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SpikeInterface
Mountainsort 5 on Neuropixel Data
Hi, I first preprocessed the neuropixel data from spikeglx with highpass filter, phase shift, concatenation, and motion correction.
I passed the data to multiple sorters including Kilosrot 3, kilosort 2.5 and moutainsort 5.
I simply ran the sorter using:
mountainsort_test = si.run_sorter(sorter_name='mountainsort5', recording=probe0_preprocessed_corrected, output_folder=dst_folder+'/sorters/mountainsort5/probe0',docker_image=True)
Kilosorts ran smoothly on my data but moutainsort5 has the following error that doesnt say what was wrong: `SpikeSortingError Traceback (most recent call last) Cell In[25], line 1 ----> 1 mountainsort_test = si.run_sorter(sorter_name='mountainsort5', recording=probe0_preprocessed_corrected, output_folder=dst_folder+'/sorters/mountainsort5/probe0',docker_image=True)
File ~/anaconda3/envs/si_env/lib/python3.10/site-packages/spikeinterface/sorters/runsorter.py:141, in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, **sorter_params) 139 else: 140 container_image = singularity_image --> 141 return run_sorter_container( 142 container_image=container_image, 143 mode=mode, 144 **common_kwargs, 145 ) 147 return run_sorter_local(**common_kwargs)
File ~/anaconda3/envs/si_env/lib/python3.10/site-packages/spikeinterface/sorters/runsorter.py:606, in run_sorter_container(sorter_name, recording, mode, container_image, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, delete_container_files, extra_requirements, **sorter_params) 604 if run_error: 605 if raise_error: --> 606 raise SpikeSortingError(f"Spike sorting in {mode} failed with the following error:\n{run_sorter_output}") 607 else: 608 if with_output:
SpikeSortingError: Spike sorting in docker failed with the following error: Number of channels: 339 Number of timepoints: 9000000 Sampling frequency: 30000.0 Hz Channel 0: [16. 40.] Channel 1: [48. 40.] Channel 2: [ 0. 60.] Channel 3: [32. 60.] Channel 4: [16. 80.] Channel 5: [48. 80.] Channel 6: [ 0. 100.] Channel 7: [ 32. 100.] Channel 8: [ 16. 120.] Channel 9: [ 48. 120.] Channel 10: [ 0. 140.] Channel 11: [ 32. 140.] Channel 12: [ 16. 160.] Channel 13: [ 48. 160.] Channel 14: [ 0. 180.] Channel 15: [ 32. 180.] Channel 16: [ 16. 200.] Channel 17: [ 48. 200.] Channel 18: [ 0. 220.] Channel 19: [ 32. 220.] Channel 20: [ 16. 240.] Channel 21: [ 48. 240.] Channel 22: [ 0. 260.] Channel 23: [ 32. 260.] Channel 24: [ 16. 280.] Channel 25: [ 48. 280.] Channel 26: [ 0. 300.] Channel 27: [ 32. 300.] Channel 28: [ 16. 320.] Channel 29: [ 48. 320.] Channel 30: [ 0. 340.] Channel 31: [ 32. 340.] Channel 32: [ 16. 360.] Channel 33: [ 48. 360.] Channel 34: [ 0. 380.] Channel 35: [ 32. 380.] Channel 36: [ 16. 400.] Channel 37: [ 48. 400.] Channel 38: [ 0. 420.] Channel 39: [ 32. 420.] Channel 40: [ 16. 440.] Channel 41: [ 48. 440.] Channel 42: [ 0. 460.] Channel 43: [ 32. 460.] Channel 44: [ 16. 480.] Channel 45: [ 48. 480.] Channel 46: [ 0. 500.] Channel 47: [ 32. 500.] Channel 48: [ 16. 520.] Channel 49: [ 48. 520.] Channel 50: [ 0. 540.] Channel 51: [ 32. 540.] Channel 52: [ 16. 560.] Channel 53: [ 48. 560.] Channel 54: [ 0. 580.] Channel 55: [ 32. 580.] Channel 56: [ 16. 600.] Channel 57: [ 48. 600.] Channel 58: [ 0. 620.] Channel 59: [ 32. 620.] Channel 60: [ 16. 640.] Channel 61: [ 48. 640.] Channel 62: [ 0. 660.] Channel 63: [ 32. 660.] Channel 64: [ 16. 680.] Channel 65: [ 48. 680.] Channel 66: [ 0. 700.] Channel 67: [ 32. 700.] Channel 68: [ 16. 720.] Channel 69: [ 48. 720.] Channel 70: [ 0. 740.] Channel 71: [ 32. 740.] Channel 72: [ 16. 760.] Channel 73: [ 48. 760.] Channel 74: [ 0. 780.] Channel 75: [ 32. 780.] Channel 76: [ 16. 800.] Channel 77: [ 48. 800.] Channel 78: [ 0. 820.] Channel 79: [ 32. 820.] Channel 80: [ 16. 840.] Channel 81: [ 48. 840.] Channel 82: [ 0. 860.] Channel 83: [ 32. 860.] Channel 84: [ 16. 880.] Channel 85: [ 48. 880.] Channel 86: [ 0. 900.] Channel 87: [ 32. 900.] Channel 88: [ 16. 920.] Channel 89: [ 48. 920.] Channel 90: [ 0. 940.] Channel 91: [ 32. 940.] Channel 92: [ 16. 960.] Channel 93: [ 48. 960.] Channel 94: [ 0. 980.] Channel 95: [ 32. 980.] Channel 96: [ 16. 1000.] Channel 97: [ 48. 1000.] Channel 98: [ 0. 1020.] Channel 99: [ 32. 1020.] Channel 100: [ 16. 1040.] Channel 101: [ 48. 1040.] Channel 102: [ 0. 1060.] Channel 103: [ 32. 1060.] Channel 104: [ 16. 1080.] Channel 105: [ 48. 1080.] Channel 106: [ 0. 1100.] Channel 107: [ 32. 1100.] Channel 108: [ 16. 1120.] Channel 109: [ 48. 1120.] Channel 110: [ 0. 1140.] Channel 111: [ 32. 1140.] Channel 112: [ 16. 1160.] Channel 113: [ 48. 1160.] Channel 114: [ 0. 1180.] Channel 115: [ 32. 1180.] Channel 116: [ 16. 1200.] Channel 117: [ 48. 1200.] Channel 118: [ 0. 1220.] Channel 119: [ 32. 1220.] Channel 120: [ 16. 1240.] Channel 121: [ 48. 1240.] Channel 122: [ 0. 1260.] Channel 123: [ 32. 1260.] Channel 124: [ 16. 1280.] Channel 125: [ 48. 1280.] Channel 126: [ 0. 1300.] Channel 127: [ 32. 1300.] Channel 128: [ 16. 1320.] Channel 129: [ 48. 1320.] Channel 130: [ 0. 1340.] Channel 131: [ 32. 1340.] Channel 132: [ 16. 1360.] Channel 133: [ 48. 1360.] Channel 134: [ 0. 1380.] Channel 135: [ 32. 1380.] Channel 136: [ 16. 1400.] Channel 137: [ 48. 1400.] Channel 138: [ 0. 1420.] Channel 139: [ 32. 1420.] Channel 140: [ 16. 1440.] Channel 141: [ 48. 1440.] Channel 142: [ 0. 1460.] Channel 143: [ 32. 1460.] Channel 144: [ 16. 1480.] Channel 145: [ 48. 1480.] Channel 146: [ 0. 1500.] Channel 147: [ 32. 1500.] Channel 148: [ 16. 1520.] Channel 149: [ 48. 1520.] Channel 150: [ 0. 1540.] Channel 151: [ 32. 1540.] Channel 152: [ 16. 1560.] Channel 153: [ 48. 1560.] Channel 154: [ 0. 1580.] Channel 155: [ 32. 1580.] Channel 156: [ 16. 1600.] Channel 157: [ 48. 1600.] Channel 158: [ 0. 1620.] Channel 159: [ 32. 1620.] Channel 160: [ 16. 1640.] Channel 161: [ 48. 1640.] Channel 162: [ 0. 1660.] Channel 163: [ 32. 1660.] Channel 164: [ 16. 1680.] Channel 165: [ 48. 1680.] Channel 166: [ 0. 1700.] Channel 167: [ 32. 1700.] Channel 168: [ 16. 1720.] Channel 169: [ 48. 1720.] Channel 170: [ 0. 1740.] Channel 171: [ 32. 1740.] Channel 172: [ 16. 1760.] Channel 173: [ 48. 1760.] Channel 174: [ 0. 1780.] Channel 175: [ 32. 1780.] Channel 176: [ 16. 1800.] Channel 177: [ 48. 1800.] Channel 178: [ 0. 1820.] Channel 179: [ 32. 1820.] Channel 180: [ 16. 1840.] Channel 181: [ 48. 1840.] Channel 182: [ 0. 1860.] Channel 183: [ 32. 1860.] Channel 184: [ 16. 1880.] Channel 185: [ 48. 1880.] Channel 186: [ 0. 1900.] Channel 187: [ 16. 1920.] Channel 188: [ 48. 1920.] Channel 189: [ 0. 1940.] Channel 190: [ 32. 1940.] Channel 191: [ 16. 1960.] Channel 192: [ 48. 1960.] Channel 193: [ 0. 1980.] Channel 194: [ 32. 1980.] Channel 195: [ 16. 2000.] Channel 196: [ 48. 2000.] Channel 197: [ 0. 2020.] Channel 198: [ 32. 2020.] Channel 199: [ 16. 2040.] Channel 200: [ 48. 2040.] Channel 201: [ 0. 2060.] Channel 202: [ 32. 2060.] Channel 203: [ 16. 2080.] Channel 204: [ 48. 2080.] Channel 205: [ 0. 2100.] Channel 206: [ 32. 2100.] Channel 207: [ 16. 2120.] Channel 208: [ 48. 2120.] Channel 209: [ 0. 2140.] Channel 210: [ 32. 2140.] Channel 211: [ 16. 2160.] Channel 212: [ 48. 2160.] Channel 213: [ 0. 2180.] Channel 214: [ 32. 2180.] Channel 215: [ 16. 2200.] Channel 216: [ 48. 2200.] Channel 217: [ 0. 2220.] Channel 218: [ 32. 2220.] Channel 219: [ 16. 2240.] Channel 220: [ 48. 2240.] Channel 221: [ 0. 2260.] Channel 222: [ 32. 2260.] Channel 223: [ 16. 2280.] Channel 224: [ 48. 2280.] Channel 225: [ 0. 2300.] Channel 226: [ 32. 2300.] Channel 227: [ 16. 2320.] Channel 228: [ 48. 2320.] Channel 229: [ 0. 2340.] Channel 230: [ 32. 2340.] Channel 231: [ 16. 2360.] Channel 232: [ 48. 2360.] Channel 233: [ 0. 2380.] Channel 234: [ 32. 2380.] Channel 235: [ 16. 2400.] Channel 236: [ 48. 2400.] Channel 237: [ 0. 2420.] Channel 238: [ 32. 2420.] Channel 239: [ 16. 2440.] Channel 240: [ 48. 2440.] Channel 241: [ 0. 2460.] Channel 242: [ 32. 2460.] Channel 243: [ 16. 2480.] Channel 244: [ 48. 2480.] Channel 245: [ 0. 2500.] Channel 246: [ 32. 2500.] Channel 247: [ 16. 2520.] Channel 248: [ 48. 2520.] Channel 249: [ 0. 2540.] Channel 250: [ 32. 2540.] Channel 251: [ 16. 2560.] Channel 252: [ 48. 2560.] Channel 253: [ 0. 2580.] Channel 254: [ 32. 2580.] Channel 255: [ 16. 2600.] Channel 256: [ 48. 2600.] Channel 257: [ 0. 2620.] Channel 258: [ 32. 2620.] Channel 259: [ 16. 2640.] Channel 260: [ 48. 2640.] Channel 261: [ 0. 2660.] Channel 262: [ 32. 2660.] Channel 263: [ 16. 2680.] Channel 264: [ 48. 2680.] Channel 265: [ 0. 2700.] Channel 266: [ 32. 2700.] Channel 267: [ 16. 2720.] Channel 268: [ 48. 2720.] Channel 269: [ 0. 2740.] Channel 270: [ 32. 2740.] Channel 271: [ 16. 2760.] Channel 272: [ 48. 2760.] Channel 273: [ 0. 2780.] Channel 274: [ 32. 2780.] Channel 275: [ 16. 2800.] Channel 276: [ 48. 2800.] Channel 277: [ 0. 2820.] Channel 278: [ 32. 2820.] Channel 279: [ 16. 2840.] Channel 280: [ 48. 2840.] Channel 281: [ 0. 2860.] Channel 282: [ 32. 2860.] Channel 283: [ 16. 2880.] Channel 284: [ 48. 2880.] Channel 285: [ 0. 2900.] Channel 286: [ 32. 2900.] Channel 287: [ 16. 2920.] Channel 288: [ 48. 2920.] Channel 289: [ 0. 2940.] Channel 290: [ 32. 2940.] Channel 291: [ 16. 2960.] Channel 292: [ 48. 2960.] Channel 293: [ 0. 2980.] Channel 294: [ 32. 2980.] Channel 295: [ 16. 3000.] Channel 296: [ 48. 3000.] Channel 297: [ 0. 3020.] Channel 298: [ 32. 3020.] Channel 299: [ 16. 3040.] Channel 300: [ 48. 3040.] Channel 301: [ 0. 3060.] Channel 302: [ 32. 3060.] Channel 303: [ 16. 3080.] Channel 304: [ 48. 3080.] Channel 305: [ 0. 3100.] Channel 306: [ 32. 3100.] Channel 307: [ 16. 3120.] Channel 308: [ 48. 3120.] Channel 309: [ 0. 3140.] Channel 310: [ 32. 3140.] Channel 311: [ 16. 3160.] Channel 312: [ 48. 3160.] Channel 313: [ 0. 3180.] Channel 314: [ 32. 3180.] Channel 315: [ 16. 3200.] Channel 316: [ 48. 3200.] Channel 317: [ 0. 3220.] Channel 318: [ 32. 3220.] Channel 319: [ 16. 3240.] Channel 320: [ 48. 3240.] Channel 321: [ 0. 3260.] Channel 322: [ 32. 3260.] Channel 323: [ 16. 3280.] Channel 324: [ 48. 3280.] Channel 325: [ 0. 3300.] Channel 326: [ 32. 3300.] Channel 327: [ 16. 3320.] Channel 328: [ 48. 3320.] Channel 329: [ 0. 3340.] Channel 330: [ 32. 3340.] Channel 331: [ 16. 3360.] Channel 332: [ 48. 3360.] Channel 333: [ 0. 3380.] Channel 334: [ 32. 3380.] Channel 335: [ 16. 3400.] Channel 336: [ 48. 3400.] Channel 337: [ 0. 3420.] Channel 338: [ 32. 3420.] Loading traces Detecting spikes
Adjacency for detect spikes with channel radius 200 [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39], [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41], [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42], [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43], [4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44], [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45], [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46], [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47], [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48], [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49], [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51], [12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52], [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53], [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54], [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55], [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56], [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57], [18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58], [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 59], [20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60], [21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61], [22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62], [23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63], [24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64], [25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65], [26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66], [27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67], [28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68], [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69], [30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70], [31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71], [32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72], [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73], [34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74], [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 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140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158], [119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141,
It's hard to say what could be going wrong. Maybe it's running out of memory?
It might be helpful to try with a smaller subset of the data -- perhaps and/or a channel slice or a time slice.
@atombysx
You can do that with this (e.g., running on 10 minutes data):
probe0_preprocessed_corrected_stub = probe0_preprocessed_corrected.frame_slice(
start_frame=0, end_frame=int(600 * probe0_preprocessed_corrected.sampling_frequency)
)
and then use the run_sorter function with the probe0_preprocessed_corrected_stub object
@atombysx
You can do that with this (e.g., running on 10 minutes data):
probe0_preprocessed_corrected_stub = probe0_preprocessed_corrected.frame_slice( start_frame=0, end_frame=int(600 * probe0_preprocessed_corrected.sampling_frequency) )and then use the
run_sorterfunction with theprobe0_preprocessed_corrected_stubobject
Hi I just tried what you said:
probe0_preprocessed_corrected_stub = probe0_preprocessed_corrected.frame_slice( start_frame=0, end_frame=int(600 * probe0_preprocessed_corrected.sampling_frequency) )
job_list = [ {'sorter_name':'mountainsort5','recording':probe0_preprocessed_corrected_stub,'output_folder':dst_folder+'/probe0/sorters/mountainsort5/','docker_image':True}] probe0_fragment_moutainsort5 = si.run_sorter_jobs(job_list = job_list, engine = 'loop')
The same error happens.
It was only successful when I reduced it to 1 min slice....
We have 64GB RAM on this machine,
@magland did you have any further thoughts on this? @atombysx were you able to find any other workaround? 🤔
@magland did you have any further thoughts on this? @atombysx were you able to find any other workaround? 🤔
I'm not sure. I guess we still don't know if it's a memory issue...
Since this is ultimately an issue interacting with MS5 I'll close this here. Feel free to open issues on the sorter repo directly for more help.
