, using indices [[0, 1]]
read 10791 SNPs from file msmc_input.IND.chromosome110.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome111.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome112.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome113.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome114.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome115.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome116.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome117.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome118.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome119.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome12.txt, using indices [[0, 1]]
read 41 SNPs from file msmc_input.IND.chromosome120.txt, using indices [[0, 1]]
read 3162 SNPs from file msmc_input.IND.chromosome121.txt, using indices [[0, 1]]
read 397 SNPs from file msmc_input.IND.chromosome122.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome124.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome125.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome126.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome127.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome128.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome129.txt, using indices [[0, 1]]
read 13823 SNPs from file msmc_input.IND.chromosome13.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome130.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome131.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome132.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome133.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome134.txt, using indices [[0, 1]]
read 281 SNPs from file msmc_input.IND.chromosome135.txt, using indices [[0, 1]]
read 55773 SNPs from file msmc_input.IND.chromosome136.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome137.txt, using indices [[0, 1]]
read 153 SNPs from file msmc_input.IND.chromosome138.txt, using indices [[0, 1]]
read 2145 SNPs from file msmc_input.IND.chromosome139.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome14.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome140.txt, using indices [[0, 1]]
read 1738 SNPs from file msmc_input.IND.chromosome141.txt, using indices [[0, 1]]
read 7 SNPs from file msmc_input.IND.chromosome142.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome143.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome144.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome145.txt, using indices [[0, 1]]
read 18788 SNPs from file msmc_input.IND.chromosome146.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome147.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome148.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome149.txt, using indices [[0, 1]]
read 29 SNPs from file msmc_input.IND.chromosome150.txt, using indices [[0, 1]]
read 232 SNPs from file msmc_input.IND.chromosome151.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome152.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome153.txt, using indices [[0, 1]]
read 20569 SNPs from file msmc_input.IND.chromosome154.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome155.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome156.txt, using indices [[0, 1]]
read 16 SNPs from file msmc_input.IND.chromosome157.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome158.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome159.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome16.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome160.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome161.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome162.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome163.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome164.txt, using indices [[0, 1]]
read 27198 SNPs from file msmc_input.IND.chromosome165.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome166.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome167.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome168.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome169.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome17.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome170.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome171.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome172.txt, using indices [[0, 1]]
read 990 SNPs from file msmc_input.IND.chromosome173.txt, using indices [[0, 1]]
read 32587 SNPs from file msmc_input.IND.chromosome174.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome175.txt, using indices [[0, 1]]
read 46 SNPs from file msmc_input.IND.chromosome176.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome177.txt, using indices [[0, 1]]
read 29107 SNPs from file msmc_input.IND.chromosome179.txt, using indices [[0, 1]]
read 6 SNPs from file msmc_input.IND.chromosome18.txt, using indices [[0, 1]]
read 21536 SNPs from file msmc_input.IND.chromosome180.txt, using indices [[0, 1]]
read 2822 SNPs from file msmc_input.IND.chromosome181.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome182.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome183.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome184.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome185.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome186.txt, using indices [[0, 1]]
read 60 SNPs from file msmc_input.IND.chromosome187.txt, using indices [[0, 1]]
read 1427 SNPs from file msmc_input.IND.chromosome188.txt, using indices [[0, 1]]
read 28 SNPs from file msmc_input.IND.chromosome189.txt, using indices [[0, 1]]
read 20398 SNPs from file msmc_input.IND.chromosome19.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome190.txt, using indices [[0, 1]]
read 9 SNPs from file msmc_input.IND.chromosome191.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome192.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome193.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome194.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome197.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome198.txt, using indices [[0, 1]]
read 965 SNPs from file msmc_input.IND.chromosome199.txt, using indices [[0, 1]]
read 335 SNPs from file msmc_input.IND.chromosome2.txt, using indices [[0, 1]]
read 959 SNPs from file msmc_input.IND.chromosome20.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome200.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome201.txt, using indices [[0, 1]]
read 799 SNPs from file msmc_input.IND.chromosome202.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome203.txt, using indices [[0, 1]]
read 83 SNPs from file msmc_input.IND.chromosome204.txt, using indices [[0, 1]]
read 40 SNPs from file msmc_input.IND.chromosome205.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome206.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome207.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome208.txt, using indices [[0, 1]]
read 247 SNPs from file msmc_input.IND.chromosome209.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome21.txt, using indices [[0, 1]]
read 116 SNPs from file msmc_input.IND.chromosome210.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome211.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome212.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome213.txt, using indices [[0, 1]]
read 103 SNPs from file msmc_input.IND.chromosome214.txt, using indices [[0, 1]]
read 26383 SNPs from file msmc_input.IND.chromosome215.txt, using indices [[0, 1]]
read 29190 SNPs from file msmc_input.IND.chromosome216.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome218.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome219.txt, using indices [[0, 1]]
read 93 SNPs from file msmc_input.IND.chromosome22.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome220.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome222.txt, using indices [[0, 1]]
read 17 SNPs from file msmc_input.IND.chromosome223.txt, using indices [[0, 1]]
read 2105 SNPs from file msmc_input.IND.chromosome224.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome225.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome226.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome227.txt, using indices [[0, 1]]
read 23 SNPs from file msmc_input.IND.chromosome228.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome229.txt, using indices [[0, 1]]
read 56 SNPs from file msmc_input.IND.chromosome23.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome231.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome232.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome233.txt, using indices [[0, 1]]
read 6740 SNPs from file msmc_input.IND.chromosome234.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome235.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome236.txt, using indices [[0, 1]]
read 359 SNPs from file msmc_input.IND.chromosome237.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome238.txt, using indices [[0, 1]]
read 9504 SNPs from file msmc_input.IND.chromosome239.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome24.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome240.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome241.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome242.txt, using indices [[0, 1]]
read 5690 SNPs from file msmc_input.IND.chromosome243.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome245.txt, using indices [[0, 1]]
read 22334 SNPs from file msmc_input.IND.chromosome246.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome247.txt, using indices [[0, 1]]
read 12067 SNPs from file msmc_input.IND.chromosome248.txt, using indices [[0, 1]]
read 9 SNPs from file msmc_input.IND.chromosome249.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome25.txt, using indices [[0, 1]]
read 30 SNPs from file msmc_input.IND.chromosome250.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome251.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome252.txt, using indices [[0, 1]]
read 119 SNPs from file msmc_input.IND.chromosome253.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome254.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome255.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome256.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome257.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome258.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome259.txt, using indices [[0, 1]]
read 2450 SNPs from file msmc_input.IND.chromosome26.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome260.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome261.txt, using indices [[0, 1]]
read 33660 SNPs from file msmc_input.IND.chromosome262.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome263.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome264.txt, using indices [[0, 1]]
read 99 SNPs from file msmc_input.IND.chromosome265.txt, using indices [[0, 1]]
read 298 SNPs from file msmc_input.IND.chromosome266.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome267.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome268.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome269.txt, using indices [[0, 1]]
read 12 SNPs from file msmc_input.IND.chromosome27.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome270.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome271.txt, using indices [[0, 1]]
read 78 SNPs from file msmc_input.IND.chromosome272.txt, using indices [[0, 1]]
read 18077 SNPs from file msmc_input.IND.chromosome273.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome274.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome276.txt, using indices [[0, 1]]
read 75 SNPs from file msmc_input.IND.chromosome277.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome278.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome279.txt, using indices [[0, 1]]
read 18 SNPs from file msmc_input.IND.chromosome28.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome280.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome281.txt, using indices [[0, 1]]
read 193 SNPs from file msmc_input.IND.chromosome282.txt, using indices [[0, 1]]
read 222 SNPs from file msmc_input.IND.chromosome283.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome284.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome285.txt, using indices [[0, 1]]
read 73 SNPs from file msmc_input.IND.chromosome286.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome287.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome288.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome289.txt, using indices [[0, 1]]
read 7 SNPs from file msmc_input.IND.chromosome29.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome290.txt, using indices [[0, 1]]
read 19868 SNPs from file msmc_input.IND.chromosome291.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome292.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome293.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome294.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome295.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome296.txt, using indices [[0, 1]]
read 65 SNPs from file msmc_input.IND.chromosome297.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome298.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome299.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome3.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome300.txt, using indices [[0, 1]]
read 20149 SNPs from file msmc_input.IND.chromosome301.txt, using indices [[0, 1]]
read 19 SNPs from file msmc_input.IND.chromosome302.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome303.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome304.txt, using indices [[0, 1]]
read 246 SNPs from file msmc_input.IND.chromosome305.txt, using indices [[0, 1]]
read 8 SNPs from file msmc_input.IND.chromosome306.txt, using indices [[0, 1]]
read 14 SNPs from file msmc_input.IND.chromosome307.txt, using indices [[0, 1]]
read 26217 SNPs from file msmc_input.IND.chromosome308.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome309.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome31.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome311.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome312.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome313.txt, using indices [[0, 1]]
read 2815 SNPs from file msmc_input.IND.chromosome314.txt, using indices [[0, 1]]
read 27 SNPs from file msmc_input.IND.chromosome315.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome316.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome317.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome318.txt, using indices [[0, 1]]
read 65 SNPs from file msmc_input.IND.chromosome319.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome32.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome320.txt, using indices [[0, 1]]
read 61 SNPs from file msmc_input.IND.chromosome321.txt, using indices [[0, 1]]
read 435 SNPs from file msmc_input.IND.chromosome322.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome323.txt, using indices [[0, 1]]
read 6 SNPs from file msmc_input.IND.chromosome324.txt, using indices [[0, 1]]
read 9 SNPs from file msmc_input.IND.chromosome325.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome326.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome328.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome329.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome33.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome331.txt, using indices [[0, 1]]
read 1006 SNPs from file msmc_input.IND.chromosome332.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome333.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome334.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome335.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome336.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome337.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome339.txt, using indices [[0, 1]]
read 46426 SNPs from file msmc_input.IND.chromosome34.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome340.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome341.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome342.txt, using indices [[0, 1]]
read 30 SNPs from file msmc_input.IND.chromosome343.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome344.txt, using indices [[0, 1]]
read 27 SNPs from file msmc_input.IND.chromosome345.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome346.txt, using indices [[0, 1]]
read 26 SNPs from file msmc_input.IND.chromosome347.txt, using indices [[0, 1]]
read 123 SNPs from file msmc_input.IND.chromosome348.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome349.txt, using indices [[0, 1]]
read 34513 SNPs from file msmc_input.IND.chromosome35.txt, using indices [[0, 1]]
read 1378 SNPs from file msmc_input.IND.chromosome351.txt, using indices [[0, 1]]
read 25 SNPs from file msmc_input.IND.chromosome352.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome353.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome354.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome355.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome356.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome357.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome358.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome359.txt, using indices [[0, 1]]
read 442 SNPs from file msmc_input.IND.chromosome36.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome360.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome361.txt, using indices [[0, 1]]
read 170 SNPs from file msmc_input.IND.chromosome362.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome363.txt, using indices [[0, 1]]
read 134 SNPs from file msmc_input.IND.chromosome364.txt, using indices [[0, 1]]
read 28 SNPs from file msmc_input.IND.chromosome365.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome366.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome367.txt, using indices [[0, 1]]
read 984 SNPs from file msmc_input.IND.chromosome368.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome369.txt, using indices [[0, 1]]
read 21 SNPs from file msmc_input.IND.chromosome37.txt, using indices [[0, 1]]
read 19 SNPs from file msmc_input.IND.chromosome370.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome371.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome372.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome373.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome374.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome375.txt, using indices [[0, 1]]
read 30 SNPs from file msmc_input.IND.chromosome376.txt, using indices [[0, 1]]
read 75 SNPs from file msmc_input.IND.chromosome377.txt, using indices [[0, 1]]
read 83 SNPs from file msmc_input.IND.chromosome379.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome38.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome380.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome381.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome382.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome383.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome384.txt, using indices [[0, 1]]
read 2168 SNPs from file msmc_input.IND.chromosome385.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome386.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome388.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome389.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome39.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome390.txt, using indices [[0, 1]]
read 4 SNPs from file msmc_input.IND.chromosome391.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome392.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome393.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome394.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome395.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome396.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome397.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome399.txt, using indices [[0, 1]]
read 7 SNPs from file msmc_input.IND.chromosome4.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome40.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome400.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome401.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome402.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome403.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome404.txt, using indices [[0, 1]]
read 23 SNPs from file msmc_input.IND.chromosome406.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome407.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome408.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome409.txt, using indices [[0, 1]]
read 970 SNPs from file msmc_input.IND.chromosome41.txt, using indices [[0, 1]]
read 1810 SNPs from file msmc_input.IND.chromosome410.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome411.txt, using indices [[0, 1]]
read 42 SNPs from file msmc_input.IND.chromosome412.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome413.txt, using indices [[0, 1]]
read 69 SNPs from file msmc_input.IND.chromosome414.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome415.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome417.txt, using indices [[0, 1]]
read 281 SNPs from file msmc_input.IND.chromosome418.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome419.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome42.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome420.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome422.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome423.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome424.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome425.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome427.txt, using indices [[0, 1]]
read 471 SNPs from file msmc_input.IND.chromosome428.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome429.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome43.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome430.txt, using indices [[0, 1]]
read 104 SNPs from file msmc_input.IND.chromosome431.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome432.txt, using indices [[0, 1]]
read 44 SNPs from file msmc_input.IND.chromosome433.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome434.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome435.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome436.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome437.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome438.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome44.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome440.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome441.txt, using indices [[0, 1]]
read 231 SNPs from file msmc_input.IND.chromosome442.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome443.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome444.txt, using indices [[0, 1]]
read 128 SNPs from file msmc_input.IND.chromosome445.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome446.txt, using indices [[0, 1]]
read 13 SNPs from file msmc_input.IND.chromosome448.txt, using indices [[0, 1]]
read 2 SNPs from file msmc_input.IND.chromosome449.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome45.txt, using indices [[0, 1]]
read 93 SNPs from file msmc_input.IND.chromosome450.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome451.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome452.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome453.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome454.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome455.txt, using indices [[0, 1]]
read 489 SNPs from file msmc_input.IND.chromosome456.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome457.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome458.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome459.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome46.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome460.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome461.txt, using indices [[0, 1]]
read 17 SNPs from file msmc_input.IND.chromosome463.txt, using indices [[0, 1]]
read 515 SNPs from file msmc_input.IND.chromosome464.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome465.txt, using indices [[0, 1]]
read 14 SNPs from file msmc_input.IND.chromosome466.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome467.txt, using indices [[0, 1]]
read 27 SNPs from file msmc_input.IND.chromosome468.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome469.txt, using indices [[0, 1]]
read 73 SNPs from file msmc_input.IND.chromosome47.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome470.txt, using indices [[0, 1]]
read 5517 SNPs from file msmc_input.IND.chromosome471.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome472.txt, using indices [[0, 1]]
read 202 SNPs from file msmc_input.IND.chromosome473.txt, using indices [[0, 1]]
read 190 SNPs from file msmc_input.IND.chromosome474.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome475.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome476.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome477.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome478.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome479.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome481.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome482.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome483.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome484.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome485.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome486.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome487.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome488.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome489.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome49.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome490.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome491.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome492.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome493.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome494.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome495.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome496.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome497.txt, using indices [[0, 1]]
read 23 SNPs from file msmc_input.IND.chromosome498.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome499.txt, using indices [[0, 1]]
read 5 SNPs from file msmc_input.IND.chromosome50.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome500.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome501.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome502.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome503.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome504.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome505.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome506.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome507.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome508.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome51.txt, using indices [[0, 1]]
read 26 SNPs from file msmc_input.IND.chromosome52.txt, using indices [[0, 1]]
read 3907 SNPs from file msmc_input.IND.chromosome53.txt, using indices [[0, 1]]
read 56 SNPs from file msmc_input.IND.chromosome54.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome55.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome56.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome57.txt, using indices [[0, 1]]
read 120 SNPs from file msmc_input.IND.chromosome59.txt, using indices [[0, 1]]
read 8 SNPs from file msmc_input.IND.chromosome6.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome60.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome61.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome62.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome63.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome64.txt, using indices [[0, 1]]
read 10347 SNPs from file msmc_input.IND.chromosome65.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome66.txt, using indices [[0, 1]]
read 316 SNPs from file msmc_input.IND.chromosome67.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome68.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome69.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome7.txt, using indices [[0, 1]]
read 50 SNPs from file msmc_input.IND.chromosome70.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome71.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome73.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome74.txt, using indices [[0, 1]]
read 287 SNPs from file msmc_input.IND.chromosome75.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome76.txt, using indices [[0, 1]]
read 11 SNPs from file msmc_input.IND.chromosome77.txt, using indices [[0, 1]]
read 167 SNPs from file msmc_input.IND.chromosome78.txt, using indices [[0, 1]]
read 3 SNPs from file msmc_input.IND.chromosome79.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome8.txt, using indices [[0, 1]]
read 43 SNPs from file msmc_input.IND.chromosome80.txt, using indices [[0, 1]]
read 10 SNPs from file msmc_input.IND.chromosome81.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome82.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome83.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome84.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome85.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome86.txt, using indices [[0, 1]]
read 1 SNPs from file msmc_input.IND.chromosome87.txt, using indices [[0, 1]]
read 8719 SNPs from file msmc_input.IND.chromosome88.txt, using indices [[0, 1]]
read 91 SNPs from file msmc_input.IND.chromosome89.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome9.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome90.txt, using indices [[0, 1]]
read 7449 SNPs from file msmc_input.IND.chromosome91.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome92.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome94.txt, using indices [[0, 1]]
read 95 SNPs from file msmc_input.IND.chromosome95.txt, using indices [[0, 1]]
read 102 SNPs from file msmc_input.IND.chromosome96.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome97.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome98.txt, using indices [[0, 1]]
read 0 SNPs from file msmc_input.IND.chromosome99.txt, using indices [[0, 1]]
estimating mutation rate: 0.00129584
Version: 2.1.1
input files: ["msmc_input.IND.chromosome1.txt", "msmc_input.IND.chromosome10.txt", "msmc_input.IND.chromosome100.txt", "msmc_input.IND.chromosome104.txt", "msmc_input.IND.chromosome105.txt", "msmc_input.IND.chromosome106.txt", "msmc_input.IND.chromosome107.txt", "msmc_input.IND.chromosome108.txt", "msmc_input.IND.chromosome109.txt", "msmc_input.IND.chromosome11.txt", "msmc_input.IND.chromosome110.txt", "msmc_input.IND.chromosome111.txt", "msmc_input.IND.chromosome112.txt", "msmc_input.IND.chromosome113.txt", "msmc_input.IND.chromosome114.txt", "msmc_input.IND.chromosome115.txt", "msmc_input.IND.chromosome116.txt", "msmc_input.IND.chromosome117.txt", "msmc_input.IND.chromosome118.txt", "msmc_input.IND.chromosome119.txt", "msmc_input.IND.chromosome12.txt", "msmc_input.IND.chromosome120.txt", "msmc_input.IND.chromosome121.txt", "msmc_input.IND.chromosome122.txt", "msmc_input.IND.chromosome124.txt", "msmc_input.IND.chromosome125.txt", "msmc_input.IND.chromosome126.txt", "msmc_input.IND.chromosome127.txt", "msmc_input.IND.chromosome128.txt", "msmc_input.IND.chromosome129.txt", "msmc_input.IND.chromosome13.txt", "msmc_input.IND.chromosome130.txt", "msmc_input.IND.chromosome131.txt", "msmc_input.IND.chromosome132.txt", "msmc_input.IND.chromosome133.txt", "msmc_input.IND.chromosome134.txt", "msmc_input.IND.chromosome135.txt", "msmc_input.IND.chromosome136.txt", "msmc_input.IND.chromosome137.txt", "msmc_input.IND.chromosome138.txt", "msmc_input.IND.chromosome139.txt", "msmc_input.IND.chromosome14.txt", "msmc_input.IND.chromosome140.txt", "msmc_input.IND.chromosome141.txt", "msmc_input.IND.chromosome142.txt", "msmc_input.IND.chromosome143.txt", "msmc_input.IND.chromosome144.txt", "msmc_input.IND.chromosome145.txt", "msmc_input.IND.chromosome146.txt", "msmc_input.IND.chromosome147.txt", "msmc_input.IND.chromosome148.txt", "msmc_input.IND.chromosome149.txt", "msmc_input.IND.chromosome150.txt", "msmc_input.IND.chromosome151.txt", "msmc_input.IND.chromosome152.txt", "msmc_input.IND.chromosome153.txt", "msmc_input.IND.chromosome154.txt", "msmc_input.IND.chromosome155.txt", "msmc_input.IND.chromosome156.txt", "msmc_input.IND.chromosome157.txt", "msmc_input.IND.chromosome158.txt", "msmc_input.IND.chromosome159.txt", "msmc_input.IND.chromosome16.txt", "msmc_input.IND.chromosome160.txt", "msmc_input.IND.chromosome161.txt", "msmc_input.IND.chromosome162.txt", "msmc_input.IND.chromosome163.txt", "msmc_input.IND.chromosome164.txt", "msmc_input.IND.chromosome165.txt", "msmc_input.IND.chromosome166.txt", "msmc_input.IND.chromosome167.txt", "msmc_input.IND.chromosome168.txt", "msmc_input.IND.chromosome169.txt", "msmc_input.IND.chromosome17.txt", "msmc_input.IND.chromosome170.txt", "msmc_input.IND.chromosome171.txt", "msmc_input.IND.chromosome172.txt", "msmc_input.IND.chromosome173.txt", "msmc_input.IND.chromosome174.txt", "msmc_input.IND.chromosome175.txt", "msmc_input.IND.chromosome176.txt", "msmc_input.IND.chromosome177.txt", "msmc_input.IND.chromosome179.txt", "msmc_input.IND.chromosome18.txt", "msmc_input.IND.chromosome180.txt", "msmc_input.IND.chromosome181.txt", "msmc_input.IND.chromosome182.txt", "msmc_input.IND.chromosome183.txt", "msmc_input.IND.chromosome184.txt", "msmc_input.IND.chromosome185.txt", "msmc_input.IND.chromosome186.txt", "msmc_input.IND.chromosome187.txt", "msmc_input.IND.chromosome188.txt", "msmc_input.IND.chromosome189.txt", "msmc_input.IND.chromosome19.txt", "msmc_input.IND.chromosome190.txt", "msmc_input.IND.chromosome191.txt", "msmc_input.IND.chromosome192.txt", "msmc_input.IND.chromosome193.txt", "msmc_input.IND.chromosome194.txt", "msmc_input.IND.chromosome197.txt", "msmc_input.IND.chromosome198.txt", "msmc_input.IND.chromosome199.txt", "msmc_input.IND.chromosome2.txt", "msmc_input.IND.chromosome20.txt", "msmc_input.IND.chromosome200.txt", "msmc_input.IND.chromosome201.txt", "msmc_input.IND.chromosome202.txt", "msmc_input.IND.chromosome203.txt", "msmc_input.IND.chromosome204.txt", "msmc_input.IND.chromosome205.txt", "msmc_input.IND.chromosome206.txt", "msmc_input.IND.chromosome207.txt", "msmc_input.IND.chromosome208.txt", "msmc_input.IND.chromosome209.txt", "msmc_input.IND.chromosome21.txt", "msmc_input.IND.chromosome210.txt", "msmc_input.IND.chromosome211.txt", "msmc_input.IND.chromosome212.txt", "msmc_input.IND.chromosome213.txt", "msmc_input.IND.chromosome214.txt", "msmc_input.IND.chromosome215.txt", "msmc_input.IND.chromosome216.txt", "msmc_input.IND.chromosome218.txt", "msmc_input.IND.chromosome219.txt", "msmc_input.IND.chromosome22.txt", "msmc_input.IND.chromosome220.txt", "msmc_input.IND.chromosome222.txt", "msmc_input.IND.chromosome223.txt", "msmc_input.IND.chromosome224.txt", "msmc_input.IND.chromosome225.txt", "msmc_input.IND.chromosome226.txt", "msmc_input.IND.chromosome227.txt", "msmc_input.IND.chromosome228.txt", "msmc_input.IND.chromosome229.txt", "msmc_input.IND.chromosome23.txt", "msmc_input.IND.chromosome231.txt", "msmc_input.IND.chromosome232.txt", "msmc_input.IND.chromosome233.txt", "msmc_input.IND.chromosome234.txt", "msmc_input.IND.chromosome235.txt", "msmc_input.IND.chromosome236.txt", "msmc_input.IND.chromosome237.txt", "msmc_input.IND.chromosome238.txt", "msmc_input.IND.chromosome239.txt", "msmc_input.IND.chromosome24.txt", "msmc_input.IND.chromosome240.txt", "msmc_input.IND.chromosome241.txt", "msmc_input.IND.chromosome242.txt", "msmc_input.IND.chromosome243.txt", "msmc_input.IND.chromosome245.txt", "msmc_input.IND.chromosome246.txt", "msmc_input.IND.chromosome247.txt", "msmc_input.IND.chromosome248.txt", "msmc_input.IND.chromosome249.txt", "msmc_input.IND.chromosome25.txt", "msmc_input.IND.chromosome250.txt", "msmc_input.IND.chromosome251.txt", "msmc_input.IND.chromosome252.txt", "msmc_input.IND.chromosome253.txt", "msmc_input.IND.chromosome254.txt", "msmc_input.IND.chromosome255.txt", "msmc_input.IND.chromosome256.txt", "msmc_input.IND.chromosome257.txt", "msmc_input.IND.chromosome258.txt", "msmc_input.IND.chromosome259.txt", "msmc_input.IND.chromosome26.txt", "msmc_input.IND.chromosome260.txt", "msmc_input.IND.chromosome261.txt", "msmc_input.IND.chromosome262.txt", "msmc_input.IND.chromosome263.txt", "msmc_input.IND.chromosome264.txt", "msmc_input.IND.chromosome265.txt", "msmc_input.IND.chromosome266.txt", "msmc_input.IND.chromosome267.txt", "msmc_input.IND.chromosome268.txt", "msmc_input.IND.chromosome269.txt", "msmc_input.IND.chromosome27.txt", "msmc_input.IND.chromosome270.txt", "msmc_input.IND.chromosome271.txt", "msmc_input.IND.chromosome272.txt", "msmc_input.IND.chromosome273.txt", "msmc_input.IND.chromosome274.txt", "msmc_input.IND.chromosome276.txt", "msmc_input.IND.chromosome277.txt", "msmc_input.IND.chromosome278.txt", "msmc_input.IND.chromosome279.txt", "msmc_input.IND.chromosome28.txt", "msmc_input.IND.chromosome280.txt", "msmc_input.IND.chromosome281.txt", "msmc_input.IND.chromosome282.txt", "msmc_input.IND.chromosome283.txt", "msmc_input.IND.chromosome284.txt", "msmc_input.IND.chromosome285.txt", "msmc_input.IND.chromosome286.txt", "msmc_input.IND.chromosome287.txt", "msmc_input.IND.chromosome288.txt", "msmc_input.IND.chromosome289.txt", "msmc_input.IND.chromosome29.txt", "msmc_input.IND.chromosome290.txt", "msmc_input.IND.chromosome291.txt", "msmc_input.IND.chromosome292.txt", "msmc_input.IND.chromosome293.txt", "msmc_input.IND.chromosome294.txt", "msmc_input.IND.chromosome295.txt", "msmc_input.IND.chromosome296.txt", "msmc_input.IND.chromosome297.txt", "msmc_input.IND.chromosome298.txt", "msmc_input.IND.chromosome299.txt", "msmc_input.IND.chromosome3.txt", "msmc_input.IND.chromosome300.txt", "msmc_input.IND.chromosome301.txt", "msmc_input.IND.chromosome302.txt", "msmc_input.IND.chromosome303.txt", "msmc_input.IND.chromosome304.txt", "msmc_input.IND.chromosome305.txt", "msmc_input.IND.chromosome306.txt", "msmc_input.IND.chromosome307.txt", "msmc_input.IND.chromosome308.txt", "msmc_input.IND.chromosome309.txt", "msmc_input.IND.chromosome31.txt", "msmc_input.IND.chromosome311.txt", "msmc_input.IND.chromosome312.txt", "msmc_input.IND.chromosome313.txt", "msmc_input.IND.chromosome314.txt", "msmc_input.IND.chromosome315.txt", "msmc_input.IND.chromosome316.txt", "msmc_input.IND.chromosome317.txt", "msmc_input.IND.chromosome318.txt", "msmc_input.IND.chromosome319.txt", "msmc_input.IND.chromosome32.txt", "msmc_input.IND.chromosome320.txt", "msmc_input.IND.chromosome321.txt", "msmc_input.IND.chromosome322.txt", "msmc_input.IND.chromosome323.txt", "msmc_input.IND.chromosome324.txt", "msmc_input.IND.chromosome325.txt", "msmc_input.IND.chromosome326.txt", "msmc_input.IND.chromosome328.txt", "msmc_input.IND.chromosome329.txt", "msmc_input.IND.chromosome33.txt", "msmc_input.IND.chromosome331.txt", "msmc_input.IND.chromosome332.txt", "msmc_input.IND.chromosome333.txt", "msmc_input.IND.chromosome334.txt", "msmc_input.IND.chromosome335.txt", "msmc_input.IND.chromosome336.txt", "msmc_input.IND.chromosome337.txt", "msmc_input.IND.chromosome339.txt", "msmc_input.IND.chromosome34.txt", "msmc_input.IND.chromosome340.txt", "msmc_input.IND.chromosome341.txt", "msmc_input.IND.chromosome342.txt", "msmc_input.IND.chromosome343.txt", "msmc_input.IND.chromosome344.txt", "msmc_input.IND.chromosome345.txt", "msmc_input.IND.chromosome346.txt", "msmc_input.IND.chromosome347.txt", "msmc_input.IND.chromosome348.txt", "msmc_input.IND.chromosome349.txt", "msmc_input.IND.chromosome35.txt", "msmc_input.IND.chromosome351.txt", "msmc_input.IND.chromosome352.txt", "msmc_input.IND.chromosome353.txt", "msmc_input.IND.chromosome354.txt", "msmc_input.IND.chromosome355.txt", "msmc_input.IND.chromosome356.txt", "msmc_input.IND.chromosome357.txt", "msmc_input.IND.chromosome358.txt", "msmc_input.IND.chromosome359.txt", "msmc_input.IND.chromosome36.txt", "msmc_input.IND.chromosome360.txt", "msmc_input.IND.chromosome361.txt", "msmc_input.IND.chromosome362.txt", "msmc_input.IND.chromosome363.txt", "msmc_input.IND.chromosome364.txt", "msmc_input.IND.chromosome365.txt", "msmc_input.IND.chromosome366.txt", "msmc_input.IND.chromosome367.txt", "msmc_input.IND.chromosome368.txt", "msmc_input.IND.chromosome369.txt", "msmc_input.IND.chromosome37.txt", "msmc_input.IND.chromosome370.txt", "msmc_input.IND.chromosome371.txt", "msmc_input.IND.chromosome372.txt", "msmc_input.IND.chromosome373.txt", "msmc_input.IND.chromosome374.txt", "msmc_input.IND.chromosome375.txt", "msmc_input.IND.chromosome376.txt", "msmc_input.IND.chromosome377.txt", "msmc_input.IND.chromosome379.txt", "msmc_input.IND.chromosome38.txt", "msmc_input.IND.chromosome380.txt", "msmc_input.IND.chromosome381.txt", "msmc_input.IND.chromosome382.txt", "msmc_input.IND.chromosome383.txt", "msmc_input.IND.chromosome384.txt", "msmc_input.IND.chromosome385.txt", "msmc_input.IND.chromosome386.txt", "msmc_input.IND.chromosome388.txt", "msmc_input.IND.chromosome389.txt", "msmc_input.IND.chromosome39.txt", "msmc_input.IND.chromosome390.txt", "msmc_input.IND.chromosome391.txt", "msmc_input.IND.chromosome392.txt", "msmc_input.IND.chromosome393.txt", "msmc_input.IND.chromosome394.txt", "msmc_input.IND.chromosome395.txt", "msmc_input.IND.chromosome396.txt", "msmc_input.IND.chromosome397.txt", "msmc_input.IND.chromosome399.txt", "msmc_input.IND.chromosome4.txt", "msmc_input.IND.chromosome40.txt", "msmc_input.IND.chromosome400.txt", "msmc_input.IND.chromosome401.txt", "msmc_input.IND.chromosome402.txt", "msmc_input.IND.chromosome403.txt", "msmc_input.IND.chromosome404.txt", "msmc_input.IND.chromosome406.txt", "msmc_input.IND.chromosome407.txt", "msmc_input.IND.chromosome408.txt", "msmc_input.IND.chromosome409.txt", "msmc_input.IND.chromosome41.txt", "msmc_input.IND.chromosome410.txt", "msmc_input.IND.chromosome411.txt", "msmc_input.IND.chromosome412.txt", "msmc_input.IND.chromosome413.txt", "msmc_input.IND.chromosome414.txt", "msmc_input.IND.chromosome415.txt", "msmc_input.IND.chromosome417.txt", "msmc_input.IND.chromosome418.txt", "msmc_input.IND.chromosome419.txt", "msmc_input.IND.chromosome42.txt", "msmc_input.IND.chromosome420.txt", "msmc_input.IND.chromosome422.txt", "msmc_input.IND.chromosome423.txt", "msmc_input.IND.chromosome424.txt", "msmc_input.IND.chromosome425.txt", "msmc_input.IND.chromosome427.txt", "msmc_input.IND.chromosome428.txt", "msmc_input.IND.chromosome429.txt", "msmc_input.IND.chromosome43.txt", "msmc_input.IND.chromosome430.txt", "msmc_input.IND.chromosome431.txt", "msmc_input.IND.chromosome432.txt", "msmc_input.IND.chromosome433.txt", "msmc_input.IND.chromosome434.txt", "msmc_input.IND.chromosome435.txt", "msmc_input.IND.chromosome436.txt", "msmc_input.IND.chromosome437.txt", "msmc_input.IND.chromosome438.txt", "msmc_input.IND.chromosome44.txt", "msmc_input.IND.chromosome440.txt", "msmc_input.IND.chromosome441.txt", "msmc_input.IND.chromosome442.txt", "msmc_input.IND.chromosome443.txt", "msmc_input.IND.chromosome444.txt", "msmc_input.IND.chromosome445.txt", "msmc_input.IND.chromosome446.txt", "msmc_input.IND.chromosome448.txt", "msmc_input.IND.chromosome449.txt", "msmc_input.IND.chromosome45.txt", "msmc_input.IND.chromosome450.txt", "msmc_input.IND.chromosome451.txt", "msmc_input.IND.chromosome452.txt", "msmc_input.IND.chromosome453.txt", "msmc_input.IND.chromosome454.txt", "msmc_input.IND.chromosome455.txt", "msmc_input.IND.chromosome456.txt", "msmc_input.IND.chromosome457.txt", "msmc_input.IND.chromosome458.txt", "msmc_input.IND.chromosome459.txt", "msmc_input.IND.chromosome46.txt", "msmc_input.IND.chromosome460.txt", "msmc_input.IND.chromosome461.txt", "msmc_input.IND.chromosome463.txt", "msmc_input.IND.chromosome464.txt", "msmc_input.IND.chromosome465.txt", "msmc_input.IND.chromosome466.txt", "msmc_input.IND.chromosome467.txt", "msmc_input.IND.chromosome468.txt", "msmc_input.IND.chromosome469.txt", "msmc_input.IND.chromosome47.txt", "msmc_input.IND.chromosome470.txt", "msmc_input.IND.chromosome471.txt", "msmc_input.IND.chromosome472.txt", "msmc_input.IND.chromosome473.txt", "msmc_input.IND.chromosome474.txt", "msmc_input.IND.chromosome475.txt", "msmc_input.IND.chromosome476.txt", "msmc_input.IND.chromosome477.txt", "msmc_input.IND.chromosome478.txt", "msmc_input.IND.chromosome479.txt", "msmc_input.IND.chromosome481.txt", "msmc_input.IND.chromosome482.txt", "msmc_input.IND.chromosome483.txt", "msmc_input.IND.chromosome484.txt", "msmc_input.IND.chromosome485.txt", "msmc_input.IND.chromosome486.txt", "msmc_input.IND.chromosome487.txt", "msmc_input.IND.chromosome488.txt", "msmc_input.IND.chromosome489.txt", "msmc_input.IND.chromosome49.txt", "msmc_input.IND.chromosome490.txt", "msmc_input.IND.chromosome491.txt", "msmc_input.IND.chromosome492.txt", "msmc_input.IND.chromosome493.txt", "msmc_input.IND.chromosome494.txt", "msmc_input.IND.chromosome495.txt", "msmc_input.IND.chromosome496.txt", "msmc_input.IND.chromosome497.txt", "msmc_input.IND.chromosome498.txt", "msmc_input.IND.chromosome499.txt", "msmc_input.IND.chromosome50.txt", "msmc_input.IND.chromosome500.txt", "msmc_input.IND.chromosome501.txt", "msmc_input.IND.chromosome502.txt", "msmc_input.IND.chromosome503.txt", "msmc_input.IND.chromosome504.txt", "msmc_input.IND.chromosome505.txt", "msmc_input.IND.chromosome506.txt", "msmc_input.IND.chromosome507.txt", "msmc_input.IND.chromosome508.txt", "msmc_input.IND.chromosome51.txt", "msmc_input.IND.chromosome52.txt", "msmc_input.IND.chromosome53.txt", "msmc_input.IND.chromosome54.txt", "msmc_input.IND.chromosome55.txt", "msmc_input.IND.chromosome56.txt", "msmc_input.IND.chromosome57.txt", "msmc_input.IND.chromosome59.txt", "msmc_input.IND.chromosome6.txt", "msmc_input.IND.chromosome60.txt", "msmc_input.IND.chromosome61.txt", "msmc_input.IND.chromosome62.txt", "msmc_input.IND.chromosome63.txt", "msmc_input.IND.chromosome64.txt", "msmc_input.IND.chromosome65.txt", "msmc_input.IND.chromosome66.txt", "msmc_input.IND.chromosome67.txt", "msmc_input.IND.chromosome68.txt", "msmc_input.IND.chromosome69.txt", "msmc_input.IND.chromosome7.txt", "msmc_input.IND.chromosome70.txt", "msmc_input.IND.chromosome71.txt", "msmc_input.IND.chromosome73.txt", "msmc_input.IND.chromosome74.txt", "msmc_input.IND.chromosome75.txt", "msmc_input.IND.chromosome76.txt", "msmc_input.IND.chromosome77.txt", "msmc_input.IND.chromosome78.txt", "msmc_input.IND.chromosome79.txt", "msmc_input.IND.chromosome8.txt", "msmc_input.IND.chromosome80.txt", "msmc_input.IND.chromosome81.txt", "msmc_input.IND.chromosome82.txt", "msmc_input.IND.chromosome83.txt", "msmc_input.IND.chromosome84.txt", "msmc_input.IND.chromosome85.txt", "msmc_input.IND.chromosome86.txt", "msmc_input.IND.chromosome87.txt", "msmc_input.IND.chromosome88.txt", "msmc_input.IND.chromosome89.txt", "msmc_input.IND.chromosome9.txt", "msmc_input.IND.chromosome90.txt", "msmc_input.IND.chromosome91.txt", "msmc_input.IND.chromosome92.txt", "msmc_input.IND.chromosome94.txt", "msmc_input.IND.chromosome95.txt", "msmc_input.IND.chromosome96.txt", "msmc_input.IND.chromosome97.txt", "msmc_input.IND.chromosome98.txt", "msmc_input.IND.chromosome99.txt"]
maxIterations: 100
mutationRate: 0.00129584
recombinationRate: 0.000323961
timeSegmentPattern: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2]
nrThreads: 32
outFilePrefix: /Msmc/OUTPUT
hmmStrideWidth: 1000
fixedRecombination: false
initialLambdaVec: []
skipAmbiguous: true
pairIndices: [[0, 1]]
logging information written to /Msmc/OUTPUT.log
loop information written to /Msmc/OUTPUT.loop.txt
final results written to /Msmc/OUTPUT.final.txt
time factor: 1
[1/100] Baumwelch iteration

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• [10/473] Expectation Stepcore.exception.ArrayIndexError@model/psmc_hmm.d(124): index [0] exceeds array of length 0

---

??:? onArrayIndexError [0x154fe0b0315c]
??:? _d_arraybounds_index [0x154fe0b0375d]
??:? [0x46726a]
??:? [0x4665ca]
??:? [0x46adfb]
??:? void std.parallelism.TaskPool.executeWorkLoop() [0x154fe0e2048f]
??:? thread_entryPoint [0x154fe0b282a9]
??:? [0x154fe0a1d608]
??:? clone [0x154fe07d8102]
core.exception.ArrayIndexError@model/psmc_hmm.d(124): index [0] exceeds array of length 0

[Meer9234]

I think there is something wrong with my files so ill first look at that. In the meantime, could you explain a bit more or refer me to an article about the -p value? How do you know which p is a good one?

I would like to make the same graphs as in this article: https://www.cell.com/current-biology/pdf/S0960-9822(15)00400-5.pdf
They reccomended a p value of 4+30*2+4+6+10 using psmc. Only I tried this one and it was not valid in msmc2

[stschiff]

Out of the top of my head, I see two problems:
1.) Some of your input data contain 0 SNPs. I think you should remove them from the input.
2.) Your command line msmc2 -t 32 -p 12+251+12+13 -i 100 -o /Msmc/OUTPUT -I 0,1 $NAMES suggests nearly 300 time segments. Way too many and clearly overfitting.