INFO 2025-06-26 21:34:13,776 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 21:34:13,776 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB Spring 2015 - ctdToUse = ctd1 INFO 2025-06-26 21:34:13,776 process.py process_mission():449 [1] Processing CANON May 2015 mission 2015.156.00 by user docker_user on host 355841a7028c INFO 2025-06-26 21:34:13,776 process.py download_process():165 [1] Download and processing steps for 2015.156.00 INFO 2025-06-26 21:34:13,776 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2015/2015156/2015.156.00 INFO 2025-06-26 21:34:13,776 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2015/2015156/2015.156.00 to /data/auv_data/dorado/missionlogs/2015.156.00 INFO 2025-06-26 21:34:18,102 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2015.156.00 INFO 2025-06-26 21:34:18,102 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/ctdDriver.log (9975174 bytes) INFO 2025-06-26 21:34:18,922 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/ctdDriver2.log (9975263 bytes) INFO 2025-06-26 21:34:19,653 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/gps.log (114116 bytes) INFO 2025-06-26 21:34:19,673 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/hydroscatlog.log (8731990 bytes) INFO 2025-06-26 21:34:20,589 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.156.00/hydroscatlog.log: [24110] INFO 2025-06-26 21:34:20,618 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/navigation.log (37388610 bytes) INFO 2025-06-26 21:34:23,304 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/isuslog.log (644949 bytes) INFO 2025-06-26 21:34:23,369 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/parosci.log (12252230 bytes) INFO 2025-06-26 21:34:24,397 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/tailCone.log (6241339 bytes) INFO 2025-06-26 21:34:25,169 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/biolume.log (7265426 bytes) INFO 2025-06-26 21:34:25,868 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 21:34:26,226 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.12 seconds INFO 2025-06-26 21:34:26,226 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2015.156.00/lopc.bin (208243 bytes) INFO 2025-06-26 21:34:26,226 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 21:34:26 2025 INFO 2025-06-26 21:34:26,227 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2015.156.00/parosci.nc INFO 2025-06-26 21:34:26,227 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 21:34:26,227 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2015.156.00/parosci.nc INFO 2025-06-26 21:34:26,230 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1433514753.3, sensor_off_time = 1433540755.8 INFO 2025-06-26 21:34:26,231 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 26002 seconds. Expecting to read 52004 L frames from the lopc.bin file. INFO 2025-06-26 21:34:26,231 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 52004 records from the lopc.bin file. INFO 2025-06-26 21:34:26,533 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2015-06-05 14:32:33 Z and endTime = 2015-06-05 21:45:55 Z with 52004 records expected to be read from lopc.bin INFO 2025-06-26 21:34:26,534 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2015.156.00/lopc.bin INFO 2025-06-26 21:34:26,534 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2015.156.00/lopc.nc INFO 2025-06-26 21:34:26,552 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 21:34:26,552 lopcToNetCDF.py main():2346 [1] lFrameCount = 0, mFrameCount = 0 ERROR 2025-06-26 21:34:26,552 lopcToNetCDF.py main():2376 [1] KeyError: sampleCountList or cFrameEsecsList not found in self.dataStructure INFO 2025-06-26 21:34:26,552 lopcToNetCDF.py main():2379 [1] No lopc.nc file created INFO 2025-06-26 21:34:26,552 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 21:34:26 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 21:34:26,553 process.py calibrate():227 [1] Calibration steps for 2015.156.00 INFO 2025-06-26 21:34:26,767 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 21:34:26,769 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 21:34:27,668 calibrate.py _nudge_pos():1806 [1] 128: 0.030 0.0006172 -0.0002615 2135 7.11 12.902 -6.812 2015-06-05T14:41:39.908231680 INFO 2025-06-26 21:34:28,384 calibrate.py _nudge_pos():1806 [1] 200: 0.040 0.0031867 -0.0016725 11555 38.51 12.302 -8.047 2015-06-05T15:21:21.905053952 INFO 2025-06-26 21:34:29,202 calibrate.py _nudge_pos():1806 [1] 275: 0.040 0.0030436 -0.0015351 12380 41.26 10.964 -6.894 2015-06-05T16:03:51.910366464 INFO 2025-06-26 21:34:29,748 calibrate.py _nudge_pos():1806 [1] 330: 0.050 0.0030629 -0.0013811 11670 38.90 11.702 -6.579 2015-06-05T16:43:39.906777600 INFO 2025-06-26 21:34:30,465 calibrate.py _nudge_pos():1806 [1] 405: 0.060 0.0031322 -0.0015120 11450 38.16 12.195 -7.342 2015-06-05T17:23:03.904832512 INFO 2025-06-26 21:34:30,486 calibrate.py _nudge_pos():1806 [1] 407: 0.050 -0.0000207 -0.0000172 140 0.46 -6.641 -6.864 2015-06-05T17:23:32.912845312 INFO 2025-06-26 21:34:31,281 calibrate.py _nudge_pos():1806 [1] 489: 0.060 0.0001184 -0.0005517 4670 15.56 1.130 -6.568 2015-06-05T17:40:27.903313920 INFO 2025-06-26 21:34:31,881 calibrate.py _nudge_pos():1806 [1] 551: 0.060 -0.0043521 -0.0004070 10795 35.98 -17.970 -2.096 2015-06-05T18:17:27.911233024 INFO 2025-06-26 21:34:31,999 calibrate.py _nudge_pos():1806 [1] 563: 0.060 0.0000073 -0.0000131 15 0.05 23.169 -52.186 2015-06-05T18:17:41.910273792 INFO 2025-06-26 21:34:32,562 calibrate.py _nudge_pos():1806 [1] 621: 0.070 -0.0044808 -0.0002187 10805 36.01 -18.484 -1.125 2015-06-05T18:54:39.908330752 INFO 2025-06-26 21:34:33,276 calibrate.py _nudge_pos():1806 [1] 695: 0.080 -0.0047343 -0.0000128 11515 38.38 -18.324 -0.062 2015-06-05T19:34:15.905563648 INFO 2025-06-26 21:34:33,943 calibrate.py _nudge_pos():1806 [1] 764: 0.080 -0.0046627 -0.0001712 10940 36.46 -18.995 -0.870 2015-06-05T20:11:51.911016704 INFO 2025-06-26 21:34:34,617 calibrate.py _nudge_pos():1806 [1] 830: 0.080 -0.0010523 0.0000131 2675 8.91 -17.536 0.273 2015-06-05T20:21:51.909914112 INFO 2025-06-26 21:34:35,339 calibrate.py _nudge_pos():1806 [1] 904: 0.090 -0.0004322 -0.0019623 10555 35.18 -1.824 -10.336 2015-06-05T20:58:15.910299904 INFO 2025-06-26 21:34:36,046 calibrate.py _nudge_pos():1806 [1] 976: 0.100 -0.0012919 -0.0016050 10895 36.31 -5.282 -8.190 2015-06-05T21:35:45.906164480 INFO 2025-06-26 21:34:38,725 calibrate.py _nudge_pos():1806 [1] 1246: 0.100 -0.0000100 0.0000071 20 0.06 -23.333 20.837 2015-06-05T21:40:18.907462656 INFO 2025-06-26 21:34:39,202 calibrate.py _nudge_pos():1806 [1] 1289: 0.100 0.0000361 0.0000021 30 0.10 55.488 4.051 2015-06-05T21:41:06.904174592 INFO 2025-06-26 21:34:40,436 calibrate.py _nudge_pos():1806 [1] 1404: 0.100 -0.0000058 0.0000015 30 0.10 -8.894 2.860 2015-06-05T21:43:06.905953792 INFO 2025-06-26 21:34:42,180 calibrate.py _nudge_pos():1862 [1] 1526: - - - 4 0.01 - - INFO 2025-06-26 21:34:42,180 calibrate.py _nudge_pos():1868 [1] Points in final series = 129813 INFO 2025-06-26 21:34:59,286 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:35:00,284 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:35:01,234 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:35:01,237 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2015.156.00/ctd1.nc INFO 2025-06-26 21:35:01,239 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 21:35:01,240 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 21:35:01,240 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 21:35:02,369 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:35:03,444 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:35:03,447 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2015.156.00/ctd2.nc WARNING 2025-06-26 21:35:03,450 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (74343) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 21:35:03,450 calibrate.py _range_qc_combined_nc():898 [1] Setting 74343 ctd2_salinity values to NaN INFO 2025-06-26 21:35:03,451 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 21:35:03,451 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 21:35:03,492 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 21:35:04,702 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 300 301 302 303 304 305] INFO 2025-06-26 21:35:04,958 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 21:35:31,880 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.156.00 ERROR 2025-06-26 21:35:31,881 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.156.00 INFO 2025-06-26 21:35:31,984 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_cal.nc INFO 2025-06-26 21:35:32,164 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 21:35:32,170 process.py align():251 [1] Alignment steps for 2015.156.00 INFO 2025-06-26 21:35:32,220 align.py process_cal():139 [1] Processing dorado_2015.156.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2015.156.00 INFO 2025-06-26 21:35:32,259 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:35:32,264 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:35:32,353 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:35:32,360 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:35:32,447 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:35:32,454 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:35:32,523 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 21:35:32,523 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 21:35:32,578 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:35:32,587 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:35:32,720 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:32,728 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:32,850 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:32,858 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:32,980 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:32,988 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,112 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,120 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,215 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,221 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,295 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,300 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,373 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,378 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,452 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,457 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,531 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,536 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,618 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,694 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,699 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,777 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,782 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,858 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,863 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:33,940 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:33,945 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,024 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,030 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,108 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,115 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,193 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,199 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,279 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,285 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,364 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,370 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,465 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,473 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,599 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,607 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,730 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.156.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:35:34,738 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:35:34,880 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:35:34,983 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:35:35,087 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:35:35,184 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:35:35,263 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:35:35,388 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 21:35:36,125 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:35:36,189 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_align.nc INFO 2025-06-26 21:35:36,380 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 21:35:36,385 process.py resample():273 [1] Resampling steps for 2015.156.00 INFO 2025-06-26 21:35:36,387 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 21:35:36,450 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_align.nc mission netCDF file INFO 2025-06-26 21:35:36,456 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_align.nc mission netCDF file INFO 2025-06-26 21:35:36,457 resample.py get_mission_start_end():1145 [1] navigation: 2015-06-05T14:33:13.372931840 to 2015-06-05T21:45:55.704390400 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 21:35:36,459 resample.py get_mission_start_end():1145 [1] hs2 : 2015-06-05T14:32:39.485253376 to 2015-06-05T21:45:55.844380928 (0 days 00:00:00 before mission_end) INFO 2025-06-26 21:35:36,461 resample.py get_mission_start_end():1145 [1] ctd1 : 2015-06-05T14:33:01.373753856 to 2015-06-05T21:45:55.624395776 (0 days 00:00:00.219985152 before mission_end) INFO 2025-06-26 21:35:36,463 resample.py get_mission_start_end():1145 [1] ctd2 : 2015-06-05T14:33:01.183766784 to 2015-06-05T21:45:55.774385408 (0 days 00:00:00.069995520 before mission_end) INFO 2025-06-26 21:35:36,464 resample.py get_mission_start_end():1145 [1] isus : 2015-06-05T14:33:46.650652160 to 2015-06-05T21:45:55.204424704 (0 days 00:00:00.639956224 before mission_end) INFO 2025-06-26 21:35:36,465 resample.py get_mission_start_end():1145 [1] biolume : 2015-06-05T14:32:32.435702016 to 2015-06-05T21:45:54.834415616 (0 days 00:00:01.009965312 before mission_end) INFO 2025-06-26 21:35:36,467 resample.py get_mission_start_end():1145 [1] tailcone : 2015-06-05T14:32:32.585725952 to 2015-06-05T21:45:55.744387584 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 21:35:36,468 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_align.nc mission netCDF file INFO 2025-06-26 21:35:36,468 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:36,918 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:36,985 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,033 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,082 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,126 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,169 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,209 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,249 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,286 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,323 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,360 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,398 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,435 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,473 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,513 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,552 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,591 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,632 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,672 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:37,988 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,029 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,069 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,110 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,151 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,170 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,191 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,216 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,240 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,265 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:38,274 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 21:35:38,274 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 21:35:39,233 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 21:35:39,441 resample.py add_biolume_proxies():633 [1] Zero flow values found: 26003 of 26003 - replaced with 350 ml/s INFO 2025-06-26 21:35:39,441 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 21:35:39,581 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 21:35:39,643 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 21:35:39,686 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 21:35:39,686 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 21:35:39,767 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 21:35:40,116 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_1S.nc INFO 2025-06-26 21:35:42,516 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 21:36:05,870 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2015.156.00/dorado_2015.156.00_1S_Gulper.txt INFO 2025-06-26 21:36:05,870 process.py archive():337 [1] Archiving steps for 2015.156.00 INFO 2025-06-26 21:36:05,870 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00, BASE_PATH = /data/auv_data INFO 2025-06-26 21:36:05,872 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00 files to /Volumes/AUVCTD/surveys/2015/netcdf INFO 2025-06-26 21:36:05,873 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.156.00_1S.nc INFO 2025-06-26 21:36:05,904 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_1S.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:36:05,905 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.156.00_cal.nc INFO 2025-06-26 21:36:06,076 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_cal.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:36:06,077 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.156.00_align.nc INFO 2025-06-26 21:36:06,321 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_align.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:36:06,360 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,393 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,401 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,433 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,550 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,558 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,594 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,620 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,706 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015156/2015.156.00 done. INFO 2025-06-26 21:36:06,706 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 21:36:06,709 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2015/odv/dorado_2015.156.00_1S_Gulper.txt INFO 2025-06-26 21:36:06,714 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2015.156.00/dorado_2015.156.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2015/odv done. INFO 2025-06-26 21:36:06,715 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.156.00/dorado_2015.156.00_processing.log /Volumes/AUVCTD/surveys/2015/netcdf