INFO 2025-06-26 10:58:18,491 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 10:58:18,491 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled by DMO 9/6/05 - ctdToUse = ctd1 INFO 2025-06-26 10:58:18,491 process.py process_mission():449 [1] Processing LOCO mission 2005.249.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:58:18,491 process.py download_process():165 [1] Download and processing steps for 2005.249.00 INFO 2025-06-26 10:58:18,491 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005249/2005.249.00 INFO 2025-06-26 10:58:18,492 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005249/2005.249.00 to /data/auv_data/dorado/missionlogs/2005.249.00 INFO 2025-06-26 10:58:21,457 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.249.00 INFO 2025-06-26 10:58:21,458 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/ctdDriver.log (8190555 bytes) INFO 2025-06-26 10:58:22,076 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/ctdDriver2.log (8190461 bytes) INFO 2025-06-26 10:58:22,676 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/gps.log (80348 bytes) INFO 2025-06-26 10:58:22,694 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/hydroscatlog.log (5587754 bytes) INFO 2025-06-26 10:58:23,357 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.249.00/hydroscatlog.log: [1370] INFO 2025-06-26 10:58:23,372 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/navigation.log (27462030 bytes) INFO 2025-06-26 10:58:25,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/isuslog.log (498453 bytes) INFO 2025-06-26 10:58:25,349 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/parosci.log (11954102 bytes) INFO 2025-06-26 10:58:26,310 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.249.00/parosci.log: [248983] INFO 2025-06-26 10:58:26,340 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/tailCone.log (5590411 bytes) INFO 2025-06-26 10:58:27,020 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.249.00/biolume.log (6339372 bytes) INFO 2025-06-26 10:58:27,617 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:58:27,938 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.48 seconds WARNING 2025-06-26 10:58:27,938 process.py download_process():196 [1] No lopc.bin file for 2005.249.00 INFO 2025-06-26 10:58:27,938 process.py calibrate():227 [1] Calibration steps for 2005.249.00 INFO 2025-06-26 10:58:28,140 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 10:58:28,142 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:58:28,899 calibrate.py _nudge_pos():1806 [1] 97: 0.120 -0.0003789 -0.0002113 1265 4.21 -13.320 -9.291 2005-09-06T16:04:32.740859520 INFO 2025-06-26 10:58:29,816 calibrate.py _nudge_pos():1806 [1] 192: 0.130 -0.0000534 -0.0000171 8050 26.83 -0.295 -0.118 2005-09-06T16:32:56.734128000 INFO 2025-06-26 10:58:30,845 calibrate.py _nudge_pos():1806 [1] 301: 0.140 -0.0000887 0.0000450 8190 27.30 -0.482 0.306 2005-09-06T17:02:02.734518784 INFO 2025-06-26 10:58:31,605 calibrate.py _nudge_pos():1806 [1] 381: 0.130 -0.0002047 0.0000214 8425 28.08 -1.081 0.141 2005-09-06T17:31:26.733676416 INFO 2025-06-26 10:58:32,324 calibrate.py _nudge_pos():1806 [1] 456: 0.120 -0.0002234 -0.0000060 8420 28.06 -1.181 -0.039 2005-09-06T18:00:44.743244672 INFO 2025-06-26 10:58:32,920 calibrate.py _nudge_pos():1806 [1] 518: 0.130 -0.0002107 -0.0000912 8305 27.68 -1.129 -0.611 2005-09-06T18:29:26.735280000 INFO 2025-06-26 10:58:33,077 calibrate.py _nudge_pos():1806 [1] 534: 0.150 0.0000040 0.0000719 25 0.08 7.490 166.505 2005-09-06T18:29:46.733910144 INFO 2025-06-26 10:58:33,694 calibrate.py _nudge_pos():1806 [1] 598: 0.120 -0.0004667 -0.0012226 9635 32.11 -2.157 -7.054 2005-09-06T19:02:56.737585536 INFO 2025-06-26 10:58:34,234 calibrate.py _nudge_pos():1806 [1] 654: 0.120 -0.0013237 0.0001182 8815 29.38 -6.683 0.745 2005-09-06T19:33:14.743043456 INFO 2025-06-26 10:58:34,622 calibrate.py _nudge_pos():1806 [1] 694: 0.140 -0.0016482 0.0004073 8475 28.25 -8.653 2.672 2005-09-06T20:02:08.734257024 INFO 2025-06-26 10:58:35,277 calibrate.py _nudge_pos():1806 [1] 761: 0.130 -0.0013128 0.0004727 7865 26.21 -7.425 3.342 2005-09-06T20:29:27.741977216 INFO 2025-06-26 10:58:35,436 calibrate.py _nudge_pos():1806 [1] 777: 0.130 -0.0000186 -0.0000075 15 0.05 -59.148 -29.889 2005-09-06T20:29:45.740744320 INFO 2025-06-26 10:58:35,535 calibrate.py _nudge_pos():1806 [1] 787: 0.130 0.0000598 0.0000259 15 0.05 189.852 102.999 2005-09-06T20:29:57.739922304 INFO 2025-06-26 10:58:35,957 calibrate.py _nudge_pos():1806 [1] 830: 0.140 -0.0010462 0.0002371 5725 19.08 -8.127 2.303 2005-09-06T20:49:44.738607360 INFO 2025-06-26 10:58:36,561 calibrate.py _nudge_pos():1806 [1] 892: 0.130 -0.0018956 -0.0019781 6925 23.08 -12.172 -15.882 2005-09-06T21:13:50.739549440 INFO 2025-06-26 10:58:37,255 calibrate.py _nudge_pos():1806 [1] 963: 0.150 -0.0025732 -0.0022175 8080 26.93 -14.157 -15.258 2005-09-06T21:41:56.734050944 INFO 2025-06-26 10:58:37,714 calibrate.py _nudge_pos():1806 [1] 1010: 0.140 -0.0026361 -0.0022085 8260 27.53 -14.184 -14.865 2005-09-06T22:10:14.737729792 INFO 2025-06-26 10:58:38,334 calibrate.py _nudge_pos():1806 [1] 1073: 0.140 -0.0015518 -0.0010816 4550 15.16 -15.157 -13.218 2005-09-06T22:26:26.741143040 INFO 2025-06-26 10:58:38,642 calibrate.py _nudge_pos():1862 [1] 1082: - - - 2 0.00 - - INFO 2025-06-26 10:58:38,642 calibrate.py _nudge_pos():1868 [1] Points in final series = 116356 WARNING 2025-06-26 10:58:42,642 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:58:55,011 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:58:55,889 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:58:56,588 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:58:56,590 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.249.00/ctd1.nc INFO 2025-06-26 10:58:56,591 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 10:58:56,592 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 10:58:56,592 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:58:57,417 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:58:58,135 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:58:58,137 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.249.00/ctd2.nc INFO 2025-06-26 10:58:58,138 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:58:58,139 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 10:58:58,139 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:58:58,174 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:58:59,308 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 3780 4980 21960 796260 910560 1138920 1181400 1338180] INFO 2025-06-26 10:58:59,523 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:58:59,529 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 10:58:59,529 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.249.00 ERROR 2025-06-26 10:58:59,529 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.249.00 INFO 2025-06-26 10:58:59,620 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_cal.nc INFO 2025-06-26 10:58:59,724 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 10:58:59,729 process.py align():251 [1] Alignment steps for 2005.249.00 INFO 2025-06-26 10:58:59,757 align.py process_cal():139 [1] Processing dorado_2005.249.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.249.00 INFO 2025-06-26 10:58:59,791 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:58:59,795 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:58:59,878 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:58:59,883 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:58:59,963 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:58:59,968 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:59:00,022 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:59:00,022 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:59:00,056 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:59:00,062 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:59:00,140 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:59:00,145 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,215 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:59:00,220 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,292 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:59:00,297 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,368 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,373 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,445 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,449 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,518 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,522 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,592 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,597 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,667 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,672 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,742 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,747 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,816 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,821 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,892 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,896 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:00,966 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:00,970 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,041 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,045 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,116 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,121 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,212 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,216 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,293 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,364 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,369 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,440 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,444 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,515 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,520 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,591 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:59:01,596 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:59:01,685 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:59:01,749 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:59:01,812 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:59:01,877 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:59:01,946 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:59:02,003 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_align.nc INFO 2025-06-26 10:59:02,087 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 10:59:02,089 process.py resample():273 [1] Resampling steps for 2005.249.00 INFO 2025-06-26 10:59:02,090 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:59:02,116 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_align.nc mission netCDF file INFO 2025-06-26 10:59:02,122 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_align.nc mission netCDF file INFO 2025-06-26 10:59:02,123 resample.py get_mission_start_end():1145 [1] navigation: 2005-09-06T15:59:06.143232768 to 2005-09-06T22:26:57.139060480 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 10:59:02,125 resample.py get_mission_start_end():1145 [1] hs2 : 2005-09-06T15:58:48.724426240 to 2005-09-06T22:26:57.049066752 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 10:59:02,127 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-09-06T15:59:11.302879616 to 2005-09-06T22:26:57.229054464 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:59:02,128 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-09-06T15:59:11.452869120 to 2005-09-06T22:26:57.159059072 (0 days 00:00:00.069995392 before mission_end) INFO 2025-06-26 10:59:02,130 resample.py get_mission_start_end():1145 [1] isus : 2005-09-06T16:00:17.518343424 to 2005-09-06T22:26:57.219054976 (0 days 00:00:00.009999488 before mission_end) INFO 2025-06-26 10:59:02,131 resample.py get_mission_start_end():1145 [1] biolume : 2005-09-06T15:58:43.954718592 to 2005-09-06T22:26:56.479071360 (0 days 00:00:00.749983104 before mission_end) INFO 2025-06-26 10:59:02,133 resample.py get_mission_start_end():1145 [1] tailcone : 2005-09-06T15:58:44.384723456 to 2005-09-06T22:26:57.139060480 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 10:59:02,133 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_align.nc mission netCDF file INFO 2025-06-26 10:59:02,134 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,390 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,434 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,477 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,519 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,557 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,595 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,631 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,667 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,701 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,734 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,768 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,801 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,835 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,867 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,900 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,933 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:02,970 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,006 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,041 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,077 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,111 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,146 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,162 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,178 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,192 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,208 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,248 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:59:03,479 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_1S.nc INFO 2025-06-26 10:59:04,809 create_products.py gulper_odv():401 [1] No gulper times found for 2005.249.00 INFO 2025-06-26 10:59:04,809 process.py archive():337 [1] Archiving steps for 2005.249.00 INFO 2025-06-26 10:59:04,809 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00, BASE_PATH = /data/auv_data INFO 2025-06-26 10:59:04,810 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:59:04,811 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.249.00_1S.nc INFO 2025-06-26 10:59:04,832 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:59:04,833 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.249.00_cal.nc INFO 2025-06-26 10:59:04,941 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:59:04,942 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.249.00_align.nc INFO 2025-06-26 10:59:05,037 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:59:05,066 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,092 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,097 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,116 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,190 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,197 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,232 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,256 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,324 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005249/2005.249.00 done. INFO 2025-06-26 10:59:05,325 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:59:05,325 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.249.00/dorado_2005.249.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf