INFO 2025-06-26 19:27:33,737 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 19:27:33,738 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - drifter tracking T-REX mission, 2 Gulpers on .05 , 8 Gulpers on .06 - stitched together - ctdToUse = ctd1 INFO 2025-06-26 19:27:33,738 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.075.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:27:33,738 process.py download_process():165 [1] Download and processing steps for 2013.075.05 INFO 2025-06-26 19:27:33,738 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013075/2013.075.05 INFO 2025-06-26 19:27:33,738 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013075/2013.075.05 to /data/auv_data/dorado/missionlogs/2013.075.05 INFO 2025-06-26 19:27:35,165 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.075.05 INFO 2025-06-26 19:27:35,165 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/ctdDriver.log (1552710 bytes) INFO 2025-06-26 19:27:35,283 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/ctdDriver2.log (1552799 bytes) INFO 2025-06-26 19:27:35,401 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/gps.log (41972 bytes) INFO 2025-06-26 19:27:35,412 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/hydroscatlog.log (1366030 bytes) INFO 2025-06-26 19:27:35,556 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.075.05/hydroscatlog.log: [12009] INFO 2025-06-26 19:27:35,560 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/navigation.log (5489094 bytes) INFO 2025-06-26 19:27:35,962 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/isuslog.log (119445 bytes) INFO 2025-06-26 19:27:35,978 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/parosci.log (1655558 bytes) INFO 2025-06-26 19:27:36,120 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.95 seconds INFO 2025-06-26 19:27:36,120 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.05/lopc.bin (20354933 bytes) INFO 2025-06-26 19:27:36,120 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:27:36 2025 INFO 2025-06-26 19:27:36,120 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.075.05/parosci.nc INFO 2025-06-26 19:27:36,120 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:27:36,120 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.075.05/parosci.nc INFO 2025-06-26 19:27:36,122 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363453844.9, sensor_off_time = 1363457914.3 INFO 2025-06-26 19:27:36,123 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 4069 seconds. Expecting to read 8138 L frames from the lopc.bin file. INFO 2025-06-26 19:27:36,123 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 8138 records from the lopc.bin file. INFO 2025-06-26 19:27:36,170 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-16 17:10:44 Z and endTime = 2013-03-16 18:18:34 Z with 8138 records expected to be read from lopc.bin INFO 2025-06-26 19:27:36,171 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.075.05/lopc.bin INFO 2025-06-26 19:27:36,171 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.075.05/lopc.nc INFO 2025-06-26 19:27:36,171 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.075.05/lopc.nc INFO 2025-06-26 19:27:36,171 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.075.05 INFO 2025-06-26 19:27:36,171 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:27:36,175 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = ERROR 2025-06-26 19:27:36,222 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:27:36,223 process.py calibrate():227 [1] Calibration steps for 2013.075.05 INFO 2025-06-26 19:27:36,301 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 19:27:36,302 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:27:39,034 calibrate.py _nudge_pos():1806 [1] 327: 0.070 0.0014597 -0.0038624 8555 28.51 7.901 -25.100 2013-03-16T17:44:40.127934208 INFO 2025-06-26 19:27:41,095 calibrate.py _nudge_pos():1806 [1] 553: 0.070 0.0010478 -0.0029498 8958 29.86 5.415 -18.303 2013-03-16T18:18:17.129760256 INFO 2025-06-26 19:27:41,254 calibrate.py _nudge_pos():1862 [1] 535: - - - 0 0.00 - - INFO 2025-06-26 19:27:41,254 calibrate.py _nudge_pos():1868 [1] Points in final series = 20172 WARNING 2025-06-26 19:27:41,285 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:27:43,293 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 16249 INFO 2025-06-26 19:27:43,423 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:27:43,594 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:27:43,717 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:27:43,718 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.075.05/ctd1.nc INFO 2025-06-26 19:27:43,719 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:27:43,720 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 19:27:43,720 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:27:43,876 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:27:43,999 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:27:44,001 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.075.05/ctd2.nc INFO 2025-06-26 19:27:44,002 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:27:44,002 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 19:27:44,002 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:27:44,011 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.05 ERROR 2025-06-26 19:27:44,011 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.075.05 ERROR 2025-06-26 19:27:44,011 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.05 ERROR 2025-06-26 19:27:44,012 calibrate.py process_logs():3542 [1] Error processing tailcone: tailcone has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.05 INFO 2025-06-26 19:27:44,012 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_cal.nc INFO 2025-06-26 19:27:44,059 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, time INFO 2025-06-26 19:27:44,063 process.py align():251 [1] Alignment steps for 2013.075.05 INFO 2025-06-26 19:27:44,085 align.py process_cal():139 [1] Processing dorado_2013.075.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.075.05 INFO 2025-06-26 19:27:44,094 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:27:44,096 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:27:44,117 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:27:44,120 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:27:44,139 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:27:44,141 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:27:44,153 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:27:44,153 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:27:44,161 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:27:44,163 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:27:44,184 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,186 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,206 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,208 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,227 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,229 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,248 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,251 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,269 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,272 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,290 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,292 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,311 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,313 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,333 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,335 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,354 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,356 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,375 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,378 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,397 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,399 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,418 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,420 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,439 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,442 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,461 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,463 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,482 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,485 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,504 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,506 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,526 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,528 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,548 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,550 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,570 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,572 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,592 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,594 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,613 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,616 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,636 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:27:44,638 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:27:44,661 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:27:44,681 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:27:44,701 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:27:44,711 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_align.nc INFO 2025-06-26 19:27:44,751 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 INFO 2025-06-26 19:27:44,753 process.py resample():273 [1] Resampling steps for 2013.075.05 INFO 2025-06-26 19:27:44,753 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:27:44,773 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_align.nc mission netCDF file INFO 2025-06-26 19:27:44,776 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_align.nc mission netCDF file INFO 2025-06-26 19:27:44,777 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-16T17:11:19.544983552 to 2013-03-16T18:18:34.128595712 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 19:27:44,779 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-16T17:10:50.186994688 to 2013-03-16T18:18:34.298584064 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:27:44,780 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-16T17:11:12.585460480 to 2013-03-16T18:18:34.238588160 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 19:27:44,781 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-16T17:11:12.295480320 to 2013-03-16T18:18:34.178592256 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 19:27:44,782 resample.py get_mission_start_end():1145 [1] isus : 2013-03-16T17:11:59.472248320 to 2013-03-16T18:18:33.958607360 (0 days 00:00:00.339976704 before mission_end) INFO 2025-06-26 19:27:44,783 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_align.nc mission netCDF file INFO 2025-06-26 19:27:44,783 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,849 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,863 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,877 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,890 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,903 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,916 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,928 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,940 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,952 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,963 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,974 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,985 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:44,996 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,007 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,019 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,031 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,042 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,055 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,068 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,080 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,093 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,105 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,117 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,129 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,139 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,149 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,158 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:27:45,270 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_1S.nc INFO 2025-06-26 19:27:48,173 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:27:48,587 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.075.05/dorado_2013.075.05_1S_Gulper.txt INFO 2025-06-26 19:27:48,587 process.py archive():337 [1] Archiving steps for 2013.075.05 INFO 2025-06-26 19:27:48,587 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05, BASE_PATH = /data/auv_data INFO 2025-06-26 19:27:48,587 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:27:48,588 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.05_1S.nc INFO 2025-06-26 19:27:48,596 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:27:48,597 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.05_cal.nc INFO 2025-06-26 19:27:48,620 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:27:48,621 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.05_align.nc INFO 2025-06-26 19:27:48,640 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:27:48,651 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,661 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,665 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,673 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,693 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,697 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,707 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,712 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.05 done. INFO 2025-06-26 19:27:48,712 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:27:48,715 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.075.05_1S_Gulper.txt INFO 2025-06-26 19:27:48,720 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.075.05/dorado_2013.075.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:27:48,720 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.05/dorado_2013.075.05_processing.log /Volumes/AUVCTD/surveys/2013/netcdf