hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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GMTK does not allow last number of loadAccRange to be greater than 9999 #75

Open EricR86 opened 8 years ago

EricR86 commented 8 years ago

Original report (BitBucket issue) by Rachel Chan (Bitbucket: rcwchan).


Upon bundling, I received an error in which GMTK says maximum possible range specification is 9999 (but my segway run has 11942 possible windows):

#!python

ERROR: Last value of range specification '1860,2698,57,7640,7973,9823,5738,2101,5563,10260,3660,2594,2238,1845,3800,10453,10567,1691,7554,11724,11025,1038,8150,6245,233,5176,5027,8653,1983,11936,7035,11568,6455,8955,1542,10065,7115,11872,5931,3063,3770,4453,6431,480,8282,5534,2841,8277,8753,6218,2103,9126,5082,7436,7032,9241,2494,6662,6442,7405,4017,1465,7895,7656,4409,6473,9231,8655,8516,2577,7062,546,5498,9403,1791,10983,4737,5929,1809,8279,9371,8559,3671,7587,11424,5935,9205,2843,6202,11776,6107,5996,756,7658,1320,86,70,7394,2215,11507,803,5805,6024,11375,7738,857,9024,11019,11148,3850,5029,1032,9320,9402,4156,6621,5972,8455,5462,787,3673,7713,7262,2332,3137,5692,8427,8534,10925,5599,7308,7855,5034,6533,4163,8340,7246,1434,7958,330,3126,8444,4985,1993,7609,1785,5283,7818,9294,6903,7941,10109,1422,9528,4283,557,11320,1532,3081,831,605,4477,10073,7337,898,10105,4147,2596,4642,293,5885,8014,9349,3497,8412,7808,8779,3870,6918,5371,4470,3961,3779,153,805,11603,8035,10621,3540,7227,469,8018,3478,3866,11331,5458,9353,8526,2889,10230,2373,10137,10921,3675,5592,9069,10975,9810,7724,9631,6060,9264,9929,4198,9722,10536,9411,500,5736,11302,3896,3341,285,8658,9552,10262,3858,723,5388,6485,11353,3479,367,935,10842,2414,1365,11555,7532,3187,6021,6854,7853,116,10235,317,6525,3508,8421,3913,9464,2454,888,2042,1050,8090,2191,2138,876,3689,11648,4913,3358,2972,2750,2422,5764,9728,11363,7432,11719,11638,1180,731,11178,3148,9498,6213,4481,6220,5794,8291,5406,9811,779,8581,4866,4182,635,4730,1330,10475,2342,8161,9821,976,8631,10244,4761,20,7711,2906,8520,9548,4399,4547,8317,9532,2140,9218,1187,8332,1967,9991,4055,4450,11891,1245,1229,3635,7862,7235,5389,8088,11129,8625,5258,11335,7160,5468,10438,310,802,11751,11283,6075,11571,1881,10232,7070,5701,6249,9607,10683,11741,3876,11850,7986,9595,5302,7749,9008,881,5411,3147,6120,4764,4554,11397,9968,5769,1760,3202,5417,9491,9951,3374,10027,10181,1930,4996,4318,7261,5602,6044,5579,11494,1051,10710,3593,394,11930,7141,11738,11862,7641,3253,10690,2262,11633,1488,2440,1156,7581,6260,10953,10447,9432,8867,7435,10973,11828,5683,11827,3920,272,4237,10533,9828,5347,10994,6586,3789,4875,5632,9901,2087,7696,6966,3310,5116,9694,10809,4276,2139,7771,9252,5032,9770,9750,5559,3906,1158,3254,10014,7714,4164,4734,3998,722,9139,9541,3872,2902,9628,4098,5711,10801,1414,1747,11522,4582,7458,1137,9232,1275,10543,1565,7400,9173,2663,50,3451,7439,10704,11265,7117,9522,11116,5681,9104,6769,9590,2149,9237,3349,58,4842,9376,3751,6037,8069,5094,2431,112,3788,1665,11043,9333,11840,4685,5431,2232,1578,157,1285,4036,10026,8781,3176,3188,5861,4869,10943,7283,3812,9690,10427,11119,9798,8646,3371,9185,3015,1325,6263,7384,3878,9159,4071,11722,3435,2496,10041,10247,6812,8699,9246,687,5547,6910,4490,10431,10635,8336,5858,947,261,4769,10135,1999,7020,4955,3044,6324,6513,9752,9245,7659,11336,10369,6340,5493,7189,9351,1902,1956,5334,10177,867,5279,1562,11419,8884,4927,5477,9399,7887,9572,9893,8521,11190,6241,6418,2731,6469,3994,4510,3526,2765,4188,6420,11333', which is 11333, is greater than the maximum possible value '9999' 

It seems that GMTK expects a sorted list (ie in the format 1:9999), and has an internal length limit of 9999 windows. So if the last number is greater than 9999, it thinks the list has length greater than 9999 (when in our case, it is actually a random list of numbers, the length of which is much less than 9999).

By comparing the params files output, I have confirmed that GMTK does not silently ignore numbers greater than 9999 (for example, the output for loadAccRange=10453,10567,11724,11025,...,50 vs loadAccRange=50 is different).

GMTK does not raise this error for loadAccRanges that do not end in a number greater than 9999, but contain numbers greater than 9999 (ie, 1,2,3,11000,5).

EricR86 commented 8 years ago

Original comment by Rachel Chan (Bitbucket: rcwchan).


EricR86 commented 8 years ago

Original comment by Rachel Chan (Bitbucket: rcwchan).