INFO 2025-06-26 05:52:29,679 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 05:52:29,679 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/12/05 - ctdToUse = ctd1 INFO 2025-06-26 05:52:29,679 process.py process_mission():449 [1] Processing BIOLUME mission 2004.211.01 by user docker_user on host 671049448ece INFO 2025-06-26 05:52:29,679 process.py download_process():165 [1] Download and processing steps for 2004.211.01 INFO 2025-06-26 05:52:29,679 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004211/2004.211.01 INFO 2025-06-26 05:52:29,679 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004211/2004.211.01 to /data/auv_data/dorado/missionlogs/2004.211.01 INFO 2025-06-26 05:52:32,395 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.211.01 INFO 2025-06-26 05:52:32,396 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/ctdDriver.log (8979563 bytes) INFO 2025-06-26 05:52:33,069 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/ctdDriver2.log (8979645 bytes) INFO 2025-06-26 05:52:33,751 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/gps.log (67388 bytes) INFO 2025-06-26 05:52:33,766 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/hydroscatlog.log (6123434 bytes) INFO 2025-06-26 05:52:34,485 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.211.01/hydroscatlog.log: [4674] INFO 2025-06-26 05:52:34,501 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/navigation.log (19897339 bytes) INFO 2025-06-26 05:52:36,016 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/isuslog.log (493909 bytes) INFO 2025-06-26 05:52:36,094 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/parosci.log (6126950 bytes) INFO 2025-06-26 05:52:36,612 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/tailCone.log (6126907 bytes) INFO 2025-06-26 05:52:37,347 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.211.01/biolume.log (6947292 bytes) INFO 2025-06-26 05:52:38,006 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:52:38,377 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.98 seconds WARNING 2025-06-26 05:52:38,378 process.py download_process():196 [1] No lopc.bin file for 2004.211.01 INFO 2025-06-26 05:52:38,378 process.py calibrate():227 [1] Calibration steps for 2004.211.01 INFO 2025-06-26 05:52:38,575 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 05:52:38,577 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:52:40,021 calibrate.py _nudge_pos():1806 [1] 165: 0.110 -0.0015522 0.0007663 10410 34.70 -6.631 4.092 2004-07-29T05:30:49.000950784 INFO 2025-06-26 05:52:40,472 calibrate.py _nudge_pos():1806 [1] 212: 0.120 -0.0014053 0.0005797 10390 34.63 -6.017 3.102 2004-07-29T06:06:12.995447168 INFO 2025-06-26 05:52:40,867 calibrate.py _nudge_pos():1806 [1] 254: 0.120 -0.0022211 0.0016840 11015 36.71 -8.974 8.500 2004-07-29T06:43:37.001722112 INFO 2025-06-26 05:52:41,378 calibrate.py _nudge_pos():1806 [1] 306: 0.120 -0.0016192 0.0020795 11230 37.43 -6.419 10.295 2004-07-29T07:21:53.994367360 INFO 2025-06-26 05:52:41,838 calibrate.py _nudge_pos():1806 [1] 353: 0.120 -0.0015805 0.0017687 11325 37.75 -6.216 8.683 2004-07-29T08:00:24.996052992 INFO 2025-06-26 05:52:42,334 calibrate.py _nudge_pos():1806 [1] 404: 0.120 -0.0001908 0.0007030 5870 19.56 -1.448 6.659 2004-07-29T08:20:49.002202752 INFO 2025-06-26 05:52:42,767 calibrate.py _nudge_pos():1806 [1] 449: 0.120 0.0032205 0.0024361 10670 35.56 13.448 12.693 2004-07-29T08:57:07.002999552 INFO 2025-06-26 05:52:43,239 calibrate.py _nudge_pos():1806 [1] 498: 0.120 0.0023295 0.0011573 11010 36.70 9.430 5.844 2004-07-29T09:34:36.998864128 INFO 2025-06-26 05:52:43,699 calibrate.py _nudge_pos():1806 [1] 545: 0.130 0.0011799 0.0008570 11650 38.83 4.516 4.090 2004-07-29T10:14:12.996097280 INFO 2025-06-26 05:52:44,142 calibrate.py _nudge_pos():1806 [1] 589: 0.130 0.0011756 0.0009501 11215 37.38 4.675 4.710 2004-07-29T10:52:18.999495296 INFO 2025-06-26 05:52:44,618 calibrate.py _nudge_pos():1806 [1] 637: 0.130 0.0012141 0.0008899 11285 37.61 4.799 4.384 2004-07-29T11:30:43.001660288 INFO 2025-06-26 05:52:45,099 calibrate.py _nudge_pos():1806 [1] 686: 0.130 0.0001943 0.0001519 3420 11.40 2.536 2.470 2004-07-29T11:42:55.001514880 INFO 2025-06-26 05:52:45,574 calibrate.py _nudge_pos():1806 [1] 734: 0.140 0.0002883 0.0002760 3605 12.01 3.569 4.258 2004-07-29T11:55:42.998903552 INFO 2025-06-26 05:52:47,484 calibrate.py _nudge_pos():1862 [1] 903: - - - 1 0.00 - - INFO 2025-06-26 05:52:47,484 calibrate.py _nudge_pos():1868 [1] Points in final series = 127539 WARNING 2025-06-26 05:52:47,585 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:53:00,413 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 102041 INFO 2025-06-26 05:53:01,169 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:53:02,099 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 05:53:02,840 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 05:53:02,842 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.211.01/ctd1.nc INFO 2025-06-26 05:53:02,844 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 05:53:02,844 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 05:53:02,844 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:53:03,730 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:53:04,496 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:53:04,499 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.211.01/ctd2.nc INFO 2025-06-26 05:53:04,500 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 05:53:04,501 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 05:53:04,501 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:53:04,538 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:53:05,947 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 05:53:05,953 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 05:53:05,954 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.211.01 ERROR 2025-06-26 05:53:05,954 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.211.01 INFO 2025-06-26 05:53:06,055 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_cal.nc INFO 2025-06-26 05:53:06,153 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 05:53:06,158 process.py align():251 [1] Alignment steps for 2004.211.01 INFO 2025-06-26 05:53:06,186 align.py process_cal():139 [1] Processing dorado_2004.211.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.211.01 INFO 2025-06-26 05:53:06,224 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:53:06,229 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:53:06,326 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:53:06,332 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:53:06,419 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:53:06,424 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:53:06,477 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:53:06,477 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:53:06,513 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:53:06,519 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:53:06,604 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:53:06,609 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:06,687 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:53:06,692 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:06,770 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:53:06,775 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:06,852 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:06,857 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:06,933 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:06,938 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,015 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,020 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,097 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,102 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,178 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,183 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,260 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,265 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,342 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,348 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,427 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,432 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,510 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,515 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,596 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,600 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,676 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,681 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,757 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,762 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,840 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,846 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:07,924 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:07,929 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:08,006 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:08,011 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:08,088 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:08,093 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:08,169 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.211.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:53:08,173 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:53:08,260 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:53:08,312 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:53:08,366 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:53:08,421 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:53:08,480 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:53:08,538 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_align.nc INFO 2025-06-26 05:53:08,627 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 05:53:08,629 process.py resample():273 [1] Resampling steps for 2004.211.01 INFO 2025-06-26 05:53:08,630 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:53:08,656 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_align.nc mission netCDF file INFO 2025-06-26 05:53:08,662 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_align.nc mission netCDF file INFO 2025-06-26 05:53:08,664 resample.py get_mission_start_end():1145 [1] navigation: 2004-07-29T04:53:44.603332480 to 2004-07-29T11:58:52.195942656 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 05:53:08,666 resample.py get_mission_start_end():1145 [1] hs2 : 2004-07-29T04:53:29.414372864 to 2004-07-29T11:58:52.275937024 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:53:08,668 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-07-29T04:53:44.363348992 to 2004-07-29T11:58:52.095949440 (0 days 00:00:00.179987584 before mission_end) INFO 2025-06-26 05:53:08,669 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-07-29T04:53:44.573334400 to 2004-07-29T11:58:52.215941248 (0 days 00:00:00.059995776 before mission_end) INFO 2025-06-26 05:53:08,671 resample.py get_mission_start_end():1145 [1] isus : 2004-07-29T04:54:41.949404032 to 2004-07-29T11:58:52.225940480 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 05:53:08,672 resample.py get_mission_start_end():1145 [1] biolume : 2004-07-29T04:53:23.784724224 to 2004-07-29T11:58:51.605948672 (0 days 00:00:00.669988352 before mission_end) INFO 2025-06-26 05:53:08,674 resample.py get_mission_start_end():1145 [1] tailcone : 2004-07-29T04:53:23.264794112 to 2004-07-29T11:58:52.185943424 (0 days 00:00:00.089993600 before mission_end) INFO 2025-06-26 05:53:08,675 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_align.nc mission netCDF file INFO 2025-06-26 05:53:08,676 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,017 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,063 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,109 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,154 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,193 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,232 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,271 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,309 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,347 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,383 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,420 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,455 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,491 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,527 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,564 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,600 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,639 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,679 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,718 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,757 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,795 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,835 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,853 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,868 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,882 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,899 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:09,942 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 05:53:10,179 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_1S.nc INFO 2025-06-26 05:53:11,424 create_products.py gulper_odv():401 [1] No gulper times found for 2004.211.01 INFO 2025-06-26 05:53:11,424 process.py archive():337 [1] Archiving steps for 2004.211.01 INFO 2025-06-26 05:53:11,424 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01, BASE_PATH = /data/auv_data INFO 2025-06-26 05:53:11,425 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 05:53:11,426 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.211.01_1S.nc INFO 2025-06-26 05:53:11,450 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:53:11,451 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.211.01_cal.nc INFO 2025-06-26 05:53:11,564 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:53:11,565 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.211.01_align.nc INFO 2025-06-26 05:53:11,675 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:53:11,705 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,733 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,737 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,759 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,824 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,848 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,875 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,949 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004211/2004.211.01 done. INFO 2025-06-26 05:53:11,950 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:53:11,950 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.211.01/dorado_2004.211.01_processing.log /Volumes/AUVCTD/surveys/2004/netcdf