INFO 2025-06-26 10:29:42,531 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 10:29:42,531 process.py process_mission():434 [1] dorado_info[mission]["comment"] = BIOLUME night missions, touched bottom on mission .00 - ctdToUse = ctd1 INFO 2025-06-26 10:29:42,531 process.py process_mission():449 [1] Processing BIOLUME mission 2005.014.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:29:42,531 process.py download_process():165 [1] Download and processing steps for 2005.014.02 INFO 2025-06-26 10:29:42,532 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005014/2005.014.02 INFO 2025-06-26 10:29:42,532 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005014/2005.014.02 to /data/auv_data/dorado/missionlogs/2005.014.02 INFO 2025-06-26 10:29:43,026 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.014.02 INFO 2025-06-26 10:29:43,027 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/ctdDriver.log (6612363 bytes) INFO 2025-06-26 10:29:43,525 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/ctdDriver2.log (6615965 bytes) INFO 2025-06-26 10:29:44,006 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/gps.log (45644 bytes) INFO 2025-06-26 10:29:44,019 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/hydroscatlog.log (4512194 bytes) INFO 2025-06-26 10:29:44,540 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.014.02/hydroscatlog.log: [17872 17873] INFO 2025-06-26 10:29:44,551 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/navigation.log (22173270 bytes) INFO 2025-06-26 10:29:46,156 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/isuslog.log (77749 bytes) INFO 2025-06-26 10:29:46,168 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/parosci.log (4419584 bytes) WARNING 2025-06-26 10:29:46,397 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 8 bytes, b = b'\x84\xf0' at record 92067, for pres_period in file /data/auv_data/dorado/missionlogs/2005.014.02/parosci.log INFO 2025-06-26 10:29:46,397 logs2netcdfs.py _read_data():224 [1] bytes read = 4419590 file size = 4419584 INFO 2025-06-26 10:29:46,397 logs2netcdfs.py _read_data():229 [1] Tried to read 8 bytes, but only 6 bytes remaining INFO 2025-06-26 10:29:46,397 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 92067 records INFO 2025-06-26 10:29:46,542 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/tailCone.log (4514395 bytes) INFO 2025-06-26 10:29:47,098 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.014.02/biolume.log (5119996 bytes) INFO 2025-06-26 10:29:47,607 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:29:47,879 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.85 seconds WARNING 2025-06-26 10:29:47,880 process.py download_process():196 [1] No lopc.bin file for 2005.014.02 INFO 2025-06-26 10:29:47,880 process.py calibrate():227 [1] Calibration steps for 2005.014.02 INFO 2025-06-26 10:29:48,055 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 10:29:48,057 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:29:48,790 calibrate.py _nudge_pos():1806 [1] 92: 0.160 -0.0031017 0.0002441 8860 29.53 -15.570 1.532 2005-01-14T04:42:00.879876352 INFO 2025-06-26 10:29:49,311 calibrate.py _nudge_pos():1806 [1] 146: 0.160 -0.0023780 0.0005305 10533 35.11 -10.042 2.800 2005-01-14T05:18:00.881906048 INFO 2025-06-26 10:29:49,921 calibrate.py _nudge_pos():1806 [1] 208: 0.150 -0.0000029 -0.0000651 225 0.75 -0.578 -16.165 2005-01-14T05:19:46.884644480 INFO 2025-06-26 10:29:50,220 calibrate.py _nudge_pos():1806 [1] 239: 0.160 -0.0039477 -0.0013096 11740 39.13 -14.966 -6.202 2005-01-14T05:59:24.881740288 INFO 2025-06-26 10:29:50,694 calibrate.py _nudge_pos():1806 [1] 288: 0.160 -0.0029119 -0.0007641 10590 35.30 -12.242 -4.011 2005-01-14T06:35:30.883359232 INFO 2025-06-26 10:29:51,184 calibrate.py _nudge_pos():1806 [1] 339: 0.160 0.0000134 -0.0000431 270 0.90 2.215 -8.915 2005-01-14T06:37:14.876235264 INFO 2025-06-26 10:29:51,252 calibrate.py _nudge_pos():1806 [1] 346: 0.160 -0.0023013 -0.0027531 10459 34.86 -9.799 -14.633 2005-01-14T07:12:12.882511872 INFO 2025-06-26 10:29:51,693 calibrate.py _nudge_pos():1806 [1] 392: 0.170 -0.0008346 -0.0009540 3465 11.55 -10.732 -15.310 2005-01-14T07:24:30.881955328 INFO 2025-06-26 10:29:52,231 calibrate.py _nudge_pos():1806 [1] 448: 0.160 0.0009563 -0.0057488 11035 36.78 3.862 -28.963 2005-01-14T08:02:12.876998144 INFO 2025-06-26 10:29:52,433 calibrate.py _nudge_pos():1806 [1] 468: 0.160 0.0000097 -0.0000669 40 0.13 11.096 -95.417 2005-01-14T08:02:39.885148032 INFO 2025-06-26 10:29:52,503 calibrate.py _nudge_pos():1806 [1] 475: 0.160 -0.0001984 0.0003413 35 0.11 -260.010 558.075 2005-01-14T08:02:52.884257536 INFO 2025-06-26 10:29:52,514 calibrate.py _nudge_pos():1806 [1] 476: 0.160 -0.0001151 0.0001240 60 0.20 -86.933 116.874 2005-01-14T08:03:04.883435520 INFO 2025-06-26 10:29:52,642 calibrate.py _nudge_pos():1806 [1] 489: 0.170 0.0000124 -0.0000301 50 0.16 11.290 -34.150 2005-01-14T08:03:26.881928448 INFO 2025-06-26 10:29:52,673 calibrate.py _nudge_pos():1806 [1] 492: 0.160 -0.0007661 -0.0026466 9215 30.71 -3.706 -15.968 2005-01-14T08:34:12.885468544 INFO 2025-06-26 10:29:53,163 calibrate.py _nudge_pos():1806 [1] 541: 0.170 -0.0017090 -0.0018966 10380 34.60 -7.341 -10.158 2005-01-14T09:09:36.879965056 INFO 2025-06-26 10:29:53,754 calibrate.py _nudge_pos():1806 [1] 600: 0.160 -0.0001897 -0.0003062 4060 13.53 -2.084 -4.194 2005-01-14T09:24:06.880365824 INFO 2025-06-26 10:29:53,968 calibrate.py _nudge_pos():1862 [1] 601: - - - 5 0.01 - - INFO 2025-06-26 10:29:53,968 calibrate.py _nudge_pos():1868 [1] Points in final series = 93946 WARNING 2025-06-26 10:29:54,043 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 10:30:04,126 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 1 seconds INFO 2025-06-26 10:30:04,844 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 1 seconds INFO 2025-06-26 10:30:05,400 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 1 seconds INFO 2025-06-26 10:30:05,402 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.014.02/ctd1.nc INFO 2025-06-26 10:30:05,403 calibrate.py _range_qc_combined_nc():898 [1] Setting 5 ctd1_salinity values to NaN INFO 2025-06-26 10:30:05,404 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 10:30:05,404 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:30:06,072 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 16 seconds, d_end_time_diff: 1 seconds INFO 2025-06-26 10:30:06,638 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 16 seconds, d_end_time_diff: 1 seconds INFO 2025-06-26 10:30:06,640 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.014.02/ctd2.nc INFO 2025-06-26 10:30:06,642 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 10:30:06,642 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 10:30:06,642 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:30:06,665 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:30:07,540 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [112920 112921 112922 112923] INFO 2025-06-26 10:30:07,703 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: 1 seconds ERROR 2025-06-26 10:30:07,709 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 10:30:07,710 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.014.02 ERROR 2025-06-26 10:30:07,710 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.014.02 INFO 2025-06-26 10:30:07,783 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_cal.nc INFO 2025-06-26 10:30:07,874 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 10:30:07,878 process.py align():251 [1] Alignment steps for 2005.014.02 INFO 2025-06-26 10:30:07,910 align.py process_cal():139 [1] Processing dorado_2005.014.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.014.02 INFO 2025-06-26 10:30:07,938 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:30:07,942 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:30:08,014 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:30:08,019 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:30:08,089 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:30:08,093 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:30:08,135 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:30:08,135 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:30:08,162 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:30:08,167 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:30:08,234 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:30:08,238 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,297 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:30:08,301 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,360 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:30:08,364 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,422 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,426 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,486 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,490 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,549 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,553 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,616 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,675 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,679 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,738 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,742 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,801 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,806 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,865 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,869 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,929 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,933 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:08,992 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:08,995 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,059 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,063 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,123 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,127 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,188 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,192 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,265 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,269 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,329 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,334 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,393 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,397 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,457 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.014.