INFO 2025-06-26 15:25:00,611 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 15:25:00,611 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - - ctdToUse = ctd1 INFO 2025-06-26 15:25:00,612 process.py process_mission():449 [1] Processing AUVCTD mission 2009.281.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:25:00,612 process.py download_process():165 [1] Download and processing steps for 2009.281.01 INFO 2025-06-26 15:25:00,612 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009281/2009.281.01 INFO 2025-06-26 15:25:00,612 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009281/2009.281.01 to /data/auv_data/dorado/missionlogs/2009.281.01 INFO 2025-06-26 15:25:03,595 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.281.01 INFO 2025-06-26 15:25:03,595 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/ctdDriver.log (5306982 bytes) INFO 2025-06-26 15:25:03,956 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.281.01/ctdDriver.log: [44331] INFO 2025-06-26 15:25:03,971 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/ctdDriver2.log (5307263 bytes) INFO 2025-06-26 15:25:04,349 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.281.01/ctdDriver2.log: [20151 51368] INFO 2025-06-26 15:25:04,370 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/gps.log (47156 bytes) INFO 2025-06-26 15:25:04,383 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/hydroscatlog.log (4649590 bytes) INFO 2025-06-26 15:25:04,867 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/navigation.log (16298994 bytes) INFO 2025-06-26 15:25:06,022 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/isuslog.log (323317 bytes) INFO 2025-06-26 15:25:06,057 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/parosci.log (5665526 bytes) INFO 2025-06-26 15:25:06,539 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/tailCone.log (3320923 bytes) INFO 2025-06-26 15:25:06,954 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.36 seconds INFO 2025-06-26 15:25:06,954 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.281.01/lopc.bin (18027967 bytes) INFO 2025-06-26 15:25:06,954 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:25:06 2025 INFO 2025-06-26 15:25:06,954 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.281.01/parosci.nc INFO 2025-06-26 15:25:06,954 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:25:06,954 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.281.01/parosci.nc INFO 2025-06-26 15:25:06,958 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1255024715.9, sensor_off_time = 1255038562.1 INFO 2025-06-26 15:25:06,958 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13846 seconds. Expecting to read 27692 L frames from the lopc.bin file. INFO 2025-06-26 15:25:06,958 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 27692 records from the lopc.bin file. INFO 2025-06-26 15:25:07,131 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-10-08 17:58:35 Z and endTime = 2009-10-08 21:49:22 Z with 27692 records expected to be read from lopc.bin INFO 2025-06-26 15:25:07,131 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.281.01/lopc.bin INFO 2025-06-26 15:25:07,131 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.281.01/lopc.nc INFO 2025-06-26 15:25:07,132 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.281.01/lopc.nc INFO 2025-06-26 15:25:07,132 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.281.01 INFO 2025-06-26 15:25:07,133 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:25:07,237 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:25:07,237 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:25:07,237 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 15:25:07,401 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 15:25:07,402 process.py calibrate():227 [1] Calibration steps for 2009.281.01 INFO 2025-06-26 15:25:07,535 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 15:25:07,537 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:25:08,159 calibrate.py _nudge_pos():1806 [1] 92: 0.040 0.0001365 0.0000371 1160 3.86 5.238 1.782 2009-10-08T18:03:58.703563520 INFO 2025-06-26 15:25:08,641 calibrate.py _nudge_pos():1806 [1] 143: 0.040 0.0002471 -0.0000402 4790 15.96 2.296 -0.467 2009-10-08T18:20:46.704510720 INFO 2025-06-26 15:25:09,120 calibrate.py _nudge_pos():1806 [1] 193: 0.040 -0.0000574 -0.0000193 55 0.18 -47.251 -19.905 2009-10-08T18:21:46.710399744 INFO 2025-06-26 15:25:09,686 calibrate.py _nudge_pos():1806 [1] 252: 0.050 0.0002660 -0.0000071 5110 17.03 2.316 -0.077 2009-10-08T18:39:46.706415104 INFO 2025-06-26 15:25:10,355 calibrate.py _nudge_pos():1806 [1] 322: 0.050 0.0005495 -0.0000593 10182 33.95 2.399 -0.324 2009-10-08T19:14:52.712143872 INFO 2025-06-26 15:25:11,023 calibrate.py _nudge_pos():1806 [1] 393: 0.060 0.0001923 -0.0001330 8077 26.93 1.058 -0.915 2009-10-08T19:42:58.706645248 INFO 2025-06-26 15:25:11,497 calibrate.py _nudge_pos():1806 [1] 443: 0.060 -0.0006794 -0.0018814 11333 37.78 -2.664 -9.228 2009-10-08T20:21:34.707988480 INFO 2025-06-26 15:25:12,122 calibrate.py _nudge_pos():1806 [1] 508: 0.060 -0.0007293 -0.0017846 11197 37.33 -2.894 -8.859 2009-10-08T20:59:58.710153216 INFO 2025-06-26 15:25:12,161 calibrate.py _nudge_pos():1806 [1] 512: 0.060 0.0001065 0.0000795 45 0.15 107.566 100.468 2009-10-08T21:00:10.709331456 INFO 2025-06-26 15:25:12,795 calibrate.py _nudge_pos():1806 [1] 578: 0.060 -0.0001906 -0.0003333 3035 10.11 -2.791 -6.107 2009-10-08T21:11:22.713295872 INFO 2025-06-26 15:25:13,249 calibrate.py _nudge_pos():1806 [1] 626: 0.070 0.0024916 0.0014757 11043 36.81 10.029 7.428 2009-10-08T21:48:58.708749824 INFO 2025-06-26 15:25:13,413 calibrate.py _nudge_pos():1862 [1] 611: - - - 37 0.12 - - INFO 2025-06-26 15:25:13,413 calibrate.py _nudge_pos():1868 [1] Points in final series = 69055 WARNING 2025-06-26 15:25:13,506 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:25:14,034 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:25:18,003 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:25:18,421 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:25:18,423 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.281.01/ctd1.nc INFO 2025-06-26 15:25:18,425 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:25:18,425 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 15:25:18,425 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:25:21,504 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:25:21,913 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:25:21,915 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.281.01/ctd2.nc INFO 2025-06-26 15:25:21,916 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 15:25:21,916 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 15:25:21,916 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 15:25:21,930 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.281.01 ERROR 2025-06-26 15:25:21,930 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.281.01 ERROR 2025-06-26 15:25:21,930 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.281.01 INFO 2025-06-26 15:25:21,985 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_cal.nc INFO 2025-06-26 15:25:28,030 calibrate.py write_netcdf():3512 [1] Data variables written: 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 15:25:28,035 process.py align():251 [1] Alignment steps for 2009.281.01 INFO 2025-06-26 15:25:28,061 align.py process_cal():139 [1] Processing dorado_2009.281.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.281.01 INFO 2025-06-26 15:25:28,084 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:25:28,087 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:25:28,138 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:25:28,142 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:25:28,192 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:25:28,195 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:25:28,227 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:25:28,227 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:25:28,248 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:25:28,252 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:25:28,302 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,305 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,349 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,352 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,396 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,400 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,443 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,447 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,491 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,495 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,537 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,541 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,585 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,589 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,631 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,635 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,679 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,683 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,727 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,731 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,776 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,779 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,822 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,826 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,870 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,874 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,917 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,920 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:28,964 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:28,968 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,012 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,016 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,061 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,065 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,109 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,113 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,158 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,161 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,204 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,208 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,254 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,258 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,302 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.281.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:25:29,306 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:25:29,360 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:25:29,397 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:25:29,435 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:25:29,475 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:25:29,511 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_align.nc INFO 2025-06-26 15:25:29,576 align.py write_netcdf():342 [1] Data variables written: 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 15:25:29,578 process.py resample():273 [1] Resampling steps for 2009.281.01 INFO 2025-06-26 15:25:29,578 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:25:29,670 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_align.nc mission netCDF file INFO 2025-06-26 15:25:29,675 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_align.nc mission netCDF file INFO 2025-06-26 15:25:29,676 resample.py get_mission_start_end():1145 [1] navigation: 2009-10-08T17:59:08.573438720 to 2009-10-08T21:49:22.107146752 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:25:29,678 resample.py get_mission_start_end():1145 [1] hs2 : 2009-10-08T17:58:41.425298432 to 2009-10-08T21:49:22.047150848 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 15:25:29,679 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-10-08T17:59:03.543783168 to 2009-10-08T21:49:22.047150848 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 15:25:29,681 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-10-08T17:59:03.293800448 to 2009-10-08T21:49:21.977155584 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 15:25:29,682 resample.py get_mission_start_end():1145 [1] isus : 2009-10-08T17:59:51.550494720 to 2009-10-08T21:49:21.367197440 (0 days 00:00:00.739949312 before mission_end) INFO 2025-06-26 15:25:29,684 resample.py get_mission_start_end():1145 [1] tailcone : 2009-10-08T17:58:38.155522560 to 2009-10-08T21:49:21.957157120 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 15:25:29,684 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_align.nc mission netCDF file INFO 2025-06-26 15:25:29,685 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,849 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,879 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,907 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,934 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,960 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:29,984 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,009 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,034 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,057 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,079 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,101 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,124 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,146 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,169 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,191 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,214 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,236 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,261 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,286 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,310 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,335 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,359 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,384 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,408 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,422 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,435 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,447 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,475 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:25:30,650 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_1S.nc INFO 2025-06-26 15:25:34,207 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 15:25:48,565 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.281.01/dorado_2009.281.01_1S_Gulper.txt INFO 2025-06-26 15:25:48,566 process.py archive():337 [1] Archiving steps for 2009.281.01 INFO 2025-06-26 15:25:48,566 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01, BASE_PATH = /data/auv_data INFO 2025-06-26 15:25:48,566 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:25:48,567 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.281.01_1S.nc INFO 2025-06-26 15:25:48,583 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:25:48,584 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.281.01_cal.nc INFO 2025-06-26 15:25:48,642 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:25:48,643 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.281.01_align.nc INFO 2025-06-26 15:25:48,699 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:25:48,720 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,738 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,742 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,758 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,804 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,809 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,828 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,843 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,849 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009281/2009.281.01 done. INFO 2025-06-26 15:25:48,849 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:25:48,850 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.281.01_1S_Gulper.txt INFO 2025-06-26 15:25:48,855 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.281.01/dorado_2009.281.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 15:25:48,855 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.281.01/dorado_2009.281.01_processing.log /Volumes/AUVCTD/surveys/2009/netcdf