INFO 2025-06-26 19:16:34,366 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 19:16:34,367 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2012 - laps around ESP drifter - battery problems - less than 1/3 of a normal mission - ctdToUse = ctd1 INFO 2025-06-26 19:16:34,367 process.py process_mission():449 [1] Processing CANON September 2012 mission 2012.256.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:16:34,367 process.py download_process():165 [1] Download and processing steps for 2012.256.00 INFO 2025-06-26 19:16:34,367 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012256/2012.256.00 INFO 2025-06-26 19:16:34,367 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012256/2012.256.00 to /data/auv_data/dorado/missionlogs/2012.256.00 INFO 2025-06-26 19:16:37,471 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.256.00 INFO 2025-06-26 19:16:37,472 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/ctdDriver.log (5997606 bytes) INFO 2025-06-26 19:16:37,923 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/ctdDriver2.log (6003743 bytes) INFO 2025-06-26 19:16:38,378 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/gps.log (63572 bytes) INFO 2025-06-26 19:16:38,393 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/hydroscatlog.log (5258506 bytes) INFO 2025-06-26 19:16:38,930 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2012.256.00/hydroscatlog.log: [1] INFO 2025-06-26 19:16:38,948 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/navigation.log (21250406 bytes) INFO 2025-06-26 19:16:40,470 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/isuslog.log (393493 bytes) INFO 2025-06-26 19:16:40,512 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/parosci.log (6375206 bytes) INFO 2025-06-26 19:16:41,070 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/tailCone.log (3758923 bytes) INFO 2025-06-26 19:16:41,543 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.256.00/biolume.log (4376010 bytes) INFO 2025-06-26 19:16:41,985 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:16:42,219 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.75 seconds WARNING 2025-06-26 19:16:42,219 process.py download_process():196 [1] No lopc.bin file for 2012.256.00 INFO 2025-06-26 19:16:42,219 process.py calibrate():227 [1] Calibration steps for 2012.256.00 INFO 2025-06-26 19:16:42,378 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 19:16:42,380 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:16:43,068 calibrate.py _nudge_pos():1806 [1] 98: 0.100 0.0004303 -0.0009237 1575 5.25 12.230 -32.623 2012-09-12T02:28:51.974960896 INFO 2025-06-26 19:16:43,930 calibrate.py _nudge_pos():1806 [1] 190: 0.100 0.0077411 -0.0118585 15111 50.38 22.919 -43.616 2012-09-12T03:20:45.971637504 INFO 2025-06-26 19:16:45,169 calibrate.py _nudge_pos():1806 [1] 321: 0.110 0.0008955 -0.0079508 12700 42.33 3.156 -34.805 2012-09-12T04:05:15.978729472 INFO 2025-06-26 19:16:46,194 calibrate.py _nudge_pos():1806 [1] 430: 0.110 0.0032130 -0.0018684 5250 17.50 27.388 -19.787 2012-09-12T04:24:33.979400960 INFO 2025-06-26 19:16:47,124 calibrate.py _nudge_pos():1806 [1] 529: 0.110 0.0006757 -0.0010893 2840 9.46 10.650 -21.329 2012-09-12T04:35:39.973777408 INFO 2025-06-26 19:16:47,144 calibrate.py _nudge_pos():1806 [1] 531: 0.120 0.0000506 -0.0000294 25 0.08 94.308 -68.178 2012-09-12T04:35:45.973366272 INFO 2025-06-26 19:16:47,266 calibrate.py _nudge_pos():1806 [1] 544: 0.110 0.0000233 -0.0000167 20 0.06 54.833 -48.856 2012-09-12T04:36:02.972201472 INFO 2025-06-26 19:16:47,893 calibrate.py _nudge_pos():1806 [1] 610: 0.110 0.0000102 -0.0000008 40 0.13 11.695 -1.211 2012-09-12T04:37:15.977200384 INFO 2025-06-26 19:16:47,903 calibrate.py _nudge_pos():1806 [1] 611: 0.110 0.0001077 0.0000232 30 0.10 166.204 44.553 2012-09-12T04:37:21.976789504 INFO 2025-06-26 19:16:48,121 calibrate.py _nudge_pos():1806 [1] 634: 0.120 0.0039309 0.0001950 15400 51.33 11.416 0.704 2012-09-12T05:29:03.974288128 INFO 2025-06-26 19:16:49,058 calibrate.py _nudge_pos():1806 [1] 733: 0.130 0.0025300 0.0004865 15620 52.06 7.240 1.732 2012-09-12T06:22:45.973565952 INFO 2025-06-26 19:16:49,212 calibrate.py _nudge_pos():1806 [1] 749: 0.130 0.0000320 -0.0000489 15 0.05 102.302 -194.198 2012-09-12T06:23:03.972333056 INFO 2025-06-26 19:16:50,055 calibrate.py _nudge_pos():1806 [1] 838: 0.120 0.0000880 -0.0007476 5230 17.43 0.752 -7.948 2012-09-12T06:41:57.974648576 INFO 2025-06-26 19:16:50,093 calibrate.py _nudge_pos():1806 [1] 842: 0.130 0.0000035 0.0000133 160 0.53 0.983 4.639 2012-09-12T06:42:32.972251136 INFO 2025-06-26 19:16:50,363 calibrate.py _nudge_pos():1862 [1] 834: - - - 0 0.00 - - INFO 2025-06-26 19:16:50,363 calibrate.py _nudge_pos():1868 [1] Points in final series = 78117 WARNING 2025-06-26 19:16:50,468 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:16:58,157 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 4 of 62588 INFO 2025-06-26 19:16:58,624 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:16:59,211 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:16:59,670 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:16:59,672 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.256.00/ctd1.nc INFO 2025-06-26 19:16:59,673 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:16:59,673 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 19:16:59,673 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:17:00,225 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:17:00,683 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:17:00,685 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.256.00/ctd2.nc INFO 2025-06-26 19:17:00,686 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:17:00,686 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 19:17:00,686 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:17:00,713 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:17:01,448 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 66600 66601] INFO 2025-06-26 19:17:01,586 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:17:15,830 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.256.00 ERROR 2025-06-26 19:17:15,830 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.256.00 INFO 2025-06-26 19:17:15,894 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_cal.nc INFO 2025-06-26 19:17:16,019 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 19:17:16,024 process.py align():251 [1] Alignment steps for 2012.256.00 INFO 2025-06-26 19:17:16,061 align.py process_cal():139 [1] Processing dorado_2012.256.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.256.00 INFO 2025-06-26 19:17:16,097 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:17:16,103 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:17:16,186 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:17:16,193 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:17:16,268 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:17:16,273 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:17:16,307 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:17:16,307 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:17:16,328 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:17:16,333 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:17:16,388 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,392 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,441 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,445 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,497 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,500 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,551 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,555 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,607 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,611 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,659 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,663 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,731 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,736 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,813 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,818 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,869 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,873 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,922 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,926 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:16,977 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:16,982 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,030 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,034 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,085 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,089 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,138 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,142 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,194 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,198 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,249 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,254 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,304 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,308 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,357 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,362 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,412 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,416 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,466 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,470 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,522 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,526 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,576 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.256.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:17:17,580 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:17:17,658 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 19:17:17,722 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 19:17:17,765 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 19:17:17,809 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:17:17,863 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:17:17,930 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:17:18,332 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:17:18,371 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_align.nc INFO 2025-06-26 19:17:18,499 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 19:17:18,501 process.py resample():273 [1] Resampling steps for 2012.256.00 INFO 2025-06-26 19:17:18,502 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:17:18,536 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_align.nc mission netCDF file INFO 2025-06-26 19:17:18,542 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_align.nc mission netCDF file INFO 2025-06-26 19:17:18,544 resample.py get_mission_start_end():1145 [1] navigation: 2012-09-12T02:22:36.980649728 to 2012-09-12T06:43:01.180318720 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 19:17:18,545 resample.py get_mission_start_end():1145 [1] hs2 : 2012-09-12T02:22:07.982636288 to 2012-09-12T06:43:01.170319360 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 19:17:18,547 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-09-12T02:22:44.420140032 to 2012-09-12T06:43:01.170319360 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 19:17:18,549 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-09-12T02:22:28.501230592 to 2012-09-12T06:43:01.250313984 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:17:18,550 resample.py get_mission_start_end():1145 [1] isus : 2012-09-12T02:23:16.177964544 to 2012-09-12T06:42:59.560429568 (0 days 00:00:01.689884416 before mission_end) INFO 2025-06-26 19:17:18,551 resample.py get_mission_start_end():1145 [1] biolume : 2012-09-12T02:22:00.403121152 to 2012-09-12T06:43:00.410337280 (0 days 00:00:00.839976704 before mission_end) INFO 2025-06-26 19:17:18,553 resample.py get_mission_start_end():1145 [1] tailcone : 2012-09-12T02:22:00.893121792 to 2012-09-12T06:43:01.250313984 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:17:18,554 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_align.nc mission netCDF file INFO 2025-06-26 19:17:18,554 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,734 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,766 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,796 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,825 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,853 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,880 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,906 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,932 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,957 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:18,981 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,005 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,030 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,054 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,078 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,102 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,126 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,149 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,175 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,202 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,227 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,253 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,279 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,305 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,331 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,346 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,359 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,370 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,382 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,393 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:19,397 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:17:19,397 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:17:19,961 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:17:20,067 resample.py add_biolume_proxies():633 [1] Zero flow values found: 870 of 15661 - replaced with 350 ml/s INFO 2025-06-26 19:17:20,068 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:17:20,123 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:17:20,148 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:17:20,170 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:17:20,170 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:17:20,204 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:17:20,401 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_1S.nc INFO 2025-06-26 19:17:20,410 create_products.py gulper_odv():401 [1] No gulper times found for 2012.256.00 INFO 2025-06-26 19:17:20,410 process.py archive():337 [1] Archiving steps for 2012.256.00 INFO 2025-06-26 19:17:20,410 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:17:20,410 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:17:20,412 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.256.00_1S.nc INFO 2025-06-26 19:17:20,431 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:17:20,432 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.256.00_cal.nc INFO 2025-06-26 19:17:20,533 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:17:20,534 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.256.00_align.nc INFO 2025-06-26 19:17:20,677 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:17:20,699 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,719 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,724 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,741 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,798 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,805 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,824 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,840 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,881 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012256/2012.256.00 done. INFO 2025-06-26 19:17:20,882 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:17:20,882 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.256.00/dorado_2012.256.00_processing.log /Volumes/AUVCTD/surveys/2012/netcdf