INFO 2025-06-26 17:23:14,988 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 17:23:14,988 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Kanna mission with automated forwarding of simulated tethys_cen position to TREX via MBARITracking/scripts/drifter.py and McCann' tres.py code - ctdToUse = ctd2 INFO 2025-06-26 17:23:14,988 process.py process_mission():449 [1] Processing AUVCTD mission 2011.062.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 17:23:14,988 process.py download_process():165 [1] Download and processing steps for 2011.062.05 INFO 2025-06-26 17:23:14,988 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011062/2011.062.05 INFO 2025-06-26 17:23:14,988 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011062/2011.062.05 to /data/auv_data/dorado/missionlogs/2011.062.05 INFO 2025-06-26 17:23:17,924 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.062.05 INFO 2025-06-26 17:23:17,924 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/ctdDriver.log (5939915 bytes) INFO 2025-06-26 17:23:18,366 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/ctdDriver2.log (5939999 bytes) INFO 2025-06-26 17:23:18,797 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/gps.log (204908 bytes) INFO 2025-06-26 17:23:18,827 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/hydroscatlog.log (5205922 bytes) INFO 2025-06-26 17:23:19,375 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/navigation.log (18237262 bytes) INFO 2025-06-26 17:23:20,679 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/isuslog.log (383285 bytes) INFO 2025-06-26 17:23:20,720 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/parosci.log (6319142 bytes) INFO 2025-06-26 17:23:21,265 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/tailCone.log (3720907 bytes) INFO 2025-06-26 17:23:21,723 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/biolume.log (4331990 bytes) INFO 2025-06-26 17:23:22,141 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 17:23:22,364 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.44 seconds INFO 2025-06-26 17:23:22,365 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.062.05/lopc.bin (16511000 bytes) INFO 2025-06-26 17:23:22,365 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 17:23:22 2025 INFO 2025-06-26 17:23:22,365 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.062.05/parosci.nc INFO 2025-06-26 17:23:22,365 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 17:23:22,365 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.062.05/parosci.nc INFO 2025-06-26 17:23:22,368 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1299177577.5, sensor_off_time = 1299193080.4 INFO 2025-06-26 17:23:22,369 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 15502 seconds. Expecting to read 31004 L frames from the lopc.bin file. INFO 2025-06-26 17:23:22,369 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 31004 records from the lopc.bin file. INFO 2025-06-26 17:23:22,550 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-03-03 18:39:37 Z and endTime = 2011-03-03 22:58:00 Z with 31004 records expected to be read from lopc.bin INFO 2025-06-26 17:23:22,550 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.062.05/lopc.bin INFO 2025-06-26 17:23:22,550 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.062.05/lopc.nc INFO 2025-06-26 17:23:22,550 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.062.05/lopc.nc INFO 2025-06-26 17:23:22,551 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.062.05 INFO 2025-06-26 17:23:22,551 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 17:23:22,584 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 17:23:22,584 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 17:23:22,584 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 17:23:23,175 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 17:23:23,176 process.py calibrate():227 [1] Calibration steps for 2011.062.05 INFO 2025-06-26 17:23:23,404 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 17:23:23,406 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 17:23:27,637 calibrate.py _nudge_pos():1806 [1] 467: 0.140 -0.0006538 -0.0005773 8820 29.40 -3.298 -3.639 2011-03-03T19:16:46.484951040 INFO 2025-06-26 17:23:28,964 calibrate.py _nudge_pos():1806 [1] 591: 0.140 0.0019923 -0.0031609 9165 30.55 9.673 -19.174 2011-03-03T19:49:22.490955264 INFO 2025-06-26 17:23:31,249 calibrate.py _nudge_pos():1806 [1] 828: 0.150 0.0008422 -0.0030915 8720 29.06 4.297 -19.711 2011-03-03T20:22:22.485316608 INFO 2025-06-26 17:23:32,076 calibrate.py _nudge_pos():1806 [1] 915: 0.150 -0.0000876 -0.0001194 1520 5.06 -2.567 -4.368 2011-03-03T20:28:52.488599296 INFO 2025-06-26 17:23:42,704 calibrate.py _nudge_pos():1806 [1] 2025: 0.150 0.0001560 -0.0001032 9030 30.10 0.769 -0.635 2011-03-03T21:17:28.488839680 INFO 2025-06-26 17:23:44,154 calibrate.py _nudge_pos():1806 [1] 2178: 0.150 0.0010403 0.0003596 9080 30.26 5.100 2.202 2011-03-03T21:50:16.494022144 INFO 2025-06-26 17:23:45,547 calibrate.py _nudge_pos():1806 [1] 2324: 0.160 0.0004662 -0.0034426 8605 28.68 2.412 -22.243 2011-03-03T22:21:22.486192896 INFO 2025-06-26 17:23:46,797 calibrate.py _nudge_pos():1806 [1] 2454: 0.160 0.0027093 -0.0025535 8445 28.15 14.281 -16.810 2011-03-03T22:51:40.491651072 INFO 2025-06-26 17:23:50,462 calibrate.py _nudge_pos():1862 [1] 2784: - - - 4 0.01 - - INFO 2025-06-26 17:23:50,462 calibrate.py _nudge_pos():1868 [1] Points in final series = 77264 WARNING 2025-06-26 17:23:50,566 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 17:23:50,675 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 8 of 61963 INFO 2025-06-26 17:23:51,154 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:23:51,737 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:23:52,197 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:23:52,199 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.062.05/ctd1.nc INFO 2025-06-26 17:23:52,200 calibrate.py _range_qc_combined_nc():898 [1] Setting 91 ctd1_salinity values to NaN INFO 2025-06-26 17:23:52,201 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 17:23:52,201 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 17:23:52,769 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:23:53,244 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:23:53,246 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.062.05/ctd2.nc INFO 2025-06-26 17:23:53,248 calibrate.py _range_qc_combined_nc():898 [1] Setting 170 ctd2_salinity values to NaN INFO 2025-06-26 17:23:53,248 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 17:23:53,248 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 17:23:53,276 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 17:23:54,137 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 17:23:54,168 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.062.05 ERROR 2025-06-26 17:23:54,168 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.062.05 INFO 2025-06-26 17:23:54,230 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_cal.nc INFO 2025-06-26 17:23:54,348 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 17:23:54,354 process.py align():251 [1] Alignment steps for 2011.062.05 INFO 2025-06-26 17:23:54,392 align.py process_cal():139 [1] Processing dorado_2011.062.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.062.05 INFO 2025-06-26 17:23:54,416 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:23:54,420 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:23:54,475 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:23:54,480 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:23:54,536 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:23:54,541 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:23:54,573 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 17:23:54,573 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 17:23:54,594 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:23:54,598 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:23:54,656 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,660 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,709 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,713 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,762 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,766 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,814 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,819 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,870 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,874 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,925 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:54,973 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:54,978 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,026 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,031 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,080 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,084 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,131 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,136 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,186 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,190 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,237 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,241 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,292 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,296 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,344 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,347 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,396 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,401 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,448 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,453 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,502 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,506 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,554 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,558 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,608 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,613 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,660 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,664 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,714 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,718 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,765 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.062.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:23:55,769 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:23:55,828 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:23:55,871 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:23:55,914 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:23:55,958 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:23:56,003 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:23:56,073 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 17:23:56,466 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:23:56,505 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_align.nc INFO 2025-06-26 17:23:56,630 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 17:23:56,632 process.py resample():273 [1] Resampling steps for 2011.062.05 INFO 2025-06-26 17:23:56,633 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 17:23:56,666 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_align.nc mission netCDF file INFO 2025-06-26 17:23:56,672 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_align.nc mission netCDF file INFO 2025-06-26 17:23:56,673 resample.py get_mission_start_end():1145 [1] navigation: 2011-03-03T18:40:26.894263040 to 2011-03-03T22:58:00.285633280 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 17:23:56,675 resample.py get_mission_start_end():1145 [1] hs2 : 2011-03-03T18:39:43.437240064 to 2011-03-03T22:58:00.385626624 (0 days 00:00:00 before mission_end) INFO 2025-06-26 17:23:56,677 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-03-03T18:40:14.035144192 to 2011-03-03T22:58:00.205638912 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 17:23:56,678 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-03-03T18:40:13.945150208 to 2011-03-03T22:58:00.345629184 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 17:23:56,679 resample.py get_mission_start_end():1145 [1] isus : 2011-03-03T18:40:52.052539648 to 2011-03-03T22:58:00.385626624 (0 days 00:00:00 before mission_end) INFO 2025-06-26 17:23:56,681 resample.py get_mission_start_end():1145 [1] biolume : 2011-03-03T18:39:36.617673216 to 2011-03-03T22:57:59.395660032 (0 days 00:00:00.989966592 before mission_end) INFO 2025-06-26 17:23:56,682 resample.py get_mission_start_end():1145 [1] tailcone : 2011-03-03T18:39:38.497578496 to 2011-03-03T22:58:00.315631104 (0 days 00:00:00.069995520 before mission_end) INFO 2025-06-26 17:23:56,683 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_align.nc mission netCDF file INFO 2025-06-26 17:23:56,683 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:56,861 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:56,893 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:56,924 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:56,956 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:56,983 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,012 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,039 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,066 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,096 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,125 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,151 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,178 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,204 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,233 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,261 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,288 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,316 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,346 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,375 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,405 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,433 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,461 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,488 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,514 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,528 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,542 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,554 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,566 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,578 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:57,582 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 17:23:57,582 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 17:23:58,058 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 17:23:58,171 resample.py add_biolume_proxies():633 [1] Zero flow values found: 3 of 15504 - replaced with 350 ml/s INFO 2025-06-26 17:23:58,172 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 17:23:58,221 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 17:23:58,245 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 17:23:58,267 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 17:23:58,267 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 17:23:58,305 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 17:23:58,507 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_1S.nc INFO 2025-06-26 17:23:59,710 create_products.py gulper_odv():401 [1] No gulper times found for 2011.062.05 INFO 2025-06-26 17:23:59,710 process.py archive():337 [1] Archiving steps for 2011.062.05 INFO 2025-06-26 17:23:59,710 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05, BASE_PATH = /data/auv_data INFO 2025-06-26 17:23:59,712 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 17:23:59,712 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.062.05_1S.nc INFO 2025-06-26 17:23:59,731 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:23:59,732 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.062.05_cal.nc INFO 2025-06-26 17:23:59,833 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:23:59,834 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.062.05_align.nc INFO 2025-06-26 17:23:59,983 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:24:00,006 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,029 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,036 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,057 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,115 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,122 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,145 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,162 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,204 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,213 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011062/2011.062.05 done. INFO 2025-06-26 17:24:00,213 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 17:24:00,213 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.062.05/dorado_2011.062.05_processing.log /Volumes/AUVCTD/surveys/2011/netcdf