INFO 2025-06-26 20:15:47,021 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 20:15:47,021 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:15:47,021 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.072.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:15:47,021 process.py download_process():165 [1] Download and processing steps for 2014.072.01 INFO 2025-06-26 20:15:47,021 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014072/2014.072.01 INFO 2025-06-26 20:15:47,021 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014072/2014.072.01 to /data/auv_data/dorado/missionlogs/2014.072.01 INFO 2025-06-26 20:15:50,470 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.072.01 INFO 2025-06-26 20:15:50,470 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/ctdDriver.log (5585670 bytes) INFO 2025-06-26 20:15:50,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/ctdDriver2.log (5585663 bytes) INFO 2025-06-26 20:15:51,258 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/gps.log (55940 bytes) INFO 2025-06-26 20:15:51,272 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/hydroscatlog.log (4892434 bytes) INFO 2025-06-26 20:15:51,767 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/navigation.log (20922210 bytes) INFO 2025-06-26 20:15:53,231 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/parosci.log (6871190 bytes) INFO 2025-06-26 20:15:53,817 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/tailCone.log (3497563 bytes) INFO 2025-06-26 20:15:54,243 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/biolume.log (4072698 bytes) INFO 2025-06-26 20:15:54,639 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:15:54,840 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.37 seconds INFO 2025-06-26 20:15:54,840 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.01/lopc.bin (52124139 bytes) INFO 2025-06-26 20:15:54,841 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:15:54 2025 INFO 2025-06-26 20:15:54,841 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.072.01/parosci.nc INFO 2025-06-26 20:15:54,841 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:15:54,841 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.072.01/parosci.nc INFO 2025-06-26 20:15:54,844 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1394734901.1, sensor_off_time = 1394749471.6 INFO 2025-06-26 20:15:54,844 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14570 seconds. Expecting to read 29140 L frames from the lopc.bin file. INFO 2025-06-26 20:15:54,844 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 29140 records from the lopc.bin file. INFO 2025-06-26 20:15:55,016 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-03-13 18:21:41 Z and endTime = 2014-03-13 22:24:31 Z with 29140 records expected to be read from lopc.bin INFO 2025-06-26 20:15:55,016 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.072.01/lopc.bin INFO 2025-06-26 20:15:55,016 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.072.01/lopc.nc INFO 2025-06-26 20:15:55,016 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.072.01/lopc.nc INFO 2025-06-26 20:15:55,017 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.072.01 INFO 2025-06-26 20:15:55,017 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:15:55,077 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:15:55,077 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:15:55,077 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:15:55,168 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:15:55,169 process.py calibrate():227 [1] Calibration steps for 2014.072.01 INFO 2025-06-26 20:15:55,317 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 20:15:55,319 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:15:55,923 calibrate.py _nudge_pos():1806 [1] 101: 0.120 -0.0027517 0.0026859 11205 37.35 -10.919 13.326 2014-03-13T19:00:39.015018752 INFO 2025-06-26 20:15:56,346 calibrate.py _nudge_pos():1806 [1] 146: 0.130 0.0004714 0.0049654 9350 31.16 2.242 29.525 2014-03-13T19:32:33.013900800 INFO 2025-06-26 20:15:56,742 calibrate.py _nudge_pos():1806 [1] 188: 0.130 0.0017046 0.0040215 8405 28.01 9.020 26.601 2014-03-13T20:01:15.015935488 INFO 2025-06-26 20:15:57,146 calibrate.py _nudge_pos():1806 [1] 231: 0.120 0.0010707 0.0000824 2250 7.50 21.174 2.038 2014-03-13T20:09:27.022230784 INFO 2025-06-26 20:15:57,629 calibrate.py _nudge_pos():1806 [1] 283: 0.130 0.0003741 0.0005931 4335 14.45 3.840 7.608 2014-03-13T20:24:45.019343616 INFO 2025-06-26 20:15:58,171 calibrate.py _nudge_pos():1806 [1] 341: 0.130 -0.0008399 -0.0002520 4455 14.85 -8.387 -3.146 2014-03-13T20:40:33.014401536 INFO 2025-06-26 20:15:58,687 calibrate.py _nudge_pos():1806 [1] 396: 0.130 -0.0011331 -0.0005923 6540 21.80 -7.706 -5.035 2014-03-13T21:03:15.021097728 INFO 2025-06-26 20:15:59,202 calibrate.py _nudge_pos():1806 [1] 451: 0.130 -0.0008490 -0.0006330 6990 23.30 -5.401 -5.035 2014-03-13T21:27:27.021628928 INFO 2025-06-26 20:15:59,662 calibrate.py _nudge_pos():1806 [1] 500: 0.140 -0.0003157 -0.0009277 7470 24.90 -1.879 -6.904 2014-03-13T21:53:09.015995136 INFO 2025-06-26 20:16:00,231 calibrate.py _nudge_pos():1806 [1] 560: 0.140 0.0000546 -0.0006320 4925 16.41 0.493 -7.135 2014-03-13T22:10:33.014476288 INFO 2025-06-26 20:16:00,648 calibrate.py _nudge_pos():1806 [1] 604: 0.150 0.0003859 -0.0002828 3175 10.58 5.404 -4.953 2014-03-13T22:21:51.018029568 INFO 2025-06-26 20:16:02,182 calibrate.py _nudge_pos():1862 [1] 719: - - - 3 0.01 - - INFO 2025-06-26 20:16:02,183 calibrate.py _nudge_pos():1868 [1] Points in final series = 72638 INFO 2025-06-26 20:16:02,396 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 58231 INFO 2025-06-26 20:16:02,832 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:03,376 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:03,803 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:03,805 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.072.01/ctd1.nc INFO 2025-06-26 20:16:03,806 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:16:03,806 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 20:16:03,806 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:16:04,318 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:04,746 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:04,748 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.072.01/ctd2.nc INFO 2025-06-26 20:16:04,749 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:16:04,749 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 20:16:04,749 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:16:04,750 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.072.01 INFO 2025-06-26 20:16:04,762 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:16:05,453 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65] INFO 2025-06-26 20:16:05,579 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:16:18,665 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.072.01 ERROR 2025-06-26 20:16:18,665 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.072.01 INFO 2025-06-26 20:16:18,723 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_cal.nc INFO 2025-06-26 20:16:18,833 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, 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 20:16:18,839 process.py align():251 [1] Alignment steps for 2014.072.01 INFO 2025-06-26 20:16:18,871 align.py process_cal():139 [1] Processing dorado_2014.072.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.072.01 INFO 2025-06-26 20:16:18,894 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:16:18,897 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:16:18,949 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:16:18,953 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:16:19,004 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:16:19,008 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:16:19,039 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:16:19,039 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:16:19,059 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:16:19,063 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:16:19,112 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,116 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,161 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,164 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,210 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,213 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,258 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,261 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,308 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,312 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,356 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,360 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,406 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,409 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,453 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,457 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,501 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,505 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,549 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,553 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,599 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,602 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,648 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,652 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,698 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,702 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,746 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,750 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,795 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,799 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,843 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,847 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,893 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,897 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,942 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,945 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:19,992 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:19,996 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:20,044 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:20,049 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:20,099 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:20,103 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:20,148 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:16:20,152 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:16:20,211 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:16:20,254 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:16:20,323 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:16:20,697 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:16:20,734 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_align.nc INFO 2025-06-26 20:16:20,846 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, 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 20:16:20,848 process.py resample():273 [1] Resampling steps for 2014.072.01 INFO 2025-06-26 20:16:20,849 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:16:20,880 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_align.nc mission netCDF file INFO 2025-06-26 20:16:20,884 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_align.nc mission netCDF file INFO 2025-06-26 20:16:20,886 resample.py get_mission_start_end():1145 [1] navigation: 2014-03-13T18:22:24.222222848 to 2014-03-13T22:24:31.617028096 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:16:20,887 resample.py get_mission_start_end():1145 [1] hs2 : 2014-03-13T18:21:47.194759168 to 2014-03-13T22:24:31.397042944 (0 days 00:00:00.219985152 before mission_end) INFO 2025-06-26 20:16:20,889 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-03-13T18:22:07.783348736 to 2014-03-13T22:24:31.427041024 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 20:16:20,890 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-03-13T18:22:07.783348736 to 2014-03-13T22:24:31.417041664 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:16:20,892 resample.py get_mission_start_end():1145 [1] biolume : 2014-03-13T18:21:38.335331840 to 2014-03-13T22:24:30.587064320 (0 days 00:00:01.029963776 before mission_end) INFO 2025-06-26 20:16:20,893 resample.py get_mission_start_end():1145 [1] tailcone : 2014-03-13T18:21:40.785198336 to 2014-03-13T22:24:31.537033472 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 20:16:20,894 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_align.nc mission netCDF file INFO 2025-06-26 20:16:20,894 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,059 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,089 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,118 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,147 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,173 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,198 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,223 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,248 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,271 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,294 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,317 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,340 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,363 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,387 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,410 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,433 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,456 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,481 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,506 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,530 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,554 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,579 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,604 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,628 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,640 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,652 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:21,656 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:16:21,656 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:16:22,158 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:16:22,261 resample.py add_biolume_proxies():633 [1] Zero flow values found: 14573 of 14573 - replaced with 350 ml/s INFO 2025-06-26 20:16:22,261 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:16:22,312 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:16:22,334 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:16:22,354 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:16:22,354 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:16:22,386 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:16:22,573 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_1S.nc INFO 2025-06-26 20:16:24,178 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:16:33,734 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.072.01/dorado_2014.072.01_1S_Gulper.txt INFO 2025-06-26 20:16:33,735 process.py archive():337 [1] Archiving steps for 2014.072.01 INFO 2025-06-26 20:16:33,735 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:16:33,735 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:16:33,736 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.01_1S.nc INFO 2025-06-26 20:16:33,807 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:16:33,808 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.01_cal.nc INFO 2025-06-26 20:16:33,912 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:16:33,914 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.01_align.nc INFO 2025-06-26 20:16:34,049 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:16:34,069 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,087 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,092 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,109 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,165 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,186 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,202 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,241 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,247 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.01 done. INFO 2025-06-26 20:16:34,247 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:16:34,248 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.072.01_1S_Gulper.txt INFO 2025-06-26 20:16:34,252 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.072.01/dorado_2014.072.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:16:34,252 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.01/dorado_2014.072.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf