INFO 2025-06-26 13:54:49,291 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 13:54:49,291 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy group missions over canyon axis between M0 & M1 (gulper trips in nice layers) - ctdToUse = ctd1 INFO 2025-06-26 13:54:49,291 process.py process_mission():449 [1] Processing AUVCTD mission 2008.010.07 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:54:49,291 process.py download_process():165 [1] Download and processing steps for 2008.010.07 INFO 2025-06-26 13:54:49,291 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.07 INFO 2025-06-26 13:54:49,291 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.07 to /data/auv_data/dorado/missionlogs/2008.010.07 INFO 2025-06-26 13:54:52,802 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.010.07 INFO 2025-06-26 13:54:52,802 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/ctdDriver.log (3116262 bytes) INFO 2025-06-26 13:54:53,028 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/ctdDriver2.log (3116447 bytes) INFO 2025-06-26 13:54:53,259 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/gps.log (80276 bytes) INFO 2025-06-26 13:54:53,276 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/hydroscatlog.log (1953374 bytes) INFO 2025-06-26 13:54:53,511 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/navigation.log (9084928 bytes) WARNING 2025-06-26 13:54:53,994 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 8 bytes, b = b'\x00\x00\x00\x00\x00\x00' at record 38486, for heading_bias in file /data/auv_data/dorado/missionlogs/2008.010.07/navigation.log INFO 2025-06-26 13:54:53,994 logs2netcdfs.py _read_data():224 [1] bytes read = 9084930 file size = 9084928 INFO 2025-06-26 13:54:53,994 logs2netcdfs.py _read_data():229 [1] Tried to read 8 bytes, but only 2 bytes remaining INFO 2025-06-26 13:54:53,995 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 38486 records WARNING 2025-06-26 13:54:54,086 logs2netcdfs.py _create_variable():536 [1] latitude: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (38487,) and arg 1 with shape (38486,). INFO 2025-06-26 13:54:54,086 logs2netcdfs.py _create_variable():537 [1] len(data) (38486) does not match shape of latitude.shape[0] (38487) WARNING 2025-06-26 13:54:54,086 logs2netcdfs.py _create_variable():544 [1] latitude data is short by one, appending the last value: 0.6421101033807444 WARNING 2025-06-26 13:54:54,091 logs2netcdfs.py _create_variable():536 [1] longitude: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (38487,) and arg 1 with shape (38486,). INFO 2025-06-26 13:54:54,091 logs2netcdfs.py _create_variable():537 [1] len(data) (38486) does not match shape of longitude.shape[0] (38487) WARNING 2025-06-26 13:54:54,091 logs2netcdfs.py _create_variable():544 [1] longitude data is short by one, appending the last value: -2.1283091555886777 INFO 2025-06-26 13:54:54,176 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/isuslog.log (201621 bytes) INFO 2025-06-26 13:54:54,199 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/parosci.log (3201110 bytes) INFO 2025-06-26 13:54:54,474 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/tailCone.log (404155 bytes) INFO 2025-06-26 13:54:54,534 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.07/biolume.log (2218572 bytes) INFO 2025-06-26 13:54:54,750 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:54:54,874 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.07 seconds WARNING 2025-06-26 13:54:54,874 process.py download_process():196 [1] No lopc.bin file for 2008.010.07 INFO 2025-06-26 13:54:54,875 process.py calibrate():227 [1] Calibration steps for 2008.010.07 INFO 2025-06-26 13:54:54,978 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 13:54:54,980 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:54:55,559 calibrate.py _nudge_pos():1806 [1] 84: 0.060 0.0001134 0.0000368 1270 4.23 3.980 1.611 2008-01-10T17:28:11.729870080 INFO 2025-06-26 13:54:57,122 calibrate.py _nudge_pos():1806 [1] 253: 0.070 0.0041448 -0.0006339 7380 24.60 25.013 -4.775 2008-01-10T17:55:35.727248384 INFO 2025-06-26 13:54:58,516 calibrate.py _nudge_pos():1806 [1] 403: 0.070 -0.0003124 0.0003537 9305 31.01 -1.495 2.113 2008-01-10T18:29:05.729553920 INFO 2025-06-26 13:55:00,613 calibrate.py _nudge_pos():1806 [1] 627: 0.080 0.0041980 0.0001590 7675 25.58 24.360 1.152 2008-01-10T18:58:23.729122560 WARNING 2025-06-26 13:55:01,983 calibrate.py _nudge_pos():1789 [1] abs(end_sec_diff) (86.484075264) > max_sec_diff_at_end (10) INFO 2025-06-26 13:55:01,983 calibrate.py _nudge_pos():1794 [1] Overriding end_lon_diff (-0.0019480523833976804) and end_lat_diff (0.0003580935743840996) by setting them to 0 INFO 2025-06-26 13:55:01,985 calibrate.py _nudge_pos():1806 [1] 775: 86.484 0.0000000 0.0000000 9153 30.51 -9.476 2.175 2008-01-10T19:31:21.323648256 INFO 2025-06-26 13:55:02,665 calibrate.py _nudge_pos():1862 [1] 747: - - - 0 0.00 - - INFO 2025-06-26 13:55:02,665 calibrate.py _nudge_pos():1868 [1] Points in final series = 38487 WARNING 2025-06-26 13:55:02,721 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 13:55:03,027 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:03,344 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:03,586 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:03,588 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.010.07/ctd1.nc INFO 2025-06-26 13:55:03,589 calibrate.py _range_qc_combined_nc():898 [1] Setting 3 ctd1_salinity values to NaN INFO 2025-06-26 13:55:03,590 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 13:55:03,590 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:55:03,886 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:04,128 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:04,130 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.010.07/ctd2.nc INFO 2025-06-26 13:55:04,131 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 13:55:04,131 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 13:55:04,131 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:55:04,149 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:55:04,625 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 780 781 782 2220 14520 14521 14522 20460 20461 20462 72240 72241 187140 244380 470220 470221 474600 486900 486901 486902 487620 487621] INFO 2025-06-26 13:55:04,700 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -8 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 13:55:04,706 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 13:55:04,706 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.010.07 ERROR 2025-06-26 13:55:04,706 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.010.07 INFO 2025-06-26 13:55:04,716 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_cal.nc INFO 2025-06-26 13:55:04,780 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_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_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 13:55:04,784 process.py align():251 [1] Alignment steps for 2008.010.07 INFO 2025-06-26 13:55:04,809 align.py process_cal():139 [1] Processing dorado_2008.010.07_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.010.07 INFO 2025-06-26 13:55:04,824 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:04,827 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:04,859 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:04,862 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:04,893 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:04,897 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:04,915 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:55:04,916 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:55:04,928 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:04,931 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:04,963 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:04,966 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:04,996 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:04,999 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,030 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,033 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,062 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,065 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,095 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,098 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,127 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,130 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,160 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,163 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,192 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,195 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,225 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,228 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,257 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,261 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,294 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,298 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,328 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,332 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,363 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,367 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,399 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,402 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,435 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,438 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,469 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,473 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,503 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,507 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,537 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,541 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,572 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,576 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,605 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,609 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,640 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,643 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,675 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:05,678 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:05,715 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:05,745 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:05,773 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:05,803 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:55:05,832 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.03 INFO 2025-06-26 13:55:05,845 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_align.nc INFO 2025-06-26 13:55:05,903 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_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_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 13:55:05,905 process.py resample():273 [1] Resampling steps for 2008.010.07 INFO 2025-06-26 13:55:05,906 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:55:05,931 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_align.nc mission netCDF file INFO 2025-06-26 13:55:05,936 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_align.nc mission netCDF file INFO 2025-06-26 13:55:05,937 resample.py get_mission_start_end():1145 [1] navigation: 2008-01-10T17:23:04.220935936 to 2008-01-10T19:31:21.323648256 (0 days 00:06:54.471606784 before mission_end) WARNING 2025-06-26 13:55:05,938 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 00:06:54.471606784 INFO 2025-06-26 13:55:05,939 resample.py get_mission_start_end():1145 [1] hs2 : 2008-01-10T17:22:37.182788096 to 2008-01-10T19:38:15.685262336 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 13:55:05,941 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-01-10T17:22:59.211278848 to 2008-01-10T19:38:15.795255040 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:55:05,943 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-01-10T17:22:59.461261824 to 2008-01-10T19:38:15.775256064 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 13:55:05,944 resample.py get_mission_start_end():1145 [1] isus : 2008-01-10T17:23:50.727749888 to 2008-01-10T19:38:14.785324032 (0 days 00:00:01.009931008 before mission_end) INFO 2025-06-26 13:55:05,946 resample.py get_mission_start_end():1145 [1] biolume : 2008-01-10T17:22:31.203163392 to 2008-01-10T19:38:15.285255680 (0 days 00:00:00.509999360 before mission_end) INFO 2025-06-26 13:55:05,947 resample.py get_mission_start_end():1145 [1] tailcone : 2008-01-10T17:22:36.322846976 to 2008-01-10T19:38:15.425280256 (0 days 00:00:00.369974784 before mission_end) INFO 2025-06-26 13:55:05,948 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_align.nc mission netCDF file INFO 2025-06-26 13:55:05,948 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,056 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,056 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 00:06:54.471606784 of NaNs to the end of mission INFO 2025-06-26 13:55:06,077 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,077 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 00:06:54.471606784 of NaNs to the end of mission INFO 2025-06-26 13:55:06,098 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,099 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 00:06:54.471606784 of NaNs to the end of mission INFO 2025-06-26 13:55:06,119 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,119 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 00:06:54.471606784 of NaNs to the end of mission INFO 2025-06-26 13:55:06,139 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,158 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,176 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,193 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,210 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,226 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,244 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,260 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,280 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,305 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,323 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,339 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,355 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,373 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,391 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,408 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,426 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,444 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,461 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,479 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,490 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,501 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,511 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,523 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,535 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:06,680 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_1S.nc INFO 2025-06-26 13:55:08,466 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:55:14,743 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.010.07/dorado_2008.010.07_1S_Gulper.txt INFO 2025-06-26 13:55:14,743 process.py archive():337 [1] Archiving steps for 2008.010.07 INFO 2025-06-26 13:55:14,743 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07, BASE_PATH = /data/auv_data INFO 2025-06-26 13:55:14,743 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 13:55:14,745 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.07_1S.nc INFO 2025-06-26 13:55:14,757 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:14,759 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.07_cal.nc INFO 2025-06-26 13:55:14,798 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:14,799 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.07_align.nc INFO 2025-06-26 13:55:14,834 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:14,849 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,861 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,866 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,876 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,902 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,907 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,920 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,926 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,951 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.07 done. INFO 2025-06-26 13:55:14,952 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:55:14,954 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.010.07_1S_Gulper.txt INFO 2025-06-26 13:55:14,959 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.010.07/dorado_2008.010.07_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 13:55:14,959 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.07/dorado_2008.010.07_processing.log /Volumes/AUVCTD/surveys/2008/netcdf