INFO 2025-06-26 20:26:54,073 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 20:26:54,073 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Summer 2014 in Bodega Bay - ctdToUse = ctd1 INFO 2025-06-26 20:26:54,073 process.py process_mission():449 [1] Processing SIMZ July 2014 mission 2014.212.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:26:54,073 process.py download_process():165 [1] Download and processing steps for 2014.212.00 INFO 2025-06-26 20:26:54,074 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014212/2014.212.00 INFO 2025-06-26 20:26:54,074 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014212/2014.212.00 to /data/auv_data/dorado/missionlogs/2014.212.00 INFO 2025-06-26 20:26:57,502 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.212.00 INFO 2025-06-26 20:26:57,502 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/ctdDriver.log (4803462 bytes) INFO 2025-06-26 20:26:57,840 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/ctdDriver2.log (4803359 bytes) INFO 2025-06-26 20:26:58,191 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/gps.log (58316 bytes) INFO 2025-06-26 20:26:58,205 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/hydroscatlog.log (4207498 bytes) INFO 2025-06-26 20:26:58,631 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/navigation.log (17984034 bytes) INFO 2025-06-26 20:26:59,905 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/isuslog.log (311253 bytes) INFO 2025-06-26 20:26:59,940 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.212.00/isuslog.log: [ 1 2 3 4 6 7 8 9 10 11 12 14 15 16 17 18 19] INFO 2025-06-26 20:26:59,941 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/parosci.log (5913398 bytes) INFO 2025-06-26 20:27:00,447 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/tailCone.log (3008395 bytes) INFO 2025-06-26 20:27:00,814 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/biolume.log (3503562 bytes) INFO 2025-06-26 20:27:01,168 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:27:01,346 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.84 seconds INFO 2025-06-26 20:27:01,347 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.212.00/lopc.bin (31753987 bytes) INFO 2025-06-26 20:27:01,347 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:27:01 2025 INFO 2025-06-26 20:27:01,347 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.212.00/parosci.nc INFO 2025-06-26 20:27:01,347 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:27:01,347 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.212.00/parosci.nc INFO 2025-06-26 20:27:01,351 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1406815050.9, sensor_off_time = 1406827584.2 INFO 2025-06-26 20:27:01,351 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 12533 seconds. Expecting to read 25066 L frames from the lopc.bin file. INFO 2025-06-26 20:27:01,351 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 25066 records from the lopc.bin file. INFO 2025-06-26 20:27:01,502 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-07-31 13:57:30 Z and endTime = 2014-07-31 17:26:24 Z with 25066 records expected to be read from lopc.bin INFO 2025-06-26 20:27:01,502 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.212.00/lopc.bin INFO 2025-06-26 20:27:01,502 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.212.00/lopc.nc INFO 2025-06-26 20:27:01,502 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.212.00/lopc.nc INFO 2025-06-26 20:27:01,503 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.212.00 INFO 2025-06-26 20:27:01,503 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:27:01,506 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:27:01,579 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:27:01,579 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:27:01,579 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:27:06,534 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:27:06,534 process.py calibrate():227 [1] Calibration steps for 2014.212.00 INFO 2025-06-26 20:27:06,677 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 20:27:06,678 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:27:07,633 calibrate.py _nudge_pos():1806 [1] 141: 0.200 -0.0001080 0.0000054 614 2.04 -7.678 0.487 2014-07-31T14:01:52.349352960 INFO 2025-06-26 20:27:08,223 calibrate.py _nudge_pos():1806 [1] 205: 0.010 -0.0010177 0.0002337 2145 7.15 -20.689 6.059 2014-07-31T14:10:04.545635328 INFO 2025-06-26 20:27:08,972 calibrate.py _nudge_pos():1806 [1] 286: 0.200 0.0025508 0.0042953 11419 38.06 9.737 20.912 2014-07-31T14:49:28.353703168 INFO 2025-06-26 20:27:09,638 calibrate.py _nudge_pos():1806 [1] 358: 0.010 -0.0025146 0.0012465 11795 39.31 -9.296 5.875 2014-07-31T15:29:58.547223552 INFO 2025-06-26 20:27:09,649 calibrate.py _nudge_pos():1806 [1] 359: 0.020 0.0000295 -0.0000322 90 0.30 14.440 -20.118 2014-07-31T15:30:16.545990656 INFO 2025-06-26 20:27:10,169 calibrate.py _nudge_pos():1806 [1] 415: 0.010 -0.0048135 0.0020343 9445 31.48 -22.222 11.974 2014-07-31T16:02:40.552817152 INFO 2025-06-26 20:27:10,860 calibrate.py _nudge_pos():1806 [1] 489: 0.020 -0.0017745 -0.0003625 4705 15.68 -16.447 -4.284 2014-07-31T16:19:34.553353216 INFO 2025-06-26 20:27:11,543 calibrate.py _nudge_pos():1806 [1] 562: 0.020 -0.0004672 0.0007531 2220 7.40 -9.180 18.867 2014-07-31T16:28:10.548005120 INFO 2025-06-26 20:27:12,174 calibrate.py _nudge_pos():1806 [1] 629: 0.020 0.0003721 0.0016071 3660 12.20 4.434 24.415 2014-07-31T16:41:28.553338112 INFO 2025-06-26 20:27:12,794 calibrate.py _nudge_pos():1806 [1] 695: 0.030 0.0007284 0.0000180 7355 24.51 4.318 0.136 2014-07-31T17:07:04.548115200 INFO 2025-06-26 20:27:13,469 calibrate.py _nudge_pos():1806 [1] 766: 0.030 0.0002206 -0.0004235 5290 17.63 1.818 -4.451 2014-07-31T17:25:52.550841856 INFO 2025-06-26 20:27:13,767 calibrate.py _nudge_pos():1862 [1] 751: - - - 3 0.01 - - INFO 2025-06-26 20:27:13,767 calibrate.py _nudge_pos():1868 [1] Points in final series = 62263 INFO 2025-06-26 20:27:13,956 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 39 of 50077 INFO 2025-06-26 20:27:14,345 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:27:14,822 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:27:15,202 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:27:15,204 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.212.00/ctd1.nc WARNING 2025-06-26 20:27:15,205 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (983) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 20:27:15,206 calibrate.py _range_qc_combined_nc():898 [1] Setting 983 ctd1_salinity values to NaN INFO 2025-06-26 20:27:15,206 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 20:27:15,206 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:27:15,650 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:27:16,030 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:27:16,033 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.212.00/ctd2.nc INFO 2025-06-26 20:27:16,034 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:27:16,035 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 20:27:16,035 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:27:16,502 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:27:17,204 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:27:17,228 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.212.00 ERROR 2025-06-26 20:27:17,229 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.212.00 INFO 2025-06-26 20:27:17,279 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_cal.nc INFO 2025-06-26 20:27:17,385 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:27:17,391 process.py align():251 [1] Alignment steps for 2014.212.00 INFO 2025-06-26 20:27:17,425 align.py process_cal():139 [1] Processing dorado_2014.212.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.212.00 INFO 2025-06-26 20:27:17,445 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:27:17,448 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:27:17,494 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:27:17,497 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:27:17,541 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:27:17,545 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:27:17,571 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:27:17,571 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:27:17,588 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:27:17,592 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:27:17,636 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,639 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 20:27:17,680 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,683 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 20:27:17,723 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,726 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 20:27:17,765 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,768 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:17,809 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,813 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:17,852 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,855 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:17,895 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,898 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:17,937 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,941 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:17,982 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:17,985 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,025 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,028 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,070 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,074 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,115 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,119 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,160 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,164 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,203 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,206 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,246 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,250 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,290 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,293 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,333 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,337 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,377 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,381 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,422 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,425 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,466 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,470 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,512 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,516 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,556 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.212.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:27:18,559 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:27:18,610 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:27:18,647 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:27:18,683 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:27:18,722 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:27:18,764 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:27:18,829 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:27:19,155 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:27:19,188 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_align.nc INFO 2025-06-26 20:27:19,303 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:27:19,306 process.py resample():273 [1] Resampling steps for 2014.212.00 INFO 2025-06-26 20:27:19,306 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:27:19,338 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_align.nc mission netCDF file INFO 2025-06-26 20:27:19,343 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_align.nc mission netCDF file INFO 2025-06-26 20:27:19,344 resample.py get_mission_start_end():1145 [1] navigation: 2014-07-31T13:58:17.164094208 to 2014-07-31T17:26:24.148677120 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 20:27:19,345 resample.py get_mission_start_end():1145 [1] hs2 : 2014-07-31T13:57:39.066704128 to 2014-07-31T17:26:24.198673664 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:27:19,347 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-07-31T13:57:57.395448320 to 2014-07-31T17:26:24.118679296 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 20:27:19,348 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-07-31T13:57:57.205461504 to 2014-07-31T17:26:24.168675584 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 20:27:19,350 resample.py get_mission_start_end():1145 [1] isus : 2014-07-31T13:58:28.643307776 to 2014-07-31T17:26:23.428726528 (0 days 00:00:00.769947136 before mission_end) INFO 2025-06-26 20:27:19,351 resample.py get_mission_start_end():1145 [1] biolume : 2014-07-31T13:57:28.957362176 to 2014-07-31T17:26:23.578681856 (0 days 00:00:00.619991808 before mission_end) INFO 2025-06-26 20:27:19,352 resample.py get_mission_start_end():1145 [1] tailcone : 2014-07-31T13:57:31.477223936 to 2014-07-31T17:26:24.058683392 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 20:27:19,353 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_align.nc mission netCDF file INFO 2025-06-26 20:27:19,354 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,500 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,527 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,552 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,578 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,602 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,625 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,647 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,669 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,689 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,713 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,734 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,755 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,776 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,797 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,818 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,838 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,858 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,880 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,902 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,923 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,945 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,966 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:19,988 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,015 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,030 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,043 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,054 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,065 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,076 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,080 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:27:20,080 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:27:20,564 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:27:20,643 resample.py add_biolume_proxies():633 [1] Zero flow values found: 12536 of 12536 - replaced with 350 ml/s INFO 2025-06-26 20:27:20,643 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:27:20,689 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:27:20,709 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:27:20,727 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:27:20,727 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:27:20,758 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:27:20,943 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_1S.nc INFO 2025-06-26 20:27:24,490 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:27:38,857 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.212.00/dorado_2014.212.00_1S_Gulper.txt INFO 2025-06-26 20:27:38,857 process.py archive():337 [1] Archiving steps for 2014.212.00 INFO 2025-06-26 20:27:38,857 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:27:38,857 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:27:38,859 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.212.00_1S.nc INFO 2025-06-26 20:27:38,877 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:27:38,878 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.212.00_cal.nc INFO 2025-06-26 20:27:38,969 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:27:38,970 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.212.00_align.nc INFO 2025-06-26 20:27:39,089 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:27:39,108 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,124 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,128 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,142 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,188 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,194 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,214 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,230 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,276 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014212/2014.212.00 done. INFO 2025-06-26 20:27:39,276 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:27:39,278 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.212.00_1S_Gulper.txt INFO 2025-06-26 20:27:39,282 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.212.00/dorado_2014.212.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:27:39,283 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.212.00/dorado_2014.212.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf