INFO 2025-06-26 15:25:48,882 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 15:25:48,882 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna mission - ctdToUse = ctd1 INFO 2025-06-26 15:25:48,882 process.py process_mission():449 [1] Processing AUVCTD mission 2009.308.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:25:48,882 process.py download_process():165 [1] Download and processing steps for 2009.308.04 INFO 2025-06-26 15:25:48,882 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009308/2009.308.04 INFO 2025-06-26 15:25:48,882 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009308/2009.308.04 to /data/auv_data/dorado/missionlogs/2009.308.04 INFO 2025-06-26 15:25:55,110 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.308.04 INFO 2025-06-26 15:25:55,111 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/ctdDriver.log (9168062 bytes) INFO 2025-06-26 15:25:55,816 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.308.04/ctdDriver.log: [ 269 1208 7504 39859 43155 46806 56434 61684 69177 70323 75887 82531 86759 90006 90009 96719 102774] INFO 2025-06-26 15:25:55,854 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/ctdDriver2.log (9168317 bytes) INFO 2025-06-26 15:25:56,530 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.308.04/ctdDriver2.log: [ 269 1209 7506 13788 30458 39862 43158 46809 69180 75890 77238 82534 86762 91241 95123 95520 96722] INFO 2025-06-26 15:25:56,564 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/gps.log (158324 bytes) INFO 2025-06-26 15:25:56,589 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/hydroscatlog.log (8755426 bytes) INFO 2025-06-26 15:25:57,498 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.308.04/hydroscatlog.log: [ 1603 2363 3301 13242 14838 16916 20799 35148 36371 36668 44070 51958 53306 54152 57142 61259 63213 75476 77510 77864 79113 88545 89655] INFO 2025-06-26 15:25:57,527 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/navigation.log (30713638 bytes) INFO 2025-06-26 15:25:59,744 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/isuslog.log (609525 bytes) INFO 2025-06-26 15:25:59,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/parosci.log (10671062 bytes) INFO 2025-06-26 15:26:00,743 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/tailCone.log (1280011 bytes) INFO 2025-06-26 15:26:00,905 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/biolume.log (7095532 bytes) INFO 2025-06-26 15:26:01,570 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:26:01,946 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.84 seconds INFO 2025-06-26 15:26:01,946 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.308.04/lopc.bin (18067403 bytes) INFO 2025-06-26 15:26:01,946 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:26:01 2025 INFO 2025-06-26 15:26:01,947 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.308.04/parosci.nc INFO 2025-06-26 15:26:01,947 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:26:01,947 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.308.04/parosci.nc INFO 2025-06-26 15:26:01,950 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257350905.9, sensor_off_time = 1257376977.6 INFO 2025-06-26 15:26:01,950 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 26071 seconds. Expecting to read 52142 L frames from the lopc.bin file. INFO 2025-06-26 15:26:01,950 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 52142 records from the lopc.bin file. INFO 2025-06-26 15:26:02,259 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-11-04 16:08:25 Z and endTime = 2009-11-04 23:22:57 Z with 52142 records expected to be read from lopc.bin INFO 2025-06-26 15:26:02,259 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.308.04/lopc.bin INFO 2025-06-26 15:26:02,259 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.308.04/lopc.nc INFO 2025-06-26 15:26:02,259 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.308.04/lopc.nc INFO 2025-06-26 15:26:02,260 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.308.04 INFO 2025-06-26 15:26:02,260 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:26:02,334 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:26:02,334 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:26:02,334 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 15:26:06,176 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 17204 8257 1 0 0 0 88 3.9 seconds, last L Frame: 52142 ERROR 2025-06-26 15:26:07,060 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 15:26:07,062 process.py calibrate():227 [1] Calibration steps for 2009.308.04 INFO 2025-06-26 15:26:07,359 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 15:26:07,361 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:26:08,182 calibrate.py _nudge_pos():1806 [1] 110: 0.080 0.0015506 -0.0000873 9815 32.76 7.024 -0.494 2009-11-04T16:42:59.255387392 INFO 2025-06-26 15:26:09,766 calibrate.py _nudge_pos():1806 [1] 273: 0.080 -0.0005894 0.0005923 10047 33.50 -2.612 3.276 2009-11-04T17:19:11.256594944 INFO 2025-06-26 15:26:11,460 calibrate.py _nudge_pos():1806 [1] 444: 0.080 0.0003739 0.0009849 9737 32.46 1.709 5.622 2009-11-04T17:54:29.261501696 INFO 2025-06-26 15:26:12,815 calibrate.py _nudge_pos():1806 [1] 581: 0.090 0.0016756 -0.0001407 10206 34.03 7.309 -0.766 2009-11-04T18:30:47.262298368 INFO 2025-06-26 15:26:12,928 calibrate.py _nudge_pos():1806 [1] 592: 0.090 0.0000038 0.0000150 15 0.05 12.242 59.678 2009-11-04T18:31:01.261339392 INFO 2025-06-26 15:26:14,366 calibrate.py _nudge_pos():1806 [1] 737: 0.090 -0.0004652 0.0005985 9736 32.46 -2.127 3.416 2009-11-04T19:05:53.258027776 INFO 2025-06-26 15:26:15,882 calibrate.py _nudge_pos():1806 [1] 890: 0.100 0.0013310 0.0000167 10335 34.46 5.733 0.090 2009-11-04T19:42:53.255947520 INFO 2025-06-26 15:26:17,658 calibrate.py _nudge_pos():1806 [1] 1065: 0.110 -0.0003452 0.0011291 9899 33.00 -1.553 6.341 2009-11-04T20:18:47.258388224 INFO 2025-06-26 15:26:19,243 calibrate.py _nudge_pos():1806 [1] 1223: 0.110 0.0022854 0.0002057 10039 33.48 10.132 1.138 2009-11-04T20:54:53.260006912 INFO 2025-06-26 15:26:20,481 