INFO 2025-06-26 21:42:48,338 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 21:42:48,338 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2015 - ctdToUse = ctd1 INFO 2025-06-26 21:42:48,338 process.py process_mission():449 [1] Processing CANON September 2015 mission 2015.286.00 by user docker_user on host 355841a7028c INFO 2025-06-26 21:42:48,338 process.py download_process():165 [1] Download and processing steps for 2015.286.00 INFO 2025-06-26 21:42:48,338 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2015/2015286/2015.286.00 INFO 2025-06-26 21:42:48,338 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2015/2015286/2015.286.00 to /data/auv_data/dorado/missionlogs/2015.286.00 INFO 2025-06-26 21:42:53,064 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2015.286.00 INFO 2025-06-26 21:42:53,065 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/ctdDriver.log (9362982 bytes) INFO 2025-06-26 21:42:53,873 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/ctdDriver2.log (9364607 bytes) INFO 2025-06-26 21:42:54,733 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/gps.log (147020 bytes) INFO 2025-06-26 21:42:54,778 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/hydroscatlog.log (8200438 bytes) INFO 2025-06-26 21:42:55,729 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.286.00/hydroscatlog.log: [13395] INFO 2025-06-26 21:42:55,770 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/navigation.log (35103618 bytes) INFO 2025-06-26 21:42:58,649 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/isuslog.log (605589 bytes) INFO 2025-06-26 21:42:58,712 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.286.00/isuslog.log: [1 3] INFO 2025-06-26 21:42:58,714 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/parosci.log (11499158 bytes) INFO 2025-06-26 21:42:59,699 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.286.00/parosci.log: [1 2 3 4] INFO 2025-06-26 21:42:59,745 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/tailCone.log (5860843 bytes) INFO 2025-06-26 21:43:00,526 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/biolume.log (6821818 bytes) INFO 2025-06-26 21:43:01,226 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 21:43:01,603 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.54 seconds INFO 2025-06-26 21:43:01,603 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2015.286.00/lopc.bin (26796232 bytes) INFO 2025-06-26 21:43:01,604 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 21:43:01 2025 INFO 2025-06-26 21:43:01,604 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2015.286.00/parosci.nc INFO 2025-06-26 21:43:01,604 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 21:43:01,604 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2015.286.00/parosci.nc INFO 2025-06-26 21:43:01,609 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1444750817.9, sensor_off_time = 1444775237.8 INFO 2025-06-26 21:43:01,609 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 24419 seconds. Expecting to read 48838 L frames from the lopc.bin file. INFO 2025-06-26 21:43:01,609 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 48838 records from the lopc.bin file. INFO 2025-06-26 21:43:01,896 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2015-10-13 15:40:17 Z and endTime = 2015-10-13 22:27:17 Z with 48838 records expected to be read from lopc.bin INFO 2025-06-26 21:43:01,896 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2015.286.00/lopc.bin INFO 2025-06-26 21:43:01,897 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2015.286.00/lopc.nc INFO 2025-06-26 21:43:01,897 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2015.286.00/lopc.nc INFO 2025-06-26 21:43:01,898 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2015.286.00 INFO 2025-06-26 21:43:01,898 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 21:43:01,963 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 21:43:01,963 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 21:43:01,963 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 21:43:05,490 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 21:43:05,492 process.py calibrate():227 [1] Calibration steps for 2015.286.00 INFO 2025-06-26 21:43:05,864 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 21:43:05,866 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 21:43:06,699 calibrate.py _nudge_pos():1806 [1] 121: 0.120 -0.0006786 -0.0005284 2610 8.70 -11.584 -11.258 2015-10-13T15:50:56.953101568 INFO 2025-06-26 21:43:06,764 calibrate.py _nudge_pos():1806 [1] 127: 0.120 -0.0000510 0.0000273 205 0.68 -11.145 7.439 2015-10-13T15:51:42.949950720 INFO 2025-06-26 21:43:08,525 calibrate.py _nudge_pos():1806 [1] 307: 0.130 -0.0016406 -0.0030369 12610 42.03 -5.793 -13.389 2015-10-13T16:36:44.944851456 INFO 2025-06-26 21:43:08,604 calibrate.py _nudge_pos():1806 [1] 315: 0.120 0.0000259 0.0000240 185 0.61 6.261 7.252 2015-10-13T16:37:28.951836672 INFO 2025-06-26 21:43:09,752 calibrate.py _nudge_pos():1806 [1] 432: 0.130 -0.0040605 -0.0033835 6850 22.83 -26.397 -27.462 2015-10-13T17:02:14.950038784 INFO 2025-06-26 21:43:11,151 calibrate.py _nudge_pos():1806 [1] 574: 0.130 -0.0012200 -0.0033401 9735 32.45 -5.580 -19.075 2015-10-13T17:37:02.947001344 INFO 2025-06-26 21:43:11,181 calibrate.py _nudge_pos():1806 [1] 577: 0.140 -0.0000445 -0.0000237 215 0.71 -9.263 -6.148 2015-10-13T17:37:47.943918592 INFO 2025-06-26 21:43:12,232 calibrate.py _nudge_pos():1806 [1] 680: 0.140 -0.0063057 -0.0010663 14625 48.75 -19.189 -4.053 2015-10-13T18:28:14.946554880 INFO 2025-06-26 21:43:13,054 calibrate.py _nudge_pos():1806 [1] 761: 0.130 -0.0072054 -0.0044112 11570 38.56 -27.718 -21.196 2015-10-13T19:08:08.952554240 INFO 2025-06-26 21:43:13,903 calibrate.py _nudge_pos():1806 [1] 843: 0.140 -0.0063311 -0.0005828 11585 38.61 -24.329 -2.797 2015-10-13T19:48:06.948280320 INFO 2025-06-26 21:43:13,978 calibrate.py _nudge_pos():1806 [1] 850: 0.150 0.0000555 -0.0000038 260 0.86 9.545 -0.821 2015-10-13T19:49:04.944307200 INFO 2025-06-26 21:43:15,121 calibrate.py _nudge_pos():1806 [1] 960: 0.140 -0.0024197 0.0008324 12764 42.55 -8.442 3.625 2015-10-13T20:33:26.951947264 INFO 2025-06-26 21:43:15,933 calibrate.py _nudge_pos():1806 [1] 1039: 0.150 -0.0015487 0.0006783 7410 24.70 -9.310 5.089 2015-10-13T20:59:26.945080320 INFO 2025-06-26 21:43:16,791 calibrate.py _nudge_pos():1806 [1] 1119: 0.150 -0.0000183 0.0000308 15 0.05 -58.357 122.407 2015-10-13T21:00:48.949462528 INFO 2025-06-26 21:43:16,907 calibrate.py _nudge_pos():1806 [1] 1130: 0.160 -0.0016876 -0.0009333 11995 39.98 -6.265 -4.326 2015-10-13T21:40:57.944435200 INFO 2025-06-26 21:43:17,516 calibrate.py _nudge_pos():1806 [1] 1189: 0.150 0.0000440 -0.0000248 35 0.11 57.662 -40.503 2015-10-13T21:42:02.949981952 INFO 2025-06-26 21:43:17,557 calibrate.py _nudge_pos():1806 [1] 1193: 0.150 -0.0010006 0.0002398 9375 31.25 -4.751 1.422 2015-10-13T22:13:20.951330304 INFO 2025-06-26 21:43:25,921 calibrate.py _nudge_pos():1862 [1] 1983: - - - 4 0.01 - - INFO 2025-06-26 21:43:25,921 calibrate.py _nudge_pos():1868 [1] Points in final series = 121878 INFO 2025-06-26 21:43:42,047 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 79 of 97611 INFO 2025-06-26 21:43:42,803 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:43:43,705 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:43:44,421 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:43:44,423 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2015.286.00/ctd1.nc INFO 2025-06-26 21:43:44,425 calibrate.py _range_qc_combined_nc():898 [1] Setting 432 ctd1_salinity values to NaN INFO 2025-06-26 21:43:44,425 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 21:43:44,425 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 21:43:45,276 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:43:45,988 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:43:45,990 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2015.286.00/ctd2.nc WARNING 2025-06-26 21:43:45,992 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (31335) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 21:43:45,992 calibrate.py _range_qc_combined_nc():898 [1] Setting 31335 ctd2_salinity values to NaN INFO 2025-06-26 21:43:45,993 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 21:43:45,993 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 21:43:46,906 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 21:43:48,019 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 21:43:48,227 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 21:44:10,571 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2015.286.00 ERROR 2025-06-26 21:44:10,571 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.286.00 INFO 2025-06-26 21:44:10,669 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_cal.nc INFO 2025-06-26 21:44:10,838 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 21:44:10,844 process.py align():251 [1] Alignment steps for 2015.286.00 INFO 2025-06-26 21:44:10,888 align.py process_cal():139 [1] Processing dorado_2015.286.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2015.286.00 INFO 2025-06-26 21:44:10,922 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:44:10,927 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:44:11,008 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:44:11,013 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:44:11,090 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:44:11,096 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:44:11,143 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 21:44:11,143 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 21:44:11,173 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:44:11,179 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:44:11,256 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,261 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 21:44:11,331 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,335 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 21:44:11,406 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,411 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 21:44:11,481 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,487 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,556 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,561 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,630 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,635 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,705 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,710 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,778 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,784 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,855 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,860 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:11,929 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:11,935 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,004 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,009 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,078 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,083 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,152 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,157 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,226 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,230 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,300 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,305 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,374 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,379 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,449 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,454 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,522 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,527 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,597 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,602 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,674 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,680 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,751 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,756 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,826 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:44:12,830 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:44:12,920 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:44:12,979 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:44:13,038 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:44:13,101 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:44:13,164 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:44:13,275 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 21:44:13,886 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:44:13,942 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_align.nc INFO 2025-06-26 21:44:14,112 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 21:44:14,115 process.py resample():273 [1] Resampling steps for 2015.286.00 INFO 2025-06-26 21:44:14,116 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 21:44:14,155 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_align.nc mission netCDF file INFO 2025-06-26 21:44:14,161 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_align.nc mission netCDF file INFO 2025-06-26 21:44:14,163 resample.py get_mission_start_end():1145 [1] navigation: 2015-10-13T15:41:01.963861248 to 2015-10-13T22:27:17.744005888 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 21:44:14,165 resample.py get_mission_start_end():1145 [1] hs2 : 2015-10-13T15:40:23.346506496 to 2015-10-13T22:27:17.824000256 (0 days 00:00:00 before mission_end) INFO 2025-06-26 21:44:14,166 resample.py get_mission_start_end():1145 [1] ctd1 : 2015-10-13T15:40:57.514166016 to 2015-10-13T22:27:17.734006528 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 21:44:14,168 resample.py get_mission_start_end():1145 [1] ctd2 : 2015-10-13T15:40:53.304454656 to 2015-10-13T22:27:17.754005248 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 21:44:14,170 resample.py get_mission_start_end():1145 [1] isus : 2015-10-13T15:41:16.102892544 to 2015-10-13T22:27:16.624082688 (0 days 00:00:01.199917568 before mission_end) INFO 2025-06-26 21:44:14,171 resample.py get_mission_start_end():1145 [1] biolume : 2015-10-13T15:40:15.487011072 to 2015-10-13T22:27:16.944026368 (0 days 00:00:00.879973888 before mission_end) INFO 2025-06-26 21:44:14,173 resample.py get_mission_start_end():1145 [1] tailcone : 2015-10-13T15:40:19.856745728 to 2015-10-13T22:27:17.664011520 (0 days 00:00:00.159988736 before mission_end) INFO 2025-06-26 21:44:14,173 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_align.nc mission netCDF file INFO 2025-06-26 21:44:14,174 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,433 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,479 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,525 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,569 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,607 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,648 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,686 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,722 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,756 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,793 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,827 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,861 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,896 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,930 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,964 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:14,998 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,034 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,071 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,109 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,206 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,243 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,281 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,317 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,354 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,372 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,388 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,402 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,417 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,431 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:15,436 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 21:44:15,436 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 21:44:16,253 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 21:44:16,428 resample.py add_biolume_proxies():633 [1] Zero flow values found: 122 of 24422 - replaced with 350 ml/s INFO 2025-06-26 21:44:16,428 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 21:44:16,525 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 21:44:16,562 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 21:44:16,593 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 21:44:16,593 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 21:44:16,642 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 21:44:16,897 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_1S.nc INFO 2025-06-26 21:44:18,679 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 21:44:40,910 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2015.286.00/dorado_2015.286.00_1S_Gulper.txt INFO 2025-06-26 21:44:40,910 process.py archive():337 [1] Archiving steps for 2015.286.00 INFO 2025-06-26 21:44:40,910 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00, BASE_PATH = /data/auv_data INFO 2025-06-26 21:44:40,912 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00 files to /Volumes/AUVCTD/surveys/2015/netcdf INFO 2025-06-26 21:44:40,913 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.286.00_1S.nc INFO 2025-06-26 21:44:40,940 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_1S.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:44:40,941 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.286.00_cal.nc INFO 2025-06-26 21:44:41,105 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_cal.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:44:41,106 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.286.00_align.nc INFO 2025-06-26 21:44:41,350 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_align.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:44:41,385 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,415 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,420 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,449 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,546 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,588 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,613 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,687 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,704 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015286/2015.286.00 done. INFO 2025-06-26 21:44:41,704 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 21:44:41,705 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2015/odv/dorado_2015.286.00_1S_Gulper.txt INFO 2025-06-26 21:44:41,713 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2015.286.00/dorado_2015.286.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2015/odv done. INFO 2025-06-26 21:44:41,713 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.286.00/dorado_2015.286.00_processing.log /Volumes/AUVCTD/surveys/2015/netcdf