INFO 2025-06-26 19:20:13,149 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 19:20:13,149 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2012 - laps around ESP drifter - last one for this campaign - ctdToUse = ctd1 INFO 2025-06-26 19:20:13,150 process.py process_mission():449 [1] Processing CANON September 2012 mission 2012.258.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:20:13,150 process.py download_process():165 [1] Download and processing steps for 2012.258.00 INFO 2025-06-26 19:20:13,150 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012258/2012.258.00 INFO 2025-06-26 19:20:13,150 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012258/2012.258.00 to /data/auv_data/dorado/missionlogs/2012.258.00 INFO 2025-06-26 19:20:17,527 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.258.00 INFO 2025-06-26 19:20:17,527 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/ctdDriver.log (13157574 bytes) INFO 2025-06-26 19:20:18,723 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/ctdDriver2.log (13157471 bytes) INFO 2025-06-26 19:20:19,987 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/gps.log (281876 bytes) INFO 2025-06-26 19:20:20,060 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/hydroscatlog.log (11521210 bytes) INFO 2025-06-26 19:20:21,817 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/navigation.log (46608150 bytes) INFO 2025-06-26 19:20:25,961 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/isuslog.log (135221 bytes) INFO 2025-06-26 19:20:25,979 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/parosci.log (13963718 bytes) INFO 2025-06-26 19:20:27,163 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/tailCone.log (8233675 bytes) INFO 2025-06-26 19:20:28,200 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.258.00/biolume.log (9582298 bytes) INFO 2025-06-26 19:20:29,178 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:20:29,718 logs2netcdfs.py download_process_logs():807 [1] Time to process: 12.19 seconds WARNING 2025-06-26 19:20:29,718 process.py download_process():196 [1] No lopc.bin file for 2012.258.00 INFO 2025-06-26 19:20:29,718 process.py calibrate():227 [1] Calibration steps for 2012.258.00 INFO 2025-06-26 19:20:30,154 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 19:20:30,156 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:20:31,183 calibrate.py _nudge_pos():1806 [1] 109: 0.020 0.0004986 -0.0007210 1680 5.60 13.309 -23.872 2012-09-14T07:45:16.024984576 INFO 2025-06-26 19:20:32,598 calibrate.py _nudge_pos():1806 [1] 214: 0.020 0.0046214 -0.0113662 13995 46.65 14.802 -45.151 2012-09-14T08:33:40.026046976 INFO 2025-06-26 19:20:33,835 calibrate.py _nudge_pos():1806 [1] 328: 0.030 0.0020807 -0.0104378 14015 46.71 6.656 -41.404 2012-09-14T09:22:16.026287360 INFO 2025-06-26 19:20:34,716 calibrate.py _nudge_pos():1806 [1] 410: 0.030 -0.0005986 -0.0087143 13845 46.15 -1.938 -34.992 2012-09-14T10:09:46.031048448 INFO 2025-06-26 19:20:36,022 calibrate.py _nudge_pos():1806 [1] 535: 0.040 0.0018673 -0.0009935 4750 15.83 17.623 -11.630 2012-09-14T10:27:40.027474944 INFO 2025-06-26 19:20:36,081 calibrate.py _nudge_pos():1806 [1] 541: 0.040 0.0000502 -0.0000072 125 0.41 18.154 -3.213 2012-09-14T10:28:10.025419776 INFO 2025-06-26 19:20:37,288 calibrate.py _nudge_pos():1806 [1] 659: 0.050 0.0069920 -0.0012289 13725 45.75 22.826 -4.978 2012-09-14T11:15:52.029359104 INFO 2025-06-26 19:20:38,295 calibrate.py _nudge_pos():1806 [1] 754: 0.060 0.0064288 0.0000880 13750 45.83 20.940 0.356 2012-09-14T12:03:16.024531968 INFO 2025-06-26 19:20:39,407 calibrate.py _nudge_pos():1806 [1] 856: 0.060 0.0020379 0.0010222 9515 31.71 9.590 5.973 2012-09-14T12:36:40.027248384 INFO 2025-06-26 19:20:40,253 calibrate.py _nudge_pos():1806 [1] 935: 0.070 0.0025973 -0.0009629 4555 15.18 25.534 -11.754 2012-09-14T12:53:10.029428736 INFO 2025-06-26 19:20:41,357 calibrate.py _nudge_pos():1806 [1] 1042: 0.080 0.0013213 0.0002338 14500 48.33 4.081 0.897 2012-09-14T13:43:16.023504128 INFO 2025-06-26 19:20:42,334 calibrate.py _nudge_pos():1806 [1] 1138: 0.080 0.0013806 0.0002836 14645 48.81 4.224 1.077 2012-09-14T14:33:40.026345472 INFO 2025-06-26 19:20:43,218 calibrate.py _nudge_pos():1806 [1] 1227: 0.080 0.0012393 0.0003851 8855 29.51 6.273 2.418 2012-09-14T15:04:40.028926720 INFO 2025-06-26 19:20:43,229 calibrate.py _nudge_pos():1806 [1] 1228: 0.090 0.0001339 -0.0000092 235 0.78 25.652 -2.180 2012-09-14T15:05:27.025707264 INFO 2025-06-26 19:20:44,150 calibrate.py _nudge_pos():1806 [1] 1320: 0.090 0.0008944 -0.0011299 4620 15.40 8.677 -13.598 2012-09-14T15:22:22.026174720 INFO 2025-06-26 19:20:45,164 calibrate.py _nudge_pos():1806 [1] 1421: 0.090 0.0066626 -0.0094352 14705 49.01 20.309 -35.671 2012-09-14T16:13:04.027783424 INFO 2025-06-26 19:20:46,195 calibrate.py _nudge_pos():1806 [1] 1524: 0.100 0.0015947 -0.0021232 4500 15.00 15.888 -26.235 2012-09-14T16:29:46.029141760 INFO 2025-06-26 19:20:46,206 calibrate.py _nudge_pos():1806 [1] 1525: 0.090 0.0000272 0.0000039 35 0.11 35.888 6.423 2012-09-14T16:29:53.028662272 INFO 2025-06-26 19:21:05,437 calibrate.py _nudge_pos():1806 [1] 3430: 0.110 0.0000518 -0.0000642 30 0.10 80.144 -123.051 2012-09-14T17:01:44.027749888 INFO 2025-06-26 19:21:05,499 calibrate.py _nudge_pos():1806 [1] 3436: 0.110 -0.0000027 -0.0000298 15 0.05 -8.542 -118.277 2012-09-14T17:01:52.027201792 INFO 2025-06-26 19:21:10,218 calibrate.py _nudge_pos():1862 [1] 3865: - - - 4 0.01 - - INFO 2025-06-26 19:21:10,218 calibrate.py _nudge_pos():1868 [1] Points in final series = 171344 INFO 2025-06-26 19:21:10,433 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=160) for self.args.mission=2012.258.00 INFO 2025-06-26 19:21:10,437 calibrate.py _depth_process():2175 [1] Setting 1 depths values to NaN WARNING 2025-06-26 19:21:10,442 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:21:10,669 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 12 of 137145 INFO 2025-06-26 19:21:11,688 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:21:12,941 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:21:13,948 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:21:13,950 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.258.00/ctd1.nc INFO 2025-06-26 19:21:13,952 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 19:21:13,952 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 19:21:13,952 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:21:15,140 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:21:16,142 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:21:16,145 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.258.00/ctd2.nc INFO 2025-06-26 19:21:16,146 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 19:21:16,146 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 19:21:16,146 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:21:16,181 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:21:17,751 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64] INFO 2025-06-26 19:21:18,038 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:21:48,824 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.258.00 ERROR 2025-06-26 19:21:48,824 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.258.00 INFO 2025-06-26 19:21:48,956 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_cal.nc INFO 2025-06-26 19:21:49,158 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 19:21:49,163 process.py align():251 [1] Alignment steps for 2012.258.00 INFO 2025-06-26 19:21:49,212 align.py process_cal():139 [1] Processing dorado_2012.258.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.258.00 INFO 2025-06-26 19:21:49,257 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:21:49,262 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:21:49,373 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:21:49,380 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:21:49,488 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:21:49,495 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:21:49,559 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:21:49,559 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:21:49,601 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:21:49,608 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:21:49,715 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:49,721 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:49,813 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:49,819 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:49,912 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:49,918 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,010 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,016 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,110 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,116 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,207 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,213 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,307 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,312 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,404 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,410 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,504 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,510 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,601 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,608 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,701 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,707 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,798 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,804 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,897 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:50,903 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:50,996 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,001 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,095 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,101 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,193 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,200 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,293 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,299 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,392 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,398 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,493 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,499 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,592 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,598 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,693 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,699 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,791 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.258.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:21:51,796 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:21:51,907 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.12 INFO 2025-06-26 19:21:51,972 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.12 INFO 2025-06-26 19:21:52,037 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.12 INFO 2025-06-26 19:21:52,107 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:21:52,186 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:21:52,327 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:21:53,176 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:21:53,247 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_align.nc INFO 2025-06-26 19:21:53,454 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 19:21:53,456 process.py resample():273 [1] Resampling steps for 2012.258.00 INFO 2025-06-26 19:21:53,457 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:21:53,501 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_align.nc mission netCDF file INFO 2025-06-26 19:21:53,508 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_align.nc mission netCDF file INFO 2025-06-26 19:21:53,510 resample.py get_mission_start_end():1145 [1] navigation: 2012-09-14T07:38:30.042796288 to 2012-09-14T17:09:38.825223936 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:21:53,512 resample.py get_mission_start_end():1145 [1] hs2 : 2012-09-14T07:37:59.464891136 to 2012-09-14T17:09:38.785226496 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 19:21:53,514 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-09-14T07:38:36.942323712 to 2012-09-14T17:09:38.715231488 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:21:53,515 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-09-14T07:38:37.222304512 to 2012-09-14T17:09:38.715231488 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:21:53,517 resample.py get_mission_start_end():1145 [1] isus : 2012-09-14T07:39:17.509544704 to 2012-09-14T17:09:35.145476096 (0 days 00:00:03.679747840 before mission_end) INFO 2025-06-26 19:21:53,518 resample.py get_mission_start_end():1145 [1] biolume : 2012-09-14T07:37:53.095293184 to 2012-09-14T17:09:37.825258240 (0 days 00:00:00.999965696 before mission_end) INFO 2025-06-26 19:21:53,520 resample.py get_mission_start_end():1145 [1] tailcone : 2012-09-14T07:37:53.825277440 to 2012-09-14T17:09:38.785226496 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 19:21:53,521 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_align.nc mission netCDF file INFO 2025-06-26 19:21:53,522 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:53,871 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:53,928 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:53,985 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,042 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,092 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,142 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,190 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,238 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,282 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,327 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,372 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,417 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,462 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,507 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,551 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,596 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,641 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,688 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,735 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,781 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,828 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,874 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,920 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,966 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,981 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:54,993 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:55,004 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:55,020 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:55,037 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:55,043 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:21:55,043 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:21:56,265 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:21:56,536 resample.py add_biolume_proxies():633 [1] Zero flow values found: 1 of 34305 - replaced with 350 ml/s INFO 2025-06-26 19:21:56,537 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:21:56,652 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:21:56,704 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:21:56,744 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:21:56,744 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:21:56,804 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:21:57,113 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_1S.nc INFO 2025-06-26 19:21:57,123 create_products.py gulper_odv():401 [1] No gulper times found for 2012.258.00 INFO 2025-06-26 19:21:57,123 process.py archive():337 [1] Archiving steps for 2012.258.00 INFO 2025-06-26 19:21:57,123 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:21:57,124 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:21:57,126 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.258.00_1S.nc INFO 2025-06-26 19:21:57,157 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:21:57,158 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.258.00_cal.nc INFO 2025-06-26 19:21:57,367 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:21:57,368 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.258.00_align.nc INFO 2025-06-26 19:21:57,659 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:21:57,699 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,742 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,775 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,899 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,908 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,949 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:57,985 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:58,069 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012258/2012.258.00 done. INFO 2025-06-26 19:21:58,069 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:21:58,070 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.258.00/dorado_2012.258.00_processing.log /Volumes/AUVCTD/surveys/2012/netcdf