INFO 2025-06-26 05:55:46,496 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 05:55:46,497 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/18/05 - ctdToUse = ctd1 INFO 2025-06-26 05:55:46,497 process.py process_mission():449 [1] Processing OCCO mission 2004.240.00 by user docker_user on host 671049448ece INFO 2025-06-26 05:55:46,497 process.py download_process():165 [1] Download and processing steps for 2004.240.00 INFO 2025-06-26 05:55:46,497 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004240/2004.240.00 INFO 2025-06-26 05:55:46,497 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004240/2004.240.00 to /data/auv_data/dorado/missionlogs/2004.240.00 INFO 2025-06-26 05:55:49,373 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.240.00 INFO 2025-06-26 05:55:49,373 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/ctdDriver.log (9203347 bytes) INFO 2025-06-26 05:55:50,066 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/ctdDriver2.log (9195069 bytes) INFO 2025-06-26 05:55:50,768 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/gps.log (67172 bytes) INFO 2025-06-26 05:55:50,783 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/hydroscatlog.log (6275954 bytes) INFO 2025-06-26 05:55:51,498 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.240.00/hydroscatlog.log: [ 53 16592] INFO 2025-06-26 05:55:51,514 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/navigation.log (20391859 bytes) INFO 2025-06-26 05:55:53,014 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/isuslog.log (507772 bytes) INFO 2025-06-26 05:55:53,067 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/parosci.log (6279062 bytes) INFO 2025-06-26 05:55:53,596 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/tailCone.log (6279403 bytes) INFO 2025-06-26 05:55:54,370 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.240.00/biolume.log (7119740 bytes) INFO 2025-06-26 05:55:55,090 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:55:55,458 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.08 seconds WARNING 2025-06-26 05:55:55,458 process.py download_process():196 [1] No lopc.bin file for 2004.240.00 INFO 2025-06-26 05:55:55,458 process.py calibrate():227 [1] Calibration steps for 2004.240.00 INFO 2025-06-26 05:55:55,664 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 05:55:55,666 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:55:56,989 calibrate.py _nudge_pos():1806 [1] 155: 0.160 -0.0000438 0.0000077 15 0.05 -139.023 30.423 2004-08-27T03:34:08.049566976 INFO 2025-06-26 05:55:57,208 calibrate.py _nudge_pos():1806 [1] 178: 0.160 0.0002247 0.0002695 1975 6.58 5.059 7.589 2004-08-27T03:41:05.051000576 INFO 2025-06-26 05:55:58,006 calibrate.py _nudge_pos():1806 [1] 260: 0.150 -0.0013732 0.0004307 10185 33.95 -5.994 2.351 2004-08-27T04:16:23.055907200 INFO 2025-06-26 05:55:58,056 calibrate.py _nudge_pos():1806 [1] 265: 0.150 -0.0014199 0.0004279 35 0.11 -1856.541 699.684 2004-08-27T04:16:34.055153664 INFO 2025-06-26 05:55:58,153 calibrate.py _nudge_pos():1806 [1] 275: 0.160 -0.0000243 -0.0000017 24 0.08 -46.968 -4.027 2004-08-27T04:16:48.054194688 INFO 2025-06-26 05:55:58,495 calibrate.py _nudge_pos():1806 [1] 310: 0.160 -0.0010631 0.0004421 10325 34.41 -4.579 2.381 2004-08-27T04:51:47.050403584 INFO 2025-06-26 05:55:58,544 calibrate.py _nudge_pos():1806 [1] 315: 0.020 -0.0000232 -0.0000192 17 0.05 -64.369 -66.847 2004-08-27T04:51:54.449896832 INFO 2025-06-26 05:55:58,906 calibrate.py _nudge_pos():1806 [1] 352: 0.020 -0.0013510 0.0003928 10017 33.39 -6.000 2.180 2004-08-27T05:25:53.450215552 INFO 2025-06-26 05:55:59,322 calibrate.py _nudge_pos():1806 [1] 394: 0.160 -0.0026903 -0.0014110 11195 37.31 -10.696 -7.007 2004-08-27T06:03:53.054052096 INFO 2025-06-26 05:55:59,787 calibrate.py _nudge_pos():1806 [1] 442: 0.160 -0.0010697 -0.0019424 11102 37.01 -4.289 -9.724 2004-08-27T06:41:41.058683136 INFO 2025-06-26 05:56:00,238 calibrate.py _nudge_pos():1806 [1] 487: 0.170 -0.0006433 -0.0024997 10670 35.56 -2.685 -13.025 2004-08-27T07:17:59.049480448 INFO 2025-06-26 05:56:00,658 calibrate.py _nudge_pos():1806 [1] 529: 0.170 -0.0003711 -0.0008749 3305 11.01 -5.003 -14.721 2004-08-27T07:29:41.051390208 INFO 2025-06-26 05:56:01,094 calibrate.py _nudge_pos():1806 [1] 572: 0.170 0.0037839 -0.0023016 11130 37.10 15.149 -11.497 2004-08-27T08:07:29.056021248 INFO 2025-06-26 05:56:01,612 calibrate.py _nudge_pos():1806 [1] 624: 0.170 0.0022583 -0.0005061 8864 29.55 11.354 -3.174 2004-08-27T08:37:53.051069056 INFO 2025-06-26 05:56:01,796 calibrate.py _nudge_pos():1806 [1] 642: 0.170 -0.0001380 0.0000561 25 0.08 -256.269 129.984 2004-08-27T08:38:16.049493376 INFO 2025-06-26 05:56:02,125 calibrate.py _nudge_pos():1806 [1] 674: 0.030 0.0017508 0.0013450 9512 31.70 8.206 7.861 2004-08-27T09:10:29.457046016 INFO 2025-06-26 05:56:02,136 calibrate.py _nudge_pos():1806 [1] 675: 0.170 0.0017618 0.0013297 153 0.51 516.743 486.321 2004-08-27T09:11:00.054949760 INFO 2025-06-26 05:56:02,270 calibrate.py _nudge_pos():1806 [1] 688: 0.170 -0.0000168 0.0000018 55 0.18 -13.834 1.803 2004-08-27T09:11:23.053374336 INFO 2025-06-26 05:56:02,679 calibrate.py _nudge_pos():1806 [1] 727: 0.170 0.0021538 0.0012738 11240 37.46 8.546 6.300 2004-08-27T09:49:29.056772480 INFO 2025-06-26 05:56:03,224 calibrate.py _nudge_pos():1806 [1] 780: 0.180 0.0018054 0.0012421 10390 34.63 7.752 6.646 2004-08-27T10:24:59.050857728 INFO 2025-06-26 05:56:03,697 calibrate.py _nudge_pos():1806 [1] 827: 0.180 0.0003539 0.0001611 2708 9.02 5.833 3.307 2004-08-27T10:34:47.050576896 INFO 2025-06-26 05:56:04,156 calibrate.py _nudge_pos():1806 [1] 873: 0.180 0.0005074 0.0003769 3375 11.25 6.710 6.210 2004-08-27T10:46:47.051253504 INFO 2025-06-26 05:56:04,632 calibrate.py _nudge_pos():1862 [1] 900: - - - 5 0.01 - - INFO 2025-06-26 05:56:04,632 calibrate.py _nudge_pos():1868 [1] Points in final series = 130708 WARNING 2025-06-26 05:56:04,735 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:56:18,431 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 05:56:19,377 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 05:56:20,151 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 05:56:20,154 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.240.00/ctd1.nc INFO 2025-06-26 05:56:20,155 calibrate.py _range_qc_combined_nc():898 [1] Setting 57 ctd1_salinity values to NaN INFO 2025-06-26 05:56:20,155 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 05:56:20,155 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:56:21,119 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:56:21,882 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:56:21,884 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.240.00/ctd2.nc INFO 2025-06-26 05:56:21,886 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 05:56:21,886 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 05:56:21,886 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:56:21,923 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:56:23,223 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 816660 1361760] INFO 2025-06-26 05:56:23,454 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 05:56:23,460 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 05:56:23,461 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.240.00 ERROR 2025-06-26 05:56:23,461 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.240.00 INFO 2025-06-26 05:56:23,567 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_cal.nc INFO 2025-06-26 05:56:23,666 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 05:56:23,671 process.py align():251 [1] Alignment steps for 2004.240.00 INFO 2025-06-26 05:56:23,700 align.py process_cal():139 [1] Processing dorado_2004.240.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.240.00 INFO 2025-06-26 05:56:23,739 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:56:23,743 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:56:23,838 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:56:23,844 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:56:23,936 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:56:23,942 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:56:23,998 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:56:23,998 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:56:24,036 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:56:24,041 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:56:24,129 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:56:24,134 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,215 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:56:24,220 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,300 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:56:24,305 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,387 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,392 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,479 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,560 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,565 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,646 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,651 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,732 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,737 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,818 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,823 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,903 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,908 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:24,992 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:24,997 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,078 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,084 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,165 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,170 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,250 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,256 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,338 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,343 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,424 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,430 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,513 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,518 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,599 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,604 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,686 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,692 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,774 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:56:25,779 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:56:25,867 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:56:25,921 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:56:25,979 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:56:26,037 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:56:26,099 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:56:26,162 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_align.nc INFO 2025-06-26 05:56:26,251 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 05:56:26,253 process.py resample():273 [1] Resampling steps for 2004.240.00 INFO 2025-06-26 05:56:26,254 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:56:26,281 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_align.nc mission netCDF file INFO 2025-06-26 05:56:26,288 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_align.nc mission netCDF file INFO 2025-06-26 05:56:26,289 resample.py get_mission_start_end():1145 [1] navigation: 2004-08-27T03:31:52.658841856 to 2004-08-27T10:47:35.077963648 (0 days 00:00:00.119991680 before mission_end) INFO 2025-06-26 05:56:26,291 resample.py get_mission_start_end():1145 [1] hs2 : 2004-08-27T03:31:36.389956480 to 2004-08-27T10:47:34.997969152 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 05:56:26,293 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-08-27T03:31:51.348931840 to 2004-08-27T10:47:35.017967744 (0 days 00:00:00.179987584 before mission_end) INFO 2025-06-26 05:56:26,295 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-08-27T03:32:15.287291776 to 2004-08-27T10:47:35.167957248 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 05:56:26,296 resample.py get_mission_start_end():1145 [1] isus : 2004-08-27T03:32:47.000000000 to 2004-08-27T10:47:31.000000000 (0 days 00:00:04.197955328 before mission_end) INFO 2025-06-26 05:56:26,298 resample.py get_mission_start_end():1145 [1] biolume : 2004-08-27T03:31:31.160280448 to 2004-08-27T10:47:33.918008832 (0 days 00:00:01.279946496 before mission_end) INFO 2025-06-26 05:56:26,300 resample.py get_mission_start_end():1145 [1] tailcone : 2004-08-27T03:31:30.440364160 to 2004-08-27T10:47:35.197955328 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:56:26,300 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_align.nc mission netCDF file INFO 2025-06-26 05:56:26,301 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,585 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,634 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,681 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,728 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,771 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,813 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,853 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,894 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,932 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:26,972 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,011 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,048 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,085 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,122 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,159 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,195 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,235 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,275 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,315 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,356 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,396 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,435 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,454 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,469 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,483 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,500 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,546 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 05:56:27,790 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_1S.nc INFO 2025-06-26 05:56:28,996 create_products.py gulper_odv():401 [1] No gulper times found for 2004.240.00 INFO 2025-06-26 05:56:28,996 process.py archive():337 [1] Archiving steps for 2004.240.00 INFO 2025-06-26 05:56:28,996 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00, BASE_PATH = /data/auv_data INFO 2025-06-26 05:56:28,996 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 05:56:28,997 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.240.00_1S.nc INFO 2025-06-26 05:56:29,021 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:56:29,022 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.240.00_cal.nc INFO 2025-06-26 05:56:29,132 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:56:29,132 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.240.00_align.nc INFO 2025-06-26 05:56:29,241 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:56:29,274 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,304 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,309 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,330 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,394 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,401 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,423 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,449 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004240/2004.240.00 done. INFO 2025-06-26 05:56:29,537 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:56:29,537 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.240.00/dorado_2004.240.00_processing.log /Volumes/AUVCTD/surveys/2004/netcdf