calibrate.py _nudge_pos():1806 [1] 1346: 0.110 0.0000296 0.0000304 80 0.26 16.679 21.401 2009-11-04T20:57:11.260553472 INFO 2025-06-26 15:26:20,683 calibrate.py _nudge_pos():1806 [1] 1366: 0.110 -0.0004293 0.0010968 10011 33.38 -1.908 6.089 2009-11-04T21:30:53.262036736 INFO 2025-06-26 15:26:21,368 calibrate.py _nudge_pos():1806 [1] 1433: 0.120 0.0000010 -0.0000136 15 0.05 3.096 -54.201 2009-11-04T21:32:02.257310208 INFO 2025-06-26 15:26:21,450 calibrate.py _nudge_pos():1806 [1] 1441: 0.120 0.0000306 0.0000269 70 0.23 19.761 21.659 2009-11-04T21:32:23.255871744 INFO 2025-06-26 15:26:22,090 calibrate.py _nudge_pos():1806 [1] 1504: 0.110 0.0021507 -0.0003265 10367 34.56 9.236 -1.750 2009-11-04T22:07:59.259545600 INFO 2025-06-26 15:26:23,686 calibrate.py _nudge_pos():1806 [1] 1661: 0.130 -0.0001537 0.0004409 9712 32.40 -0.704 2.522 2009-11-04T22:42:59.255685888 INFO 2025-06-26 15:26:25,277 calibrate.py _nudge_pos():1806 [1] 1816: 0.130 0.0002803 0.0001996 9369 31.23 1.332 1.184 2009-11-04T23:16:47.256758272 INFO 2025-06-26 15:26:29,081 calibrate.py _nudge_pos():1862 [1] 2154: - - - 2 0.00 - - INFO 2025-06-26 15:26:29,082 calibrate.py _nudge_pos():1868 [1] Points in final series = 130130 WARNING 2025-06-26 15:26:29,255 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:26:43,081 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:26:50,520 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:26:51,315 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:26:51,318 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.308.04/ctd1.nc INFO 2025-06-26 15:26:51,319 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 15:26:51,319 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 15:26:51,319 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:26:57,104 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:26:57,871 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:26:57,874 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.308.04/ctd2.nc INFO 2025-06-26 15:26:57,875 calibrate.py _range_qc_combined_nc():898 [1] Setting 171 ctd2_salinity values to NaN INFO 2025-06-26 15:26:57,875 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 15:26:57,875 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:26:57,915 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:26:59,129 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 1512366 1512367 1553460] INFO 2025-06-26 15:26:59,368 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:26:59,374 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 15:26:59,374 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.308.04 ERROR 2025-06-26 15:26:59,374 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.308.04 INFO 2025-06-26 15:26:59,398 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_cal.nc INFO 2025-06-26 15:27:07,627 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, 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 15:27:07,633 process.py align():251 [1] Alignment steps for 2009.308.04 INFO 2025-06-26 15:27:07,662 align.py process_cal():139 [1] Processing dorado_2009.308.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.308.04 INFO 2025-06-26 15:27:07,699 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:07,704 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:07,791 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:07,797 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:07,882 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:07,888 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:07,941 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:27:07,941 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:27:07,974 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:07,981 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:08,066 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,071 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,143 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,149 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,224 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,228 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,302 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,308 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,383 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,388 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,463 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,468 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,546 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,551 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,627 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,632 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,709 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,714 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,788 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,794 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,871 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,876 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:08,951 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:08,956 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,035 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,040 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,120 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,125 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,202 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,208 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,282 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,287 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,363 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,368 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,444 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,450 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,527 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,532 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,610 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.308.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:09,614 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:09,706 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:09,765 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:09,826 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:09,890 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:27:09,955 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 15:27:09,977 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_align.nc INFO 2025-06-26 15:27:10,063 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, 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 15:27:10,065 process.py resample():273 [1] Resampling steps for 2009.308.04 INFO 2025-06-26 15:27:10,065 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:27:10,091 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_align.nc mission netCDF file INFO 2025-06-26 15:27:10,097 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_align.nc mission netCDF file INFO 2025-06-26 15:27:10,099 resample.py get_mission_start_end():1145 [1] navigation: 2009-11-04T16:08:57.905229312 to 2009-11-04T23:22:57.661383936 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 15:27:10,101 resample.py get_mission_start_end():1145 [1] hs2 : 2009-11-04T16:08:30.977073920 to 2009-11-04T23:22:57.541392128 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 15:27:10,103 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-11-04T16:08:52.715584768 to 2009-11-04T23:22:57.661383936 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 15:27:10,104 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-11-04T16:08:52.705585408 to 2009-11-04T23:22:57.621386496 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 15:27:10,106 resample.py get_mission_start_end():1145 [1] isus : 2009-11-04T16:09:43.982072832 to 2009-11-04T23:22:56.771444736 (0 days 00:00:00.899938304 before mission_end) INFO 2025-06-26 15:27:10,108 resample.py get_mission_start_end():1145 [1] biolume : 2009-11-04T16:08:24.487484160 to 2009-11-04T23:22:56.501428992 (0 days 00:00:01.169954048 before mission_end) INFO 2025-06-26 15:27:10,109 resample.py get_mission_start_end():1145 [1] tailcone : 2009-11-04T16:08:30.367115776 to 2009-11-04T23:22:57.671383040 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:27:10,110 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_align.nc mission netCDF file INFO 2025-06-26 15:27:10,110 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,392 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,439 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,486 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,533 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,574 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,614 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,655 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,695 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,732 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,769 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,806 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,842 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,879 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,916 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,954 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:10,991 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,030 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,069 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,110 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,149 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,187 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,226 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,244 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,260 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,275 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,293 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,310 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:11,555 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_1S.nc INFO 2025-06-26 15:27:14,740 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 15:27:20,309 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.308.04/dorado_2009.308.04_1S_Gulper.txt INFO 2025-06-26 15:27:20,309 process.py archive():337 [1] Archiving steps for 2009.308.04 INFO 2025-06-26 15:27:20,309 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04, BASE_PATH = /data/auv_data INFO 2025-06-26 15:27:20,310 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:27:20,311 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.308.04_1S.nc INFO 2025-06-26 15:27:20,335 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:20,336 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.308.04_cal.nc INFO 2025-06-26 15:27:20,440 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:20,441 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.308.04_align.nc INFO 2025-06-26 15:27:20,533 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:20,563 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,589 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,594 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,619 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,702 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,709 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,739 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,749 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,821 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,844 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009308/2009.308.04 done. INFO 2025-06-26 15:27:20,844 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:27:20,845 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.308.04_1S_Gulper.txt INFO 2025-06-26 15:27:20,850 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.308.04/dorado_2009.308.04_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 15:27:20,850 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.308.04/dorado_2009.308.04_processing.log /Volumes/AUVCTD/surveys/2009/netcdf