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:30:09,461 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:30:09,525 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:30:09,563 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:30:09,601 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:30:09,641 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:30:09,689 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:30:09,736 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_align.nc INFO 2025-06-26 10:30:09,814 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 10:30:09,817 process.py resample():273 [1] Resampling steps for 2005.014.02 INFO 2025-06-26 10:30:09,818 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:30:09,852 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_align.nc mission netCDF file INFO 2025-06-26 10:30:09,861 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_align.nc mission netCDF file INFO 2025-06-26 10:30:09,863 resample.py get_mission_start_end():1145 [1] navigation: 2005-01-14T04:11:19.296033408 to 2005-01-14T09:24:28.878858752 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 10:30:09,865 resample.py get_mission_start_end():1145 [1] hs2 : 2005-01-14T04:11:02.967152128 to 2005-01-14T09:24:28.968852736 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 10:30:09,868 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-01-14T04:11:26.415545728 to 2005-01-14T09:24:28.968852736 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 10:30:09,870 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-01-14T04:11:15.526291840 to 2005-01-14T09:24:28.848860928 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 10:30:09,873 resample.py get_mission_start_end():1145 [1] isus : 2005-01-14T04:12:22.941673472 to 2005-01-14T09:24:26.079050752 (0 days 00:00:02.899801344 before mission_end) INFO 2025-06-26 10:30:09,875 resample.py get_mission_start_end():1145 [1] biolume : 2005-01-14T04:10:57.987458944 to 2005-01-14T09:24:28.368859520 (0 days 00:00:00.609992576 before mission_end) INFO 2025-06-26 10:30:09,877 resample.py get_mission_start_end():1145 [1] tailcone : 2005-01-14T04:10:58.807436928 to 2005-01-14T09:24:28.978852096 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:30:09,878 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_align.nc mission netCDF file INFO 2025-06-26 10:30:09,879 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,104 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,142 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,179 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,215 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,247 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,280 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,312 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,342 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,371 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,401 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,430 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,458 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,486 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,515 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,543 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,571 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,603 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,634 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,665 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,696 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,727 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,758 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,771 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,781 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,791 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,805 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:10,839 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:30:11,040 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_1S.nc INFO 2025-06-26 10:30:13,110 create_products.py gulper_odv():401 [1] No gulper times found for 2005.014.02 INFO 2025-06-26 10:30:13,110 process.py archive():337 [1] Archiving steps for 2005.014.02 INFO 2025-06-26 10:30:13,110 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02, BASE_PATH = /data/auv_data INFO 2025-06-26 10:30:13,112 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:30:13,113 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.014.02_1S.nc INFO 2025-06-26 10:30:13,132 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:30:13,133 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.014.02_cal.nc INFO 2025-06-26 10:30:13,212 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:30:13,213 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.014.02_align.nc INFO 2025-06-26 10:30:13,289 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:30:13,315 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,337 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,342 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,357 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,424 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,428 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,444 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,464 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,521 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005014/2005.014.02 done. INFO 2025-06-26 10:30:13,521 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:30:13,521 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.014.02/dorado_2005.014.02_processing.log /Volumes/AUVCTD/surveys/2005/netcdf