INFO 2025-06-26 19:24:42,204 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 19:24:42,204 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2012 - Distributed Autonomy - ctdToUse = ctd1 INFO 2025-06-26 19:24:42,204 process.py process_mission():449 [1] Processing CANON September 2012 mission 2012.270.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:24:42,204 process.py download_process():165 [1] Download and processing steps for 2012.270.04 INFO 2025-06-26 19:24:42,204 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012270/2012.270.04 INFO 2025-06-26 19:24:42,204 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012270/2012.270.04 to /data/auv_data/dorado/missionlogs/2012.270.04 INFO 2025-06-26 19:24:45,965 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.270.04 INFO 2025-06-26 19:24:45,965 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/ctdDriver.log (7908006 bytes) INFO 2025-06-26 19:24:46,792 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/ctdDriver2.log (7907999 bytes) INFO 2025-06-26 19:24:47,678 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/gps.log (493484 bytes) INFO 2025-06-26 19:24:47,743 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/hydroscatlog.log (6923806 bytes) INFO 2025-06-26 19:24:48,783 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/navigation.log (27993014 bytes) INFO 2025-06-26 19:24:50,975 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/isuslog.log (611669 bytes) INFO 2025-06-26 19:24:51,038 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/parosci.log (8362358 bytes) INFO 2025-06-26 19:24:51,907 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/tailCone.log (4948315 bytes) INFO 2025-06-26 19:24:52,621 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/biolume.log (5760226 bytes) INFO 2025-06-26 19:24:53,196 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:24:53,488 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.52 seconds INFO 2025-06-26 19:24:53,488 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.270.04/lopc.bin (84699441 bytes) INFO 2025-06-26 19:24:53,488 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:24:53 2025 INFO 2025-06-26 19:24:53,489 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.270.04/parosci.nc INFO 2025-06-26 19:24:53,489 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:24:53,489 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.270.04/parosci.nc INFO 2025-06-26 19:24:53,493 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1348674567.3, sensor_off_time = 1348695185.7 INFO 2025-06-26 19:24:53,493 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 20618 seconds. Expecting to read 41236 L frames from the lopc.bin file. INFO 2025-06-26 19:24:53,493 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 41236 records from the lopc.bin file. INFO 2025-06-26 19:24:53,744 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-09-26 15:49:27 Z and endTime = 2012-09-26 21:33:05 Z with 41236 records expected to be read from lopc.bin INFO 2025-06-26 19:24:53,744 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.270.04/lopc.bin INFO 2025-06-26 19:24:53,744 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.270.04/lopc.nc INFO 2025-06-26 19:24:53,744 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.270.04/lopc.nc INFO 2025-06-26 19:24:53,745 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.270.04 INFO 2025-06-26 19:24:53,745 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:24:53,808 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:24:53,808 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:24:53,809 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:24:55,555 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:24:55,556 process.py calibrate():227 [1] Calibration steps for 2012.270.04 INFO 2025-06-26 19:24:55,773 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 19:24:55,775 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:25:04,998 calibrate.py _nudge_pos():1806 [1] 954: 0.030 0.0052684 -0.0045495 9045 30.15 25.910 -27.964 2012-09-26T16:35:28.378650112 INFO 2025-06-26 19:25:07,288 calibrate.py _nudge_pos():1806 [1] 1199: 0.040 -0.0010973 -0.0025525 8740 29.13 -5.584 -16.237 2012-09-26T17:08:40.382188544 INFO 2025-06-26 19:25:08,281 calibrate.py _nudge_pos():1806 [1] 1305: 0.040 -0.0004189 -0.0028669 5355 17.85 -3.480 -29.767 2012-09-26T17:28:16.381627136 INFO 2025-06-26 19:25:18,233 calibrate.py _nudge_pos():1806 [1] 2285: 0.050 -0.0000733 -0.0021065 7040 23.46 -0.463 -16.636 2012-09-26T18:08:04.378038272 INFO 2025-06-26 19:25:19,398 calibrate.py _nudge_pos():1806 [1] 2406: 0.050 0.0030505 -0.0012358 8100 27.00 16.751 -8.483 2012-09-26T18:37:04.378840064 INFO 2025-06-26 19:25:21,401 calibrate.py _nudge_pos():1806 [1] 2613: 0.050 0.0021743 -0.0001633 3380 11.26 28.620 -2.687 2012-09-26T18:51:46.378418944 INFO 2025-06-26 19:25:30,417 calibrate.py _nudge_pos():1806 [1] 3561: 0.060 0.0022974 -0.0029192 8375 27.91 12.202 -19.379 2012-09-26T19:35:28.378799360 INFO 2025-06-26 19:25:31,633 calibrate.py _nudge_pos():1806 [1] 3686: 0.060 -0.0013448 -0.0023534 7114 23.71 -8.407 -18.390 2012-09-26T20:01:16.382754048 INFO 2025-06-26 19:25:32,812 calibrate.py _nudge_pos():1806 [1] 3809: 0.060 -0.0007767 -0.0019435 4610 15.36 -7.495 -23.441 2012-09-26T20:18:40.381235200 INFO 2025-06-26 19:25:38,661 calibrate.py _nudge_pos():1806 [1] 4408: 0.060 0.0003177 -0.0025424 7000 23.33 2.019 -20.193 2012-09-26T20:51:58.384362752 INFO 2025-06-26 19:25:38,920 calibrate.py _nudge_pos():1806 [1] 4434: 0.070 -0.0000184 0.0000187 25 0.08 -34.031 43.240 2012-09-26T20:52:28.382307584 INFO 2025-06-26 19:26:02,061 calibrate.py _nudge_pos():1806 [1] 6764: 0.070 0.0000174 -0.0000034 55 0.18 14.353 -3.468 2012-09-26T21:31:28.382006528 INFO 2025-06-26 19:26:02,510 calibrate.py _nudge_pos():1806 [1] 6810: 0.080 0.0000408 -0.0000351 105 0.35 17.435 -18.787 2012-09-26T21:32:34.377485824 INFO 2025-06-26 19:26:02,816 calibrate.py _nudge_pos():1862 [1] 6805: - - - 1 0.00 - - INFO 2025-06-26 19:26:02,816 calibrate.py _nudge_pos():1868 [1] Points in final series = 102907 INFO 2025-06-26 19:26:03,031 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=30) for self.args.mission=2012.270.04 INFO 2025-06-26 19:26:03,034 calibrate.py _depth_process():2175 [1] Setting 1 depths values to NaN WARNING 2025-06-26 19:26:03,038 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:26:03,797 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:26:04,567 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:26:05,167 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:26:05,169 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.270.04/ctd1.nc INFO 2025-06-26 19:26:05,171 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:26:05,171 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 19:26:05,171 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:26:05,884 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:26:06,485 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:26:06,487 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.270.04/ctd2.nc INFO 2025-06-26 19:26:06,488 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:26:06,488 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 19:26:06,489 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:26:06,524 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:26:07,460 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 1202280] INFO 2025-06-26 19:26:07,633 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:26:26,083 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.270.04 ERROR 2025-06-26 19:26:26,083 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.270.04 INFO 2025-06-26 19:26:26,165 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_cal.nc INFO 2025-06-26 19:26:26,309 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 19:26:26,315 process.py align():251 [1] Alignment steps for 2012.270.04 INFO 2025-06-26 19:26:26,356 align.py process_cal():139 [1] Processing dorado_2012.270.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.270.04 INFO 2025-06-26 19:26:26,386 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:26:26,390 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:26:26,461 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:26:26,466 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:26:26,535 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:26:26,540 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:26:26,582 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:26:26,582 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:26:26,608 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:26:26,613 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:26:26,681 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:26,686 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:26,746 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:26,750 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:26,811 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:26,815 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:26,875 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:26,879 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:26,941 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:26,945 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,005 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,010 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,071 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,076 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,136 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,141 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,201 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,206 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,266 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,272 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,332 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,337 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,397 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,401 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,463 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,467 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,528 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,532 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,594 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,599 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,660 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,664 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,726 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,730 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,791 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,795 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,858 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,862 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,923 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,928 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:27,990 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:27,994 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:28,056 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.270.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:26:28,060 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:26:28,133 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:26:28,185 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:26:28,238 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:26:28,292 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:26:28,346 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:26:28,437 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:26:28,961 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:26:29,010 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_align.nc INFO 2025-06-26 19:26:29,159 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 19:26:29,161 process.py resample():273 [1] Resampling steps for 2012.270.04 INFO 2025-06-26 19:26:29,162 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:26:29,198 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_align.nc mission netCDF file INFO 2025-06-26 19:26:29,204 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_align.nc mission netCDF file INFO 2025-06-26 19:26:29,206 resample.py get_mission_start_end():1145 [1] navigation: 2012-09-26T15:50:04.195269632 to 2012-09-26T21:33:05.575348480 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:26:29,208 resample.py get_mission_start_end():1145 [1] hs2 : 2012-09-26T15:49:33.197393152 to 2012-09-26T21:33:05.545350656 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 19:26:29,209 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-09-26T15:49:54.145957888 to 2012-09-26T21:33:05.465355776 (0 days 00:00:00.219985152 before mission_end) INFO 2025-06-26 19:26:29,211 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-09-26T15:49:54.365943040 to 2012-09-26T21:33:05.665342208 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 19:26:29,213 resample.py get_mission_start_end():1145 [1] isus : 2012-09-26T15:50:42.852621312 to 2012-09-26T21:33:05.475355392 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 19:26:29,214 resample.py get_mission_start_end():1145 [1] biolume : 2012-09-26T15:49:26.407824128 to 2012-09-26T21:33:04.205408000 (0 days 00:00:01.479932928 before mission_end) INFO 2025-06-26 19:26:29,216 resample.py get_mission_start_end():1145 [1] tailcone : 2012-09-26T15:49:27.927754240 to 2012-09-26T21:33:05.685340928 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:26:29,216 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_align.nc mission netCDF file INFO 2025-06-26 19:26:29,217 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,439 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,478 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,517 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,555 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,590 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,623 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,657 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,689 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,720 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,751 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,781 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,812 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,842 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,872 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,903 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,933 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,963 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:29,996 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,030 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,063 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,096 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,128 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,161 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,194 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,211 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,226 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,241 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,254 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,267 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:30,272 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:26:30,272 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:26:31,036 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:26:31,174 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:26:31,248 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:26:31,281 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:26:31,308 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:26:31,309 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:26:31,350 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:26:31,576 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_1S.nc INFO 2025-06-26 19:26:35,069 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:26:49,492 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2012.270.04/dorado_2012.270.04_1S_Gulper.txt INFO 2025-06-26 19:26:49,492 process.py archive():337 [1] Archiving steps for 2012.270.04 INFO 2025-06-26 19:26:49,492 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04, BASE_PATH = /data/auv_data INFO 2025-06-26 19:26:49,494 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:26:49,495 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.270.04_1S.nc INFO 2025-06-26 19:26:49,516 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:26:49,517 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.270.04_cal.nc INFO 2025-06-26 19:26:49,659 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:26:49,660 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.270.04_align.nc INFO 2025-06-26 19:26:49,849 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:26:49,875 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:49,900 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:49,906 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:49,929 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,002 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,010 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,035 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,055 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,109 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,117 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012270/2012.270.04 done. INFO 2025-06-26 19:26:50,117 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:26:50,118 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2012/odv/dorado_2012.270.04_1S_Gulper.txt INFO 2025-06-26 19:26:50,122 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2012.270.04/dorado_2012.270.04_1S_Gulper.txt /Volumes/AUVCTD/surveys/2012/odv done. INFO 2025-06-26 19:26:50,122 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.270.04/dorado_2012.270.04_processing.log /Volumes/AUVCTD/surveys/2012/netcdf