INFO 2025-06-26 20:23:33,580 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:23:33,580 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Summer 2014 in Bodega Bay - ctdToUse = ctd2 INFO 2025-06-26 20:23:33,580 process.py process_mission():449 [1] Processing SIMZ July 2014 mission 2014.210.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:23:33,580 process.py download_process():165 [1] Download and processing steps for 2014.210.01 INFO 2025-06-26 20:23:33,580 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014210/2014.210.01 INFO 2025-06-26 20:23:33,580 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014210/2014.210.01 to /data/auv_data/dorado/missionlogs/2014.210.01 INFO 2025-06-26 20:23:36,842 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.210.01 INFO 2025-06-26 20:23:36,842 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/ctdDriver.log (3329862 bytes) INFO 2025-06-26 20:23:37,073 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/ctdDriver2.log (3329855 bytes) INFO 2025-06-26 20:23:37,313 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/gps.log (40964 bytes) INFO 2025-06-26 20:23:37,324 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/hydroscatlog.log (2920282 bytes) INFO 2025-06-26 20:23:37,624 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/navigation.log (12456738 bytes) INFO 2025-06-26 20:23:38,515 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/isuslog.log (215189 bytes) INFO 2025-06-26 20:23:38,540 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.210.01/isuslog.log: [1 3] INFO 2025-06-26 20:23:38,541 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/parosci.log (4103078 bytes) INFO 2025-06-26 20:23:38,877 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/tailCone.log (2087419 bytes) INFO 2025-06-26 20:23:39,133 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/biolume.log (2433450 bytes) INFO 2025-06-26 20:23:39,371 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:23:39,492 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.65 seconds INFO 2025-06-26 20:23:39,493 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.01/lopc.bin (32238487 bytes) INFO 2025-06-26 20:23:39,493 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:23:39 2025 INFO 2025-06-26 20:23:39,493 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.210.01/parosci.nc INFO 2025-06-26 20:23:39,493 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:23:39,493 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.210.01/parosci.nc INFO 2025-06-26 20:23:39,496 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1406644892.3, sensor_off_time = 1406653588.4 INFO 2025-06-26 20:23:39,496 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8696 seconds. Expecting to read 17392 L frames from the lopc.bin file. INFO 2025-06-26 20:23:39,496 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 17392 records from the lopc.bin file. INFO 2025-06-26 20:23:39,599 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-07-29 14:41:32 Z and endTime = 2014-07-29 17:06:28 Z with 17392 records expected to be read from lopc.bin INFO 2025-06-26 20:23:39,599 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.210.01/lopc.bin INFO 2025-06-26 20:23:39,599 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.210.01/lopc.nc INFO 2025-06-26 20:23:39,600 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.210.01/lopc.nc INFO 2025-06-26 20:23:39,600 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.210.01 INFO 2025-06-26 20:23:39,600 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:23:39,678 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:23:39,678 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:23:39,678 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:23:41,011 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:23:41,012 process.py calibrate():227 [1] Calibration steps for 2014.210.01 INFO 2025-06-26 20:23:41,201 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 20:23:41,202 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:23:42,008 calibrate.py _nudge_pos():1806 [1] 127: 0.010 -0.0001810 -0.0001191 615 2.05 -12.845 -10.780 2014-07-29T14:45:40.256939776 INFO 2025-06-26 20:23:42,499 calibrate.py _nudge_pos():1806 [1] 181: 0.020 -0.0010853 -0.0000265 2225 7.41 -21.270 -0.663 2014-07-29T14:53:58.252824832 INFO 2025-06-26 20:23:43,144 calibrate.py _nudge_pos():1806 [1] 252: 0.010 0.0030531 0.0044807 10150 33.83 13.112 24.543 2014-07-29T15:28:58.258964480 INFO 2025-06-26 20:23:43,813 calibrate.py _nudge_pos():1806 [1] 325: 0.020 -0.0019749 0.0005307 11640 38.80 -7.399 2.535 2014-07-29T16:08:58.254553600 INFO 2025-06-26 20:23:44,198 calibrate.py _nudge_pos():1806 [1] 367: 0.030 -0.0047086 0.0007543 9875 32.91 -20.792 4.247 2014-07-29T16:42:34.256448000 INFO 2025-06-26 20:23:44,844 calibrate.py _nudge_pos():1806 [1] 437: 0.030 -0.0012766 0.0000778 4185 13.95 -13.302 1.034 2014-07-29T16:57:40.254382848 INFO 2025-06-26 20:23:45,500 calibrate.py _nudge_pos():1806 [1] 508: 0.030 -0.0005444 0.0006139 2050 6.83 -11.584 16.656 2014-07-29T17:05:40.251500800 INFO 2025-06-26 20:23:45,948 calibrate.py _nudge_pos():1862 [1] 509: - - - 0 0.00 - - INFO 2025-06-26 20:23:45,948 calibrate.py _nudge_pos():1868 [1] Points in final series = 43244 INFO 2025-06-26 20:23:46,345 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:46,690 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:23:46,952 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:23:46,953 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.210.01/ctd1.nc INFO 2025-06-26 20:23:46,955 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:23:46,955 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 20:23:46,955 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:23:47,279 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:23:47,538 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:23:47,540 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.210.01/ctd2.nc INFO 2025-06-26 20:23:47,541 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:23:47,541 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 20:23:47,541 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:23:47,867 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:23:48,231 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 300 301 302 303 304 305 306 307 308 309 310 311] INFO 2025-06-26 20:23:48,309 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:23:56,099 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.210.01 ERROR 2025-06-26 20:23:56,099 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.210.01 INFO 2025-06-26 20:23:56,135 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_cal.nc INFO 2025-06-26 20:23:56,222 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 20:23:56,229 process.py align():251 [1] Alignment steps for 2014.210.01 INFO 2025-06-26 20:23:56,259 align.py process_cal():139 [1] Processing dorado_2014.210.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.210.01 INFO 2025-06-26 20:23:56,274 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:56,277 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:56,312 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:56,315 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:56,349 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:56,351 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:56,371 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:23:56,371 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:23:56,384 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:56,387 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:56,421 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,424 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,455 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,458 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,498 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,501 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,531 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,534 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,564 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,567 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,596 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,599 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,629 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,631 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,661 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,664 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,694 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,697 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,727 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,730 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,761 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,764 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,796 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,826 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,829 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,859 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,862 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,893 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,896 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,926 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,929 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,960 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,963 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:56,994 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:56,997 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:57,029 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:57,032 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:57,062 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:57,065 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:57,096 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:57,099 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:57,130 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:57,132 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:57,170 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:57,199 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:57,228 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:57,259 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:23:57,290 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:23:57,337 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:23:57,566 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:57,593 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_align.nc INFO 2025-06-26 20:23:57,684 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 20:23:57,686 process.py resample():273 [1] Resampling steps for 2014.210.01 INFO 2025-06-26 20:23:57,687 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:23:57,715 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_align.nc mission netCDF file INFO 2025-06-26 20:23:57,720 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_align.nc mission netCDF file INFO 2025-06-26 20:23:57,721 resample.py get_mission_start_end():1145 [1] navigation: 2014-07-29T14:42:19.670681088 to 2014-07-29T17:06:28.258212096 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 20:23:57,722 resample.py get_mission_start_end():1145 [1] hs2 : 2014-07-29T14:41:36.403644928 to 2014-07-29T17:06:28.418201088 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:23:57,724 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-07-29T14:41:58.932101632 to 2014-07-29T17:06:28.228214272 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 20:23:57,725 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-07-29T14:41:58.792111104 to 2014-07-29T17:06:28.348206080 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 20:23:57,726 resample.py get_mission_start_end():1145 [1] isus : 2014-07-29T14:42:31.289884928 to 2014-07-29T17:06:27.898236672 (0 days 00:00:00.519964416 before mission_end) INFO 2025-06-26 20:23:57,728 resample.py get_mission_start_end():1145 [1] biolume : 2014-07-29T14:41:29.744067072 to 2014-07-29T17:06:27.848206080 (0 days 00:00:00.569995008 before mission_end) INFO 2025-06-26 20:23:57,729 resample.py get_mission_start_end():1145 [1] tailcone : 2014-07-29T14:41:33.143868160 to 2014-07-29T17:06:28.348206080 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 20:23:57,730 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_align.nc mission netCDF file INFO 2025-06-26 20:23:57,730 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,838 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,858 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,877 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,897 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,915 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,932 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,950 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,967 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:57,984 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,001 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,017 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,033 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,049 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,065 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,081 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,097 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,113 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,131 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,148 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,166 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,183 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,200 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,217 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,234 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,245 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,256 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,266 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,275 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,284 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,287 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:23:58,287 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:23:58,607 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:23:58,659 resample.py add_biolume_proxies():633 [1] Zero flow values found: 8699 of 8699 - replaced with 350 ml/s INFO 2025-06-26 20:23:58,660 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:23:58,692 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:23:58,706 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:23:58,719 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:23:58,719 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:23:58,743 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:58,900 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_1S.nc INFO 2025-06-26 20:24:00,590 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 20:24:11,423 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.210.01/dorado_2014.210.01_1S_Gulper.txt INFO 2025-06-26 20:24:11,423 process.py archive():337 [1] Archiving steps for 2014.210.01 INFO 2025-06-26 20:24:11,423 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:24:11,423 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:24:11,425 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.01_1S.nc INFO 2025-06-26 20:24:11,439 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:24:11,440 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.01_cal.nc INFO 2025-06-26 20:24:11,497 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:24:11,498 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.01_align.nc INFO 2025-06-26 20:24:11,583 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:24:11,599 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,613 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,617 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,629 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,663 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,668 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,684 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,697 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,722 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.01 done. INFO 2025-06-26 20:24:11,729 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:24:11,730 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.210.01_1S_Gulper.txt INFO 2025-06-26 20:24:11,735 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.210.01/dorado_2014.210.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:24:11,735 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.01/dorado_2014.210.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf