Function encountered error after 2h of processing

[edridgedsouza]

I ran InSituType and it proceeded for about 2h before encountering an error. The traceback was not particularly informative so I'm copying it here.

# https://github.com/Nanostring-Biostats/CosMx-Cell-Profiles/raw/refs/heads/main/Mouse/Brain/MouseBrain.profiles.csv
mouse_brain_ref <- read.csv('/home/ubuntu/data/leon-brains/reference/MouseBrain.profiles.csv') %>% column_to_rownames('X')

message_('Making cohorts') # Takes 5 min
cohort <- fastCohorting(processed_objs[[1]]@meta.data[, c('Mean.PanCK','Max.PanCK',
                                                'Mean.G','Max.G',
                                                'Mean.CD298.B2M','Max.CD298.B2M',
                                                'Mean.CD45','Max.CD45',
                                                'Mean.DAPI','Max.DAPI')], 
                                                gaussian_transform=T)
processed_objs[[1]]@meta.data$cohort <- factor(cohort)
print(table(cohort))


message_('Running InSituType')
# Made sure to transpose the counts matrix
raw <- processed_objs[[1]][['RNA']]$counts %>% t()
unsup <- insitutype(
    counts = raw[, !grepl('^NegPrb', colnames(raw))],
    neg = rowMeans(raw[, grepl('^NegPrb', colnames(raw))]),
    n_clusts = 40,
    reference_profiles = mouse_brain_ref,
    cohort=cohort,
    update_reference_profiles = T
)  # Crashed after 2h
saveRDS(unsup, '/home/ubuntu/tmp/unsup.RDS')

message_('Done')

Here is the output:

{
	"name": "ERROR",
	"message": "Error in .local(x, ...): unused argument (counts = new(\"dgCMatrix\", i = c(0, 3, 10, 14, 19, 33, 38, 40, 44, 55, 67, 70, 71, 72, 75, 76, 81, 91, 92, 97, 101, 103, 107, 109, 110, 113, 122, 132, 138, 140, 141, 145, 155, 160, 161, 164, 165, 183, 184, 187, 192, 195, 198, 199, 200, 201, 202, 208, 213, 216, 217, 218, 219, 227, 228, 230, 233, 238, 241, 244, 246, 247, 248, 257, 278, 283, 285, 286, 288, 289, 291, 292, 293, 300, 302, 303, 306, 311, 320, 321, 322, 323, 325, 327, 330, 332, 334, 339, 343, 345, 347, 352, 353, 355, 357, 368, 372, 
378, 379, 380, 384, 388, 390, 394, 397, 399, 400, 402, 412, 414, 419, 423, 435, 437, 439, 443, 444, 449, 451, 455, 462, 471, 472, 474, 475, 478, 480, 482, 483, 484, 486, 490, 493, 495, 496, 498, 499, 500, 501, 504, 505, 509, 511, 512, 520, 523, 525, 526, 529, 538, 539, 547, 555, 558, 559, 560, 562, 564, 566, 568, 572, 575, 576, 580, 584, 586, 588, 589, 591, 596, 597, 604, 609, 613, 615, 616, 618, 629, 633, 635, 636, 640, 641, 650, 652, 653, 656, 662, 666, 667, 675, 680, 681, 682, 683, 686, 691, 692, 
694, 700, 701, 704, 707, 717, 719, 720, 723, 724, 730, 732, 740, 742, 744, 745, 746, 749, 752, 753, 758, 759, 761, 764, 766, 767, 770, 772, 773, 774, 779, 780, 781, 783, 784, 785, 790, 791, 794, 796, 806, 807, 808, 809, 810, 814, 815, 817, 825, 826, 831, 835, 839, 840, 841, 843, 848, 851, 852, 853, 854, 857, 858, 862, 863, 864, 865, 872, 875, 879, 881, 882, 886, 888, 890, 892, 894, 897, 904, 906, 907, 909, 910, 911, 914, 918, 921, 922, 925, 927, 928, 929, 932, 937, 940, 941, 948, 949, 951, 956, 961, 
963, 965, 967, 968, 969, 971, 973, 980, 982, 985, 986, 988, 989, 990, 991, 994, 995, 1004, 1011, 1015, 1016, 1017, 1019, 1021, 1022, 1023, 1025, 1026, 1028, 1031, 1035, 1037, 1038, 1043, 1045, 1046, 1048, 1050, 1052, 1057, 1060, 1061, 1064, 1065, 1068, 1070, 1076, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1089, 1091, 1095, 1097, 1099, 1104, 1106, 1107, 1116, 1121, 1122, 1125, 1126, 1133, 1134, 1135, 1137, 1146, 1147, 1149, 1150, 1153, 1156, 1160, 1163, 1165, 1167, 1169, 1170, 1172, 1177, 1179, 1180, 
1183, 1184, 1186, 1191, 1193, 1195, 1201, 1203, 1207, 1209, 1210, 1212, 1213, 1214, 1215, 1216, 1219, 1220, 1222, 1223, 1230, 1237, 1239, 1240, 1241, 1244, 1246, 1247, 1248, 1249, 1252, 1253, 1255, 1258, 1259, 1261, 1263, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1277, 1278, 1282, 1283, 1285, 1286, 1287, 1293, 1298, 1303, 1304, 1305, 1311, 1313, 1314, 1315, 1317, 1318, 1319, 1322, 1323, 1324, 1325, 1326, 1327, 1329, 1330, 1332, 1333, 1336, 1338, 1340, 1341, 1342, 1344, 1345, 1346, 1347, 1348, 1356, 
1361, 1362, 1364, 1365, 1368, 1371, 1374, 1376, 1377, 1383, 1386, 1387, 1388, 1390, 1391, 1392, 1394, 1397, 1398, 1399, 1400, 1402, 1403, 1405, 1409, 1412, 1414, 1416, 1417, 1420, 1422, 1427, 1429, 1438, 1447, 1448, 1450, 1459, 1460, 1463, 1464, 1469, 1472, 1473, 1474, 1478, 1480, 1486, 1487, 1490, 1492, 1495, 1496, 1499, 1510, 1515, 1517, 1519, 1520, 1521, 1522, 1523, 1526, 1529, 1533, 1538, 1539, 1540, 1546, 1547, 1548, 1549, 1553, 1559, 1560, 1567, 1568, 1584, 1586, 1590, 1593, 1594, 1600, 1601, 
1602, 1606, 1610, 1611, 1613, 1617, 1618, 1619, 1622, 1624, 1629, 1632, 1634, 1635, 1636, 1647, 1652, 1654, 1656, 1657, 1663, 1664, 1668, 1671, 1676, 1677, 1681, 1682, 1689, 1695, 1699, 1700, 1701, 1703, 1704, 1705, 1711, 1712, 1715, 1716, 1717, 1720, 1730, 1732, 1733, 1737, 1738, 1742, 1744, 1745, 1746, 1747, 1751, 1752, 1753, 1754, 1756, 1760, 1765, 1766, 1768, 1772, 1774, 1775, 1780, 1782, 1783, 1785, 1786, 1788, 1789, 1792, 1793, 1794, 1796, 1799, 1803, 1804, 1808, 1809, 1810, 1815, 1819, 1820, 
1822, 1829, 1833, 1835, 1836, 1840, 1841, 1844, 1847, 1851, 1855, 1859, 1863, 1868, 1871, 1874, 1879, 1880, 1883, 1884, 1889, 1890, 1891, 1892, 1897, 1901, 1902, 1906, 1907, 1913, 1916, 1920, 1927, 1940, 1941, 1950, 1954, 1956, 1968, 1970, 1978, 1980, 1981, 1983, 1984, 1989, 1991, 1997, 1998, 2014, 2019, 2023, 2024, 2029, 2034, 2036, 2039, 2041, 2046, 2054, 2056, 2057, 2060, 2067, 2068, 2073, 2076, 2078, 2080, 2082, 2086, 2090, 2093, 2098, 2103, 2104, 2107, 2114, 2115, 2117, 2127, 2130, 2132, 2133, 
2136, 2137, 2140, 2148, 2149, 2151, 2154, 2157, 2166, 2172, 2173, 2176, 2178, 2185, 2190, 2191, 2192, 2193, 2199, 2202, 2207, 2210, 2211, 2212, 2213, 2217, 2221, 2226, 2228, 2230, 2233, 2234, 2236, 2237, 2239, 2240, 2243, 2244, 2245, 2256, 2257, 2258, 2260, 2262, 2264, 2268, 2270, 2274, 2275, 2278, 2285, 2287, 2290, 2296, 2298, 2299, 2304, 2306, 2307, 2308, 2311, 2313, 2318, 2320, 2324, 2326, 2327, 2329, 2330, 2335, 2336, 2345, 2348, 2350, 2351, 2352, 2358, 2362, 2365, 2370, 2375, 2380, 2382, 2385, 
2401, 2404, 2411, 2413, 2414, 2418, 2432, 2440, 2441, 2445, 2446, 2447, 2451, 2452, 2453, 2458, 2461, 2466, 2470, 2476, 2479, 2482, 2484, 2487, 2488, 2490, 2492, 2496, 2497, 2498, 2499, 2508, 2513, 2533, 2534, 2536, 2542, 2543, 2544, 2547, 2548, 2549, 2552, 2555, 2558, 2559, 2560, 2563, 2564, 2572, 2574, 2575, 2576, 2577, 2579, 2582, 2585, 2587, 2590, 2591, 2594, 2595, 2596, 2600, 2607, 2609, 2613, 2617, 2619, 2623, 2627, 2630, 2631, 2632, 2636, 2637, 2642, 2643, 2649, 2655, 2659, 2664, 2667, 2668, 
2670, 2673, 2674, 2675, 2676, 2682, 2683, 2686, 2688, 2690, 2692, 2693, 2699, 2702, 2704, 2705, 2713, 2714, 2718, 2719, 2720, 2721, 2722, 2727, 2729, 2731, 2732, 2734, 2735, 2736, 2737, 2738, 2739, 2744, 2746, 2747, 2750, 2752, 2755, 2766, 2767, 2772, 2775, 2780, 2785, 2786, 2787, 2790, 2791, 2792, 2796, 2801, 2802, 2805, 2807, 2809, 2817, 2819, 2827, 2829, 2831, 2834, 2836, 2839, 2841, 2843, 2845, 2846, 2848, 2852, 2853, 2854, 2858, 2863, 2867, 2877, 2878, 2879, 2883, 2888, 2890, 2891, 2897, 2902, 
2906, 2908, 2909, 2912, 2913, 2914, 2917, 2920, 2923, 2924, 2927, 2930, 2931, 2935, 2937, 2938, 2939, 2940, 2947, 2949, 2952, 2960, 2962, 2964, 2965, 2968, 2970, 2972, 2973, 2979, 2981, 2984, 2988, 2992, 2993, 2997, 2998, 2999, 3002, 3013, 3014, 3015, 3024, 3030, 3033, 3038, 3042, 3043, 3044, 3046, 3051, 3059, 3060, 3065, 3070, 3085, 3086, 3088, 3090, 3093, 3094, 3099, 3103, 3104, 3111, 3112, 3113, 3114, 3117, 3118, 3125, 3131, 3135, 3138, 3140, 3142, 3143, 3144, 3145, 3147, 3149, 3150, 3152, 3153, 
3155, 3159, 3160, 3163, 3167, 3168, 3169, 3170, 3178, 3182, 3188, 3190, 3192, 3193, 3194, 3198, 3200, 3201, 3204, 3205, 3206, 3210, 3211, 3213, 3217, 3219, 3220, 3229, 3232, 3234, 3237, 3238, 3241, 3242, 3243, 3245, 3246, 3247, 3248, 3250, 3252, 3255, 3257, 3259, 3261, 3262, 3264, 3265, 3266, 3268, 3269, 3271, 3272, 3273, 3281, 3284, 3286, 3291, 3293, 3299, 3300, 3302, 3306, 3309, 3310, 3312, 3314, 3316, 3322, 3324, 3325, 3326, 3328, 3330, 3331, 3335, 3342, 3345, 3346, 3352, 3353, 3357, 3358, 3360, 
3364, 3365, 3367, 3369, 3370, 3371, 3375, 3379, 3380, 3383, 3384, 3387, 3391, 3396, 3399, 3401, 3403, 3407, 3408, 3412, 3413, 3414, 3421, 3422, 3423, 3424, 3429, 3430, 3431, 3434, 3435, 3436, 3437, 3447, 3448, 3450, 3452, 3455, 3461, 3464, 3466, 3470, 3474, 3476, 3477, 3481, 3483, 3484, 3485, 3487, 3489, 3490, 3491, 3492, 3493, 3495, 3498, 3501, 3502, 3503, 3504, 3506, 3508, 3509, 3512, 3513, 3515, 3518, 3519, 3520, 3521, 3522, 3527, 3531, 3532, 3534, 3535, 3537, 3538, 3539, 3540, 3551, 3552, 3561, 
3562, 3564, 3571, 3572, 3574, 3575, 3576, 3578, 3579, 3580, 3581, 3583, 3585, 3586, 3589, 3596, 3597, 3600, 3603, 3604, 3608, 3609, 3610, 3618, 3622, 3625, 3627, 3631, 3634, 3636, 3638, 3639, 3647, 3648, 3650, 3651, 3657, 3661, 3663, 3670, 3671, 3674, 3675, 3676, 3677, 3678, 3680, 3682, 3683, 3685, 3687, 3689, 3691, 3693, 3696, 3702, 3703, 3705, 3707, 3708, 3710, 3711, 3718, 3721, 3722, 3727, 3728, 3729, 3734, 3737, 3740, 3743, 3744, 3746, 3749, 3750, 3752, 3756, 3757, 3761, 3766, 3767, 3768, 3772, 
3773, 3774, 3777, 3785, 3790, 3791, 3795, 3797, 3798, 3799, 3800, 3801, 3803, 3810, 3814, 3815, 3818, 3820, 3822, 3824, 3826, 3827, 3829, 3830, 3831, 3833, 3835, 3836, 3838, 3842, 3844, 3845, 3850, 3851, 3859, 3867, 3868, 3869, 3872, 3875, 3877, 3879, 3881, 3882, 3885, 3886, 3892, 3893, 3895, 3897, 3901, 3902, 3904, 3907, 3910, 3911, 3912, 3915, 3916, 3917, 3920, 3921, 3922, 3923, 3927, 3931, 3933, 3937, 3939, 3940, 3941, 3942, 3943, 3946, 3947, 3948, 3952, 3954, 3955, 3956, 3959, 3961, 3973, 3974, 
3975, 3982, 3986, 3990, 3993, 3995, 3996, 3998, 4003, 4005, 4006, 4009, 4010, 4015, 4020, 4029, 403
",
	"stack": "Error in .local(x, ...): unused argument (counts = new(\"dgCMatrix\", i = c(0, 3, 10, 14, 19, 33, 38, 40, 44, 55, 67, 70, 71, 72, 75, 76, 81, 91, 92, 97, 101, 103, 107, 109, 110, 113, 122, 132, 138, 140, 141, 145, 155, 160, 161, 164, 165, 183, 184, 187, 192, 195, 198, 199, 200, 201, 202, 208, 213, 216, 217, 218, 219, 227, 228, 230, 233, 238, 241, 244, 246, 247, 248, 257, 278, 283, 285, 286, 288, 289, 291, 292, 293, 300, 302, 303, 306, 311, 320, 321, 322, 323, 325, 327, 330, 332, 334, 339, 343, 345, 347, 352, 353, 355, 357, 368, 372, 
378, 379, 380, 384, 388, 390, 394, 397, 399, 400, 402, 412, 414, 419, 423, 435, 437, 439, 443, 444, 449, 451, 455, 462, 471, 472, 474, 475, 478, 480, 482, 483, 484, 486, 490, 493, 495, 496, 498, 499, 500, 501, 504, 505, 509, 511, 512, 520, 523, 525, 526, 529, 538, 539, 547, 555, 558, 559, 560, 562, 564, 566, 568, 572, 575, 576, 580, 584, 586, 588, 589, 591, 596, 597, 604, 609, 613, 615, 616, 618, 629, 633, 635, 636, 640, 641, 650, 652, 653, 656, 662, 666, 667, 675, 680, 681, 682, 683, 686, 691, 692, 
694, 700, 701, 704, 707, 717, 719, 720, 723, 724, 730, 732, 740, 742, 744, 745, 746, 749, 752, 753, 758, 759, 761, 764, 766, 767, 770, 772, 773, 774, 779, 780, 781, 783, 784, 785, 790, 791, 794, 796, 806, 807, 808, 809, 810, 814, 815, 817, 825, 826, 831, 835, 839, 840, 841, 843, 848, 851, 852, 853, 854, 857, 858, 862, 863, 864, 865, 872, 875, 879, 881, 882, 886, 888, 890, 892, 894, 897, 904, 906, 907, 909, 910, 911, 914, 918, 921, 922, 925, 927, 928, 929, 932, 937, 940, 941, 948, 949, 951, 956, 961, 
963, 965, 967, 968, 969, 971, 973, 980, 982, 985, 986, 988, 989, 990, 991, 994, 995, 1004, 1011, 1015, 1016, 1017, 1019, 1021, 1022, 1023, 1025, 1026, 1028, 1031, 1035, 1037, 1038, 1043, 1045, 1046, 1048, 1050, 1052, 1057, 1060, 1061, 1064, 1065, 1068, 1070, 1076, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1089, 1091, 1095, 1097, 1099, 1104, 1106, 1107, 1116, 1121, 1122, 1125, 1126, 1133, 1134, 1135, 1137, 1146, 1147, 1149, 1150, 1153, 1156, 1160, 1163, 1165, 1167, 1169, 1170, 1172, 1177, 1179, 1180, 
1183, 1184, 1186, 1191, 1193, 1195, 1201, 1203, 1207, 1209, 1210, 1212, 1213, 1214, 1215, 1216, 1219, 1220, 1222, 1223, 1230, 1237, 1239, 1240, 1241, 1244, 1246, 1247, 1248, 1249, 1252, 1253, 1255, 1258, 1259, 1261, 1263, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1277, 1278, 1282, 1283, 1285, 1286, 1287, 1293, 1298, 1303, 1304, 1305, 1311, 1313, 1314, 1315, 1317, 1318, 1319, 1322, 1323, 1324, 1325, 1326, 1327, 1329, 1330, 1332, 1333, 1336, 1338, 1340, 1341, 1342, 1344, 1345, 1346, 1347, 1348, 1356, 
1361, 1362, 1364, 1365, 1368, 1371, 1374, 1376, 1377, 1383, 1386, 1387, 1388, 1390, 1391, 1392, 1394, 1397, 1398, 1399, 1400, 1402, 1403, 1405, 1409, 1412, 1414, 1416, 1417, 1420, 1422, 1427, 1429, 1438, 1447, 1448, 1450, 1459, 1460, 1463, 1464, 1469, 1472, 1473, 1474, 1478, 1480, 1486, 1487, 1490, 1492, 1495, 1496, 1499, 1510, 1515, 1517, 1519, 1520, 1521, 1522, 1523, 1526, 1529, 1533, 1538, 1539, 1540, 1546, 1547, 1548, 1549, 1553, 1559, 1560, 1567, 1568, 1584, 1586, 1590, 1593, 1594, 1600, 1601, 
1602, 1606, 1610, 1611, 1613, 1617, 1618, 1619, 1622, 1624, 1629, 1632, 1634, 1635, 1636, 1647, 1652, 1654, 1656, 1657, 1663, 1664, 1668, 1671, 1676, 1677, 1681, 1682, 1689, 1695, 1699, 1700, 1701, 1703, 1704, 1705, 1711, 1712, 1715, 1716, 1717, 1720, 1730, 1732, 1733, 1737, 1738, 1742, 1744, 1745, 1746, 1747, 1751, 1752, 1753, 1754, 1756, 1760, 1765, 1766, 1768, 1772, 1774, 1775, 1780, 1782, 1783, 1785, 1786, 1788, 1789, 1792, 1793, 1794, 1796, 1799, 1803, 1804, 1808, 1809, 1810, 1815, 1819, 1820, 
1822, 1829, 1833, 1835, 1836, 1840, 1841, 1844, 1847, 1851, 1855, 1859, 1863, 1868, 1871, 1874, 1879, 1880, 1883, 1884, 1889, 1890, 1891, 1892, 1897, 1901, 1902, 1906, 1907, 1913, 1916, 1920, 1927, 1940, 1941, 1950, 1954, 1956, 1968, 1970, 1978, 1980, 1981, 1983, 1984, 1989, 1991, 1997, 1998, 2014, 2019, 2023, 2024, 2029, 2034, 2036, 2039, 2041, 2046, 2054, 2056, 2057, 2060, 2067, 2068, 2073, 2076, 2078, 2080, 2082, 2086, 2090, 2093, 2098, 2103, 2104, 2107, 2114, 2115, 2117, 2127, 2130, 2132, 2133, 
2136, 2137, 2140, 2148, 2149, 2151, 2154, 2157, 2166, 2172, 2173, 2176, 2178, 2185, 2190, 2191, 2192, 2193, 2199, 2202, 2207, 2210, 2211, 2212, 2213, 2217, 2221, 2226, 2228, 2230, 2233, 2234, 2236, 2237, 2239, 2240, 2243, 2244, 2245, 2256, 2257, 2258, 2260, 2262, 2264, 2268, 2270, 2274, 2275, 2278, 2285, 2287, 2290, 2296, 2298, 2299, 2304, 2306, 2307, 2308, 2311, 2313, 2318, 2320, 2324, 2326, 2327, 2329, 2330, 2335, 2336, 2345, 2348, 2350, 2351, 2352, 2358, 2362, 2365, 2370, 2375, 2380, 2382, 2385, 
2401, 2404, 2411, 2413, 2414, 2418, 2432, 2440, 2441, 2445, 2446, 2447, 2451, 2452, 2453, 2458, 2461, 2466, 2470, 2476, 2479, 2482, 2484, 2487, 2488, 2490, 2492, 2496, 2497, 2498, 2499, 2508, 2513, 2533, 2534, 2536, 2542, 2543, 2544, 2547, 2548, 2549, 2552, 2555, 2558, 2559, 2560, 2563, 2564, 2572, 2574, 2575, 2576, 2577, 2579, 2582, 2585, 2587, 2590, 2591, 2594, 2595, 2596, 2600, 2607, 2609, 2613, 2617, 2619, 2623, 2627, 2630, 2631, 2632, 2636, 2637, 2642, 2643, 2649, 2655, 2659, 2664, 2667, 2668, 
2670, 2673, 2674, 2675, 2676, 2682, 2683, 2686, 2688, 2690, 2692, 2693, 2699, 2702, 2704, 2705, 2713, 2714, 2718, 2719, 2720, 2721, 2722, 2727, 2729, 2731, 2732, 2734, 2735, 2736, 2737, 2738, 2739, 2744, 2746, 2747, 2750, 2752, 2755, 2766, 2767, 2772, 2775, 2780, 2785, 2786, 2787, 2790, 2791, 2792, 2796, 2801, 2802, 2805, 2807, 2809, 2817, 2819, 2827, 2829, 2831, 2834, 2836, 2839, 2841, 2843, 2845, 2846, 2848, 2852, 2853, 2854, 2858, 2863, 2867, 2877, 2878, 2879, 2883, 2888, 2890, 2891, 2897, 2902, 
2906, 2908, 2909, 2912, 2913, 2914, 2917, 2920, 2923, 2924, 2927, 2930, 2931, 2935, 2937, 2938, 2939, 2940, 2947, 2949, 2952, 2960, 2962, 2964, 2965, 2968, 2970, 2972, 2973, 2979, 2981, 2984, 2988, 2992, 2993, 2997, 2998, 2999, 3002, 3013, 3014, 3015, 3024, 3030, 3033, 3038, 3042, 3043, 3044, 3046, 3051, 3059, 3060, 3065, 3070, 3085, 3086, 3088, 3090, 3093, 3094, 3099, 3103, 3104, 3111, 3112, 3113, 3114, 3117, 3118, 3125, 3131, 3135, 3138, 3140, 3142, 3143, 3144, 3145, 3147, 3149, 3150, 3152, 3153, 
3155, 3159, 3160, 3163, 3167, 3168, 3169, 3170, 3178, 3182, 3188, 3190, 3192, 3193, 3194, 3198, 3200, 3201, 3204, 3205, 3206, 3210, 3211, 3213, 3217, 3219, 3220, 3229, 3232, 3234, 3237, 3238, 3241, 3242, 3243, 3245, 3246, 3247, 3248, 3250, 3252, 3255, 3257, 3259, 3261, 3262, 3264, 3265, 3266, 3268, 3269, 3271, 3272, 3273, 3281, 3284, 3286, 3291, 3293, 3299, 3300, 3302, 3306, 3309, 3310, 3312, 3314, 3316, 3322, 3324, 3325, 3326, 3328, 3330, 3331, 3335, 3342, 3345, 3346, 3352, 3353, 3357, 3358, 3360, 
3364, 3365, 3367, 3369, 3370, 3371, 3375, 3379, 3380, 3383, 3384, 3387, 3391, 3396, 3399, 3401, 3403, 3407, 3408, 3412, 3413, 3414, 3421, 3422, 3423, 3424, 3429, 3430, 3431, 3434, 3435, 3436, 3437, 3447, 3448, 3450, 3452, 3455, 3461, 3464, 3466, 3470, 3474, 3476, 3477, 3481, 3483, 3484, 3485, 3487, 3489, 3490, 3491, 3492, 3493, 3495, 3498, 3501, 3502, 3503, 3504, 3506, 3508, 3509, 3512, 3513, 3515, 3518, 3519, 3520, 3521, 3522, 3527, 3531, 3532, 3534, 3535, 3537, 3538, 3539, 3540, 3551, 3552, 3561, 
3562, 3564, 3571, 3572, 3574, 3575, 3576, 3578, 3579, 3580, 3581, 3583, 3585, 3586, 3589, 3596, 3597, 3600, 3603, 3604, 3608, 3609, 3610, 3618, 3622, 3625, 3627, 3631, 3634, 3636, 3638, 3639, 3647, 3648, 3650, 3651, 3657, 3661, 3663, 3670, 3671, 3674, 3675, 3676, 3677, 3678, 3680, 3682, 3683, 3685, 3687, 3689, 3691, 3693, 3696, 3702, 3703, 3705, 3707, 3708, 3710, 3711, 3718, 3721, 3722, 3727, 3728, 3729, 3734, 3737, 3740, 3743, 3744, 3746, 3749, 3750, 3752, 3756, 3757, 3761, 3766, 3767, 3768, 3772, 
3773, 3774, 3777, 3785, 3790, 3791, 3795, 3797, 3798, 3799, 3800, 3801, 3803, 3810, 3814, 3815, 3818, 3820, 3822, 3824, 3826, 3827, 3829, 3830, 3831, 3833, 3835, 3836, 3838, 3842, 3844, 3845, 3850, 3851, 3859, 3867, 3868, 3869, 3872, 3875, 3877, 3879, 3881, 3882, 3885, 3886, 3892, 3893, 3895, 3897, 3901, 3902, 3904, 3907, 3910, 3911, 3912, 3915, 3916, 3917, 3920, 3921, 3922, 3923, 3927, 3931, 3933, 3937, 3939, 3940, 3941, 3942, 3943, 3946, 3947, 3948, 3952, 3954, 3955, 3956, 3959, 3961, 3973, 3974, 
3975, 3982, 3986, 3990, 3993, 3995, 3996, 3998, 4003, 4005, 4006, 4009, 4010, 4015, 4020, 4029, 403
Traceback:

1. insitutype(counts = raw[, !grepl(\"^NegPrb\", colnames(raw))], 
 .     neg = rowMeans(raw[, grepl(\"^NegPrb\", colnames(raw))]), n_clusts = 40, 
 .     reference_profiles = mouse_brain_ref, cohort = cohort, update_reference_profiles = T)
2. .handleSimpleError(function (cnd) 
 . {
 .     watcher$capture_plot_and_output()
 .     cnd <- sanitize_call(cnd)
 .     watcher$push(cnd)
 .     switch(on_error, continue = invokeRestart(\"eval_continue\"), 
 .         stop = invokeRestart(\"eval_stop\"), error = NULL)
 . }, \"unused argument (counts = new(\\\"dgCMatrix\\\", i = c(0, 3, 10, 14, 19, 33, 38, 40, 44, 55, 67, 70, 71, 72, 75, 76, 81, 91, 92, 97, 101, 103, 107, 109, 110, 113, 122, 132, 138, 140, 141, 145, 155, 160, 161, 164, 165, 183, 184, 187, 192, 195, 198, 199, 200, 201, 202, 208, 213, 216, 217, 218, 219, 227, 228, 230, 233, 238, 241, 244, 246, 247, 248, 257, 278, 283, 285, 286, 288, 289, 291, 292, 293, 300, 302, 303, 306, 311, 320, 321, 322, 323, 325, 327, 330, 332, 334, 339, 343, 345, 347, 352, 353, 355, 357, 368, 372, \
378, 379, 380, 384, 388, 390, 394, 397, 399, 400, 402, 412, 414, 419, 423, 435, 437, 439, 443, 444, 449, 451, 455, 462, 471, 472, 474, 475, 478, 480, 482, 483, 484, 486, 490, 493, 495, 496, 498, 499, 500, 501, 504, 505, 509, 511, 512, 520, 523, 525, 526, 529, 538, 539, 547, 555, 558, 559, 560, 562, 564, 566, 568, 572, 575, 576, 580, 584, 586, 588, 589, 591, 596, 597, 604, 609, 613, 615, 616, 618, 629, 633, 635, 636, 640, 641, 650, 652, 653, 656, 662, 666, 667, 675, 680, 681, 682, 683, 686, 691, 692, \
694, 700, 701, 704, 707, 717, 719, 720, 723, 724, 730, 732, 740, 742, 744, 745, 746, 749, 752, 753, 758, 759, 761, 764, 766, 767, 770, 772, 773, 774, 779, 780, 781, 783, 784, 785, 790, 791, 794, 796, 806, 807, 808, 809, 810, 814, 815, 817, 825, 826, 831, 835, 839, 840, 841, 843, 848, 851, 852, 853, 854, 857, 858, 862, 863, 864, 865, 872, 875, 879, 881, 882, 886, 888, 890, 892, 894, 897, 904, 906, 907, 909, 910, 911, 914, 918, 921, 922, 925, 927, 928, 929, 932, 937, 940, 941, 948, 949, 951, 956, 961, \
963, 965, 967, 968, 969, 971, 973, 980, 982, 985, 986, 988, 989, 990, 991, 994, 995, 1004, 1011, 1015, 1016, 1017, 1019, 1021, 1022, 1023, 1025, 1026, 1028, 1031, 1035, 1037, 1038, 1043, 1045, 1046, 1048, 1050, 1052, 1057, 1060, 1061, 1064, 1065, 1068, 1070, 1076, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1089, 1091, 1095, 1097, 1099, 1104, 1106, 1107, 1116, 1121, 1122, 1125, 1126, 1133, 1134, 1135, 1137, 1146, 1147, 1149, 1150, 1153, 1156, 1160, 1163, 1165, 1167, 1169, 1170, 1172, 1177, 1179, 1180, \
1183, 1184, 1186, 1191, 1193, 1195, 1201, 1203, 1207, 1209, 1210, 1212, 1213, 1214, 1215, 1216, 1219, 1220, 1222, 1223, 1230, 1237, 1239, 1240, 1241, 1244, 1246, 1247, 1248, 1249, 1252, 1253, 1255, 1258, 1259, 1261, 1263, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1277, 1278, 1282, 1283, 1285, 1286, 1287, 1293, 1298, 1303, 1304, 1305, 1311, 1313, 1314, 1315, 1317, 1318, 1319, 1322, 1323, 1324, 1325, 1326, 1327, 1329, 1330, 1332, 1333, 1336, 1338, 1340, 1341, 1342, 1344, 1345, 1346, 1347, 1348, 1356, \
1361, 1362, 1364, 1365, 1368, 1371, 1374, 1376, 1377, 1383, 1386, 1387, 1388, 1390, 1391, 1392, 1394, 1397, 1398, 1399, 1400, 1402, 1403, 1405, 1409, 1412, 1414, 1416, 1417, 1420, 1422, 1427, 1429, 1438, 1447, 1448, 1450, 1459, 1460, 1463, 1464, 1469, 1472, 1473, 1474, 1478, 1480, 1486, 1487, 1490, 1492, 1495, 1496, 1499, 1510, 1515, 1517, 1519, 1520, 1521, 1522, 1523, 1526, 1529, 1533, 1538, 1539, 1540, 1546, 1547, 1548, 1549, 1553, 1559, 1560, 1567, 1568, 1584, 1586, 1590, 1593, 1594, 1600, 1601, \
1602, 1606, 1610, 1611, 1613, 1617, 1618, 1619, 1622, 1624, 1629, 1632, 1634, 1635, 1636, 1647, 1652, 1654, 1656, 1657, 1663, 1664, 1668, 1671, 1676, 1677, 1681, 1682, 1689, 1695, 1699, 1700, 1701, 1703, 1704, 1705, 1711, 1712, 1715, 1716, 1717, 1720, 1730, 1732, 1733, 1737, 1738, 1742, 1744, 1745, 1746, 1747, 1751, 1752, 1753, 1754, 1756, 1760, 1765, 1766, 1768, 1772, 1774, 1775, 1780, 1782, 1783, 1785, 1786, 1788, 1789, 1792, 1793, 1794, 1796, 1799, 1803, 1804, 1808, 1809, 1810, 1815, 1819, 1820, \
1822, 1829, 1833, 1835, 1836, 1840, 1841, 1844, 1847, 1851, 1855, 1859, 1863, 1868, 1871, 1874, 1879, 1880, 1883, 1884, 1889, 1890, 1891, 1892, 1897, 1901, 1902, 1906, 1907, 1913, 1916, 1920, 1927, 1940, 1941, 1950, 1954, 1956, 1968, 1970, 1978, 1980, 1981, 1983, 1984, 1989, 1991, 1997, 1998, 2014, 2019, 2023, 2024, 2029, 2034, 2036, 2039, 2041, 2046, 2054, 2056, 2057, 2060, 2067, 2068, 2073, 2076, 2078, 2080, 2082, 2086, 2090, 2093, 2098, 2103, 2104, 2107, 2114, 2115, 2117, 2127, 2130, 2132, 2133, \
2136, 2137, 2140, 2148, 2149, 2151, 2154, 2157, 2166, 2172, 2173, 2176, 2178, 2185, 2190, 2191, 2192, 2193, 2199, 2202, 2207, 2210, 2211, 2212, 2213, 2217, 2221, 2226, 2228, 2230, 2233, 2234, 2236, 2237, 2239, 2240, 2243, 2244, 2245, 2256, 2257, 2258, 2260, 2262, 2264, 2268, 2270, 2274, 2275, 2278, 2285, 2287, 2290, 2296, 2298, 2299, 2304, 2306, 2307, 2308, 2311, 2313, 2318, 2320, 2324, 2326, 2327, 2329, 2330, 2335, 2336, 2345, 2348, 2350, 2351, 2352, 2358, 2362, 2365, 2370, 2375, 2380, 2382, 2385, \
2401, 2404, 2411, 2413, 2414, 2418, 2432, 2440, 2441, 2445, 2446, 2447, 2451, 2452, 2453, 2458, 2461, 2466, 2470, 2476, 2479, 2482, 2484, 2487, 2488, 2490, 2492, 2496, 2497, 2498, 2499, 2508, 2513, 2533, 2534, 2536, 2542, 2543, 2544, 2547, 2548, 2549, 2552, 2555, 2558, 2559, 2560, 2563, 2564, 2572, 2574, 2575, 2576, 2577, 2579, 2582, 2585, 2587, 2590, 2591, 2594, 2595, 2596, 2600, 2607, 2609, 2613, 2617, 2619, 2623, 2627, 2630, 2631, 2632, 2636, 2637, 2642, 2643, 2649, 2655, 2659, 2664, 2667, 2668, \
2670, 2673, 2674, 2675, 2676, 2682, 2683, 2686, 2688, 2690, 2692, 2693, 2699, 2702, 2704, 2705, 2713, 2714, 2718, 2719, 2720, 2721, 2722, 2727, 2729, 2731, 2732, 2734, 2735, 2736, 2737, 2738, 2739, 2744, 2746, 2747, 2750, 2752, 2755, 2766, 2767, 2772, 2775, 2780, 2785, 2786, 2787, 2790, 2791, 2792, 2796, 2801, 2802, 2805, 2807, 2809, 2817, 2819, 2827, 2829, 2831, 2834, 2836, 2839, 2841, 2843, 2845, 2846, 2848, 2852, 2853, 2854, 2858, 2863, 2867, 2877, 2878, 2879, 2883, 2888, 2890, 2891, 2897, 2902, \
2906, 2908, 2909, 2912, 2913, 2914, 2917, 2920, 2923, 2924, 2927, 2930, 2931, 2935, 2937, 2938, 2939, 2940, 2947, 2949, 2952, 2960, 2962, 2964, 2965, 2968, 2970, 2972, 2973, 2979, 2981, 2984, 2988, 2992, 2993, 2997, 2998, 2999, 3002, 3013, 3014, 3015, 3024, 3030, 3033, 3038, 3042, 3043, 3044, 3046, 3051, 3059, 3060, 3065, 3070, 3085, 3086, 3088, 3090, 3093, 3094, 3099, 3103, 3104, 3111, 3112, 3113, 3114, 3117, 3118, 3125, 3131, 3135, 3138, 3140, 3142, 3143, 3144, 3145, 3147, 3149, 3150, 3152, 3153, \
3155, 3159, 3160, 3163, 3167, 3168, 3169, 3170, 3178, 3182, 3188, 3190, 3192, 3193, 3194, 3198, 3200, 3201, 3204, 3205, 3206, 3210, 3211, 3213, 3217, 3219, 3220, 3229, 3232, 3234, 3237, 3238, 3241, 3242, 3243, 3245, 3246, 3247, 3248, 3250, 3252, 3255, 3257, 3259, 3261, 3262, 3264, 3265, 3266, 3268, 3269, 3271, 3272, 3273, 3281, 3284, 3286, 3291, 3293, 3299, 3300, 3302, 3306, 3309, 3310, 3312, 3314, 3316, 3322, 3324, 3325, 3326, 3328, 3330, 3331, 3335, 3342, 3345, 3346, 3352, 3353, 3357, 3358, 3360, \
3364, 3365, 3367, 3369, 3370, 3371, 3375, 3379, 3380, 3383, 3384, 3387, 3391, 3396, 3399, 3401, 3403, 3407, 3408, 3412, 3413, 3414, 3421, 3422, 3423, 3424, 3429, 3430, 3431, 3434, 3435, 3436, 3437, 3447, 3448, 3450, 3452, 3455, 3461, 3464, 3466, 3470, 3474, 3476, 3477, 3481, 3483, 3484, 3485, 3487, 3489, 3490, 3491, 3492, 3493, 3495, 3498, 3501, 3502, 3503, 3504, 3506, 3508, 3509, 3512, 3513, 3515, 3518, 3519, 3520, 3521, 3522, 3527, 3531, 3532, 3534, 3535, 3537, 3538, 3539, 3540, 3551, 3552, 3561, \
3562, 3564, 3571, 3572, 3574, 3575, 3576, 3578, 3579, 3580, 3581, 3583, 3585, 3586, 3589, 3596, 3597, 3600, 3603, 3604, 3608, 3609, 3610, 3618, 3622, 3625, 3627, 3631, 3634, 3636, 3638, 3639, 3647, 3648, 3650, 3651, 3657, 3661, 3663, 3670, 3671, 3674, 3675, 3676, 3677, 3678, 3680, 3682, 3683, 3685, 3687, 3689, 3691, 3693, 3696, 3702, 3703, 3705, 3707, 3708, 3710, 3711, 3718, 3721, 3722, 3727, 3728, 3729, 3734, 3737, 3740, 3743, 3744, 3746, 3749, 3750, 3752, 3756, 3757, 3761, 3766, 3767, 3768, 3772, \
3773, 3774, 3777, 3785, 3790, 3791, 3795, 3797, 3798, 3799, 3800, 3801, 3803, 3810, 3814, 3815, 3818, 3820, 3822, 3824, 3826, 3827, 3829, 3830, 3831, 3833, 3835, 3836, 3838, 3842, 3844, 3845, 3850, 3851, 3859, 3867, 3868, 3869, 3872, 3875, 3877, 3879, 3881, 3882, 3885, 3886, 3892, 3893, 3895, 3897, 3901, 3902, 3904, 3907, 3910, 3911, 3912, 3915, 3916, 3917, 3920, 3921, 3922, 3923, 3927, 3931, 3933, 3937, 3939, 3940, 3941, 3942, 3943, 3946, 3947, 3948, 3952, 3954, 3955, 3956, 3959, 3961, 3973, 3974, \
3975, 3982, 3986, 3990, 3993, 3995, 3996, 3998, 4003, 4005, 4006, 4009, 4010, 4015, 4020, 4029, 403\", 
 .     base::quote(.local(x, ...)))"
}

I followed the tutorial in the vignette and transposed the counts matrix so that rownames are cell IDs, and kept the reference dataframe so that rownames are gene names. I'm not sure what could be the issue. One guess: the provided mouse brain reference doesn't seem to have the same gene names as the 1000-plex assay:

table(rownames(mouse_brain_ref) %in% colnames(raw))

This gives the following output:

FALSE  TRUE 
  766   184 

What is the source of this error? Is it related to the conflict in gene names? And is there a mouse brain reference with closer alignment to the genes in this particular 1000-plex assay?

[github-actions]

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