INFO 2025-06-26 20:44:06,074 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 20:44:06,075 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2014 Northern Monterey Bay gulper missions - ctdToUse = ctd1 INFO 2025-06-26 20:44:06,075 process.py process_mission():449 [1] Processing SIMZ October 2014 mission 2014.294.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:44:06,075 process.py download_process():165 [1] Download and processing steps for 2014.294.00 INFO 2025-06-26 20:44:06,075 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014294/2014.294.00 INFO 2025-06-26 20:44:06,075 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014294/2014.294.00 to /data/auv_data/dorado/missionlogs/2014.294.00 INFO 2025-06-26 20:44:09,855 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.294.00 INFO 2025-06-26 20:44:09,855 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/ctdDriver.log (7032390 bytes) INFO 2025-06-26 20:44:10,347 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/ctdDriver2.log (7032383 bytes) INFO 2025-06-26 20:44:10,856 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/gps.log (95900 bytes) INFO 2025-06-26 20:44:10,874 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/hydroscatlog.log (6157390 bytes) INFO 2025-06-26 20:44:11,522 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/navigation.log (26343810 bytes) INFO 2025-06-26 20:44:13,522 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/isuslog.log (454581 bytes) INFO 2025-06-26 20:44:13,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/parosci.log (8652374 bytes) INFO 2025-06-26 20:44:14,310 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/tailCone.log (4401163 bytes) INFO 2025-06-26 20:44:14,849 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/biolume.log (5124066 bytes) INFO 2025-06-26 20:44:15,345 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:44:15,599 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.74 seconds INFO 2025-06-26 20:44:15,599 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.294.00/lopc.bin (22004985 bytes) INFO 2025-06-26 20:44:15,599 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:44:15 2025 INFO 2025-06-26 20:44:15,599 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.294.00/parosci.nc INFO 2025-06-26 20:44:15,599 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:44:15,599 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.294.00/parosci.nc INFO 2025-06-26 20:44:15,603 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1413905416.7, sensor_off_time = 1413923754.6 INFO 2025-06-26 20:44:15,603 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 18337 seconds. Expecting to read 36674 L frames from the lopc.bin file. INFO 2025-06-26 20:44:15,603 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 36674 records from the lopc.bin file. INFO 2025-06-26 20:44:15,821 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-21 15:30:16 Z and endTime = 2014-10-21 20:35:54 Z with 36674 records expected to be read from lopc.bin INFO 2025-06-26 20:44:15,821 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.294.00/lopc.bin INFO 2025-06-26 20:44:15,821 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.294.00/lopc.nc INFO 2025-06-26 20:44:15,821 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.294.00/lopc.nc INFO 2025-06-26 20:44:15,822 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.294.00 INFO 2025-06-26 20:44:15,822 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:44:15,866 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:44:15,866 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:44:15,866 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:44:22,718 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:44:22,719 process.py calibrate():227 [1] Calibration steps for 2014.294.00 INFO 2025-06-26 20:44:22,974 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 20:44:22,976 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:44:24,814 calibrate.py _nudge_pos():1806 [1] 230: 0.180 -0.0000873 -0.0000500 1295 4.31 -2.997 -2.150 2014-10-21T15:38:23.009127424 INFO 2025-06-26 20:44:25,515 calibrate.py _nudge_pos():1806 [1] 306: 0.180 -0.0002684 -0.0002718 8590 28.63 -1.388 -1.759 2014-10-21T16:08:16.006298624 INFO 2025-06-26 20:44:26,066 calibrate.py _nudge_pos():1806 [1] 365: 0.180 -0.0004218 -0.0002920 8290 27.63 -2.262 -1.958 2014-10-21T16:36:52.008744192 INFO 2025-06-26 20:44:26,611 calibrate.py _nudge_pos():1806 [1] 424: 0.190 0.0000456 -0.0003273 6700 22.33 0.302 -2.716 2014-10-21T17:00:10.002975232 INFO 2025-06-26 20:44:27,150 calibrate.py _nudge_pos():1806 [1] 482: 0.190 0.0005885 -0.0000003 3795 12.65 6.895 -0.004 2014-10-21T17:13:46.007075072 INFO 2025-06-26 20:44:28,094 calibrate.py _nudge_pos():1806 [1] 582: 0.190 -0.0020144 -0.0002924 6315 21.05 -14.185 -2.574 2014-10-21T17:36:28.003771904 INFO 2025-06-26 20:44:28,636 calibrate.py _nudge_pos():1806 [1] 635: 0.200 -0.0032336 0.0000907 7204 24.01 -19.963 0.700 2014-10-21T18:01:22.001425920 INFO 2025-06-26 20:44:29,283 calibrate.py _nudge_pos():1806 [1] 703: 0.200 -0.0037638 0.0002750 7495 24.98 -22.338 2.040 2014-10-21T18:27:28.004147456 INFO 2025-06-26 20:44:29,875 calibrate.py _nudge_pos():1806 [1] 765: 0.200 -0.0004405 -0.0005540 1675 5.58 -11.704 -18.398 2014-10-21T18:34:04.007019520 INFO 2025-06-26 20:44:30,622 calibrate.py _nudge_pos():1806 [1] 844: 0.200 0.0007025 0.0001310 3419 11.39 9.141 2.131 2014-10-21T18:46:46.004818944 INFO 2025-06-26 20:44:31,338 calibrate.py _nudge_pos():1806 [1] 920: 0.200 -0.0003945 0.0001241 3434 11.44 -5.111 2.009 2014-10-21T18:59:28.002618624 INFO 2025-06-26 20:44:31,395 calibrate.py _nudge_pos():1806 [1] 926: 0.200 0.0000307 -0.0000240 194 0.64 7.072 -6.919 2014-10-21T19:00:12.009604096 INFO 2025-06-26 20:44:31,912 calibrate.py _nudge_pos():1806 [1] 981: 0.200 -0.0006033 -0.0003691 5749 19.16 -4.668 -3.570 2014-10-21T19:20:16.007124480 INFO 2025-06-26 20:44:32,459 calibrate.py _nudge_pos():1806 [1] 1038: 0.200 -0.0007089 -0.0006015 6379 21.26 -4.942 -5.242 2014-10-21T19:42:28.005876224 INFO 2025-06-26 20:44:33,021 calibrate.py _nudge_pos():1806 [1] 1097: 0.010 -0.0005541 -0.0005430 6955 23.18 -3.542 -4.341 2014-10-21T20:06:37.206599168 INFO 2025-06-26 20:44:33,604 calibrate.py _nudge_pos():1806 [1] 1158: 0.010 -0.0002807 -0.0001148 4755 15.85 -2.624 -1.342 2014-10-21T20:23:28.207341056 INFO 2025-06-26 20:44:34,203 calibrate.py _nudge_pos():1806 [1] 1221: 0.010 -0.0000805 -0.0002031 2930 9.76 -1.222 -3.856 2014-10-21T20:34:16.202950144 INFO 2025-06-26 20:44:35,168 calibrate.py _nudge_pos():1862 [1] 1273: - - - 2 0.00 - - INFO 2025-06-26 20:44:35,168 calibrate.py _nudge_pos():1868 [1] Points in final series = 91114 INFO 2025-06-26 20:44:36,009 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:44:36,709 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:44:37,261 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:44:37,263 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.294.00/ctd1.nc INFO 2025-06-26 20:44:37,265 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 20:44:37,265 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 20:44:37,265 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:44:37,919 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:44:38,460 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:44:38,462 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.294.00/ctd2.nc INFO 2025-06-26 20:44:38,463 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:44:38,463 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 20:44:38,463 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:44:38,494 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:44:39,412 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80] INFO 2025-06-26 20:44:39,576 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:44:56,214 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.294.00 ERROR 2025-06-26 20:44:56,215 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.294.00 INFO 2025-06-26 20:44:56,287 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_cal.nc INFO 2025-06-26 20:44:56,423 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 20:44:56,429 process.py align():251 [1] Alignment steps for 2014.294.00 INFO 2025-06-26 20:44:56,468 align.py process_cal():139 [1] Processing dorado_2014.294.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.294.00 INFO 2025-06-26 20:44:56,500 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:44:56,505 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:44:56,568 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:44:56,573 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:44:56,636 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:44:56,641 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:44:56,681 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:44:56,682 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:44:56,707 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:44:56,712 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:44:56,777 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:56,781 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:56,837 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:56,842 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:56,900 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:56,904 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:56,961 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:56,965 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,023 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,027 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,083 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,087 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,144 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,149 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,205 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,210 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,267 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,272 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,328 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,333 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,390 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,395 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,450 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,455 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,514 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,519 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,575 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,580 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,640 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,645 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,712 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,716 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,789 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,796 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,854 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,859 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,919 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,924 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:57,982 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:57,988 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:58,050 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:58,055 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:58,115 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.294.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:44:58,119 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:44:58,236 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:44:58,294 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:44:58,344 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:44:58,397 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:44:58,453 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:44:58,544 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:44:59,044 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:44:59,091 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_align.nc INFO 2025-06-26 20:44:59,239 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 20:44:59,243 process.py resample():273 [1] Resampling steps for 2014.294.00 INFO 2025-06-26 20:44:59,243 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:44:59,280 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_align.nc mission netCDF file INFO 2025-06-26 20:44:59,286 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_align.nc mission netCDF file INFO 2025-06-26 20:44:59,287 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-21T15:31:02.219323392 to 2014-10-21T20:35:54.606209024 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:44:59,289 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-21T15:30:22.882018304 to 2014-10-21T20:35:54.436220672 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 20:44:59,290 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-21T15:30:43.050636544 to 2014-10-21T20:35:54.406222848 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 20:44:59,292 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-21T15:30:43.110632448 to 2014-10-21T20:35:54.456219392 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 20:44:59,293 resample.py get_mission_start_end():1145 [1] isus : 2014-10-21T15:31:33.627171840 to 2014-10-21T20:35:54.376224768 (0 days 00:00:00.229984256 before mission_end) INFO 2025-06-26 20:44:59,295 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-21T15:30:15.862465024 to 2014-10-21T20:35:53.316263168 (0 days 00:00:01.289945856 before mission_end) INFO 2025-06-26 20:44:59,296 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-21T15:30:18.712303872 to 2014-10-21T20:35:54.496216576 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 20:44:59,297 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_align.nc mission netCDF file INFO 2025-06-26 20:44:59,297 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,507 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,544 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,594 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,646 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,684 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,725 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,771 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,815 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,857 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,899 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,931 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,960 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:44:59,990 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,026 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,056 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,085 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,115 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,147 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,179 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,212 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,243 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,273 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,304 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,335 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,351 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,366 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,380 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,394 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,406 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:00,411 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:45:00,411 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:45:01,129 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:45:01,323 resample.py add_biolume_proxies():633 [1] Zero flow values found: 18339 of 18339 - replaced with 350 ml/s INFO 2025-06-26 20:45:01,323 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:45:01,416 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:45:01,462 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:45:01,506 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:45:01,507 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:45:01,566 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:45:01,863 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_1S.nc INFO 2025-06-26 20:45:03,928 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:45:27,116 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.294.00/dorado_2014.294.00_1S_Gulper.txt INFO 2025-06-26 20:45:27,116 process.py archive():337 [1] Archiving steps for 2014.294.00 INFO 2025-06-26 20:45:27,116 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:45:27,118 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:45:27,119 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.294.00_1S.nc INFO 2025-06-26 20:45:27,140 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:45:27,141 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.294.00_cal.nc INFO 2025-06-26 20:45:27,264 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:45:27,265 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.294.00_align.nc INFO 2025-06-26 20:45:27,445 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:45:27,470 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,493 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,498 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,519 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,592 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,599 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,625 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,645 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,698 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,719 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014294/2014.294.00 done. INFO 2025-06-26 20:45:27,719 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:45:27,721 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.294.00_1S_Gulper.txt INFO 2025-06-26 20:45:27,727 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.294.00/dorado_2014.294.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:45:27,727 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.294.00/dorado_2014.294.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf