INFO 2025-06-26 21:32:50,975 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 21:32:50,975 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB Spring 2015 - ctdToUse = ctd1 INFO 2025-06-26 21:32:50,975 process.py process_mission():449 [1] Processing CANON May 2015 mission 2015.148.01 by user docker_user on host 355841a7028c INFO 2025-06-26 21:32:50,975 process.py download_process():165 [1] Download and processing steps for 2015.148.01 INFO 2025-06-26 21:32:50,975 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2015/2015148/2015.148.01 INFO 2025-06-26 21:32:50,976 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2015/2015148/2015.148.01 to /data/auv_data/dorado/missionlogs/2015.148.01 INFO 2025-06-26 21:32:55,746 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2015.148.01 INFO 2025-06-26 21:32:55,746 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/ctdDriver.log (9134886 bytes) INFO 2025-06-26 21:32:56,469 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/ctdDriver2.log (9134783 bytes) INFO 2025-06-26 21:32:57,143 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/gps.log (90356 bytes) INFO 2025-06-26 21:32:57,160 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/hydroscatlog.log (7997074 bytes) INFO 2025-06-26 21:32:57,995 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/navigation.log (34225506 bytes) INFO 2025-06-26 21:33:00,511 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/isuslog.log (590133 bytes) INFO 2025-06-26 21:33:00,571 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/parosci.log (11220950 bytes) INFO 2025-06-26 21:33:01,511 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/tailCone.log (5715691 bytes) INFO 2025-06-26 21:33:02,220 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/biolume.log (6652838 bytes) INFO 2025-06-26 21:33:02,888 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 21:33:03,222 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.48 seconds INFO 2025-06-26 21:33:03,222 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2015.148.01/lopc.bin (74411557 bytes) INFO 2025-06-26 21:33:03,223 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 21:33:03 2025 INFO 2025-06-26 21:33:03,223 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2015.148.01/parosci.nc INFO 2025-06-26 21:33:03,223 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 21:33:03,223 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2015.148.01/parosci.nc INFO 2025-06-26 21:33:03,226 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1432827760.2, sensor_off_time = 1432851573.1 INFO 2025-06-26 21:33:03,226 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23812 seconds. Expecting to read 47624 L frames from the lopc.bin file. INFO 2025-06-26 21:33:03,226 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 47624 records from the lopc.bin file. INFO 2025-06-26 21:33:03,506 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2015-05-28 15:42:40 Z and endTime = 2015-05-28 22:19:33 Z with 47624 records expected to be read from lopc.bin INFO 2025-06-26 21:33:03,506 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2015.148.01/lopc.bin INFO 2025-06-26 21:33:03,506 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2015.148.01/lopc.nc INFO 2025-06-26 21:33:03,507 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2015.148.01/lopc.nc INFO 2025-06-26 21:33:03,507 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2015.148.01 INFO 2025-06-26 21:33:03,507 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 21:33:03,565 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 21:33:03,566 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 21:33:03,566 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 21:33:05,288 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 21:33:05,289 process.py calibrate():227 [1] Calibration steps for 2015.148.01 INFO 2025-06-26 21:33:05,498 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 21:33:05,500 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 21:33:06,519 calibrate.py _nudge_pos():1806 [1] 147: 0.100 0.0012795 -0.0001957 3355 11.18 17.018 -3.244 2015-05-28T15:56:15.408737536 INFO 2025-06-26 21:33:07,218 calibrate.py _nudge_pos():1806 [1] 222: 0.100 0.0046874 -0.0009816 11150 37.16 18.752 -4.894 2015-05-28T16:34:39.410902528 INFO 2025-06-26 21:33:07,294 calibrate.py _nudge_pos():1806 [1] 230: 0.100 -0.0000122 0.0000102 125 0.41 -4.401 4.562 2015-05-28T16:35:11.408710656 INFO 2025-06-26 21:33:07,814 calibrate.py _nudge_pos():1806 [1] 286: 0.110 -0.0000093 0.0000189 15 0.05 -29.743 74.867 2015-05-28T16:36:09.404737792 INFO 2025-06-26 21:33:07,861 calibrate.py _nudge_pos():1806 [1] 291: 0.110 0.0048114 -0.0006899 11560 38.53 18.561 -3.318 2015-05-28T17:14:45.406080768 INFO 2025-06-26 21:33:07,899 calibrate.py _nudge_pos():1806 [1] 295: 0.120 -0.0000300 0.0000054 175 0.58 -7.680 1.721 2015-05-28T17:15:23.403477760 INFO 2025-06-26 21:33:08,512 calibrate.py _nudge_pos():1806 [1] 357: 0.120 0.0044474 -0.0007446 11235 37.45 17.650 -3.685 2015-05-28T17:53:51.405368832 INFO 2025-06-26 21:33:09,092 calibrate.py _nudge_pos():1806 [1] 418: 0.130 0.0042325 -0.0010233 11550 38.50 16.336 -4.926 2015-05-28T18:33:21.403012864 INFO 2025-06-26 21:33:09,870 calibrate.py _nudge_pos():1806 [1] 496: 0.130 0.0011108 -0.0002352 4535 15.11 10.920 -2.884 2015-05-28T18:49:45.405603840 INFO 2025-06-26 21:33:09,961 calibrate.py _nudge_pos():1806 [1] 505: 0.130 0.0000213 -0.0000251 155 0.51 6.177 -9.064 2015-05-28T18:50:24.402932480 INFO 2025-06-26 21:33:10,681 calibrate.py _nudge_pos():1806 [1] 578: 0.140 -0.0032831 -0.0001855 9220 30.73 -15.872 -1.119 2015-05-28T19:22:21.401608960 INFO 2025-06-26 21:33:11,376 calibrate.py _nudge_pos():1806 [1] 651: 0.140 -0.0044312 0.0000332 10920 36.40 -18.086 0.169 2015-05-28T19:59:57.407062016 INFO 2025-06-26 21:33:12,187 calibrate.py _nudge_pos():1806 [1] 735: 0.150 -0.0045645 0.0002565 10775 35.91 -18.880 1.324 2015-05-28T20:37:15.403748864 INFO 2025-06-26 21:33:12,637 calibrate.py _nudge_pos():1806 [1] 782: 0.150 -0.0052856 0.0005565 11470 38.23 -20.537 2.697 2015-05-28T21:16:15.403447808 INFO 2025-06-26 21:33:13,385 calibrate.py _nudge_pos():1806 [1] 860: 0.150 -0.0011444 0.0003155 2735 9.11 -18.654 6.414 2015-05-28T21:26:39.410700288 INFO 2025-06-26 21:33:13,416 calibrate.py _nudge_pos():1806 [1] 863: 0.150 0.0000366 0.0000025 25 0.08 68.026 5.704 2015-05-28T21:26:46.410220800 INFO 2025-06-26 21:33:13,710 calibrate.py _nudge_pos():1806 [1] 892: 0.150 0.0000076 0.0000300 15 0.05 24.303 119.175 2015-05-28T21:27:17.408097536 INFO 2025-06-26 21:33:13,867 calibrate.py _nudge_pos():1806 [1] 908: 0.150 0.0008735 -0.0016022 8765 29.21 4.440 -10.163 2015-05-28T21:56:45.406981120 INFO 2025-06-26 21:33:13,888 calibrate.py _nudge_pos():1806 [1] 910: 0.160 0.0001025 -0.0001943 955 3.18 4.786 -11.323 2015-05-28T21:59:57.403828736 INFO 2025-06-26 21:33:13,909 calibrate.py _nudge_pos():1806 [1] 912: 0.150 0.0001093 -0.0002149 955 3.18 5.102 -12.520 2015-05-28T22:03:09.410674944 INFO 2025-06-26 21:33:14,702 calibrate.py _nudge_pos():1806 [1] 981: 0.170 0.0002476 -0.0004127 3110 10.36 3.548 -7.380 2015-05-28T22:14:39.403407360 INFO 2025-06-26 21:33:14,773 calibrate.py _nudge_pos():1806 [1] 988: 0.160 0.0000090 -0.0000246 40 0.13 10.227 -35.016 2015-05-28T22:14:53.402448384 INFO 2025-06-26 21:33:14,804 calibrate.py _nudge_pos():1806 [1] 991: 0.160 -0.0000334 0.0000746 35 0.11 -43.828 122.022 2015-05-28T22:15:03.401763328 INFO 2025-06-26 21:33:15,391 calibrate.py _nudge_pos():1806 [1] 1043: 0.160 -0.0001439 0.0001002 25 0.08 -267.163 232.003 2015-05-28T22:16:00.407858176 INFO 2025-06-26 21:33:16,208 calibrate.py _nudge_pos():1806 [1] 1122: 0.160 0.0000324 -0.0000097 25 0.08 60.068 -22.464 2015-05-28T22:17:23.402172928 INFO 2025-06-26 21:33:16,471 calibrate.py _nudge_pos():1806 [1] 1149: 0.150 0.0000168 -0.0000150 30 0.10 25.784 -28.669 2015-05-28T22:17:55.409980160 INFO 2025-06-26 21:33:16,521 calibrate.py _nudge_pos():1806 [1] 1154: 0.160 0.0000385 -0.0000286 25 0.08 71.418 -66.269 2015-05-28T22:18:04.409363456 INFO 2025-06-26 21:33:17,414 calibrate.py _nudge_pos():1862 [1] 1195: - - - 3 0.01 - - INFO 2025-06-26 21:33:17,415 calibrate.py _nudge_pos():1868 [1] Points in final series = 118830 INFO 2025-06-26 21:33:18,581 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:33:19,456 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:33:20,152 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:33:20,154 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2015.148.01/ctd1.nc INFO 2025-06-26 21:33:20,155 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 21:33:20,155 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 21:33:20,155 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 21:33:20,984 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:33:21,680 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:33:21,682 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2015.148.01/ctd2.nc WARNING 2025-06-26 21:33:21,685 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (60428) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 21:33:21,685 calibrate.py _range_qc_combined_nc():898 [1] Setting 60428 ctd2_salinity values to NaN INFO 2025-06-26 21:33:21,686 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 21:33:21,686 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 21:33:21,726 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 21:33:22,779 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 600 601] INFO 2025-06-26 21:33:22,986 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 21:33:44,665 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2015.148.01 ERROR 2025-06-26 21:33:44,666 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.148.01 INFO 2025-06-26 21:33:44,758 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_cal.nc INFO 2025-06-26 21:33:44,916 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 21:33:44,922 process.py align():251 [1] Alignment steps for 2015.148.01 INFO 2025-06-26 21:33:44,970 align.py process_cal():139 [1] Processing dorado_2015.148.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2015.148.01 INFO 2025-06-26 21:33:45,003 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:33:45,008 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:33:45,086 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:33:45,091 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:33:45,165 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:33:45,171 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:33:45,217 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 21:33:45,218 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 21:33:45,248 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:33:45,253 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:33:45,328 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,333 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,400 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,405 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,471 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,476 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,541 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,546 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,617 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,682 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,687 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,754 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,759 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,824 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,829 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,896 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,900 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:45,981 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:45,986 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,054 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,059 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,125 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,129 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,197 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,201 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,267 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,271 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,338 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,343 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,410 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,415 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,482 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,487 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,555 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,560 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,627 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,632 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,699 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,704 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,770 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,775 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,841 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.148.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:33:46,846 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:33:46,934 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:33:46,992 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:33:47,052 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:33:47,111 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:33:47,172 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:33:47,284 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 21:33:47,893 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:33:47,946 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_align.nc INFO 2025-06-26 21:33:48,111 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 21:33:48,115 process.py resample():273 [1] Resampling steps for 2015.148.01 INFO 2025-06-26 21:33:48,116 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 21:33:48,159 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_align.nc mission netCDF file INFO 2025-06-26 21:33:48,165 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_align.nc mission netCDF file INFO 2025-06-26 21:33:48,166 resample.py get_mission_start_end():1145 [1] navigation: 2015-05-28T15:43:27.221362176 to 2015-05-28T22:19:33.003294464 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 21:33:48,168 resample.py get_mission_start_end():1145 [1] hs2 : 2015-05-28T15:42:44.474290432 to 2015-05-28T22:19:32.943298560 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 21:33:48,169 resample.py get_mission_start_end():1145 [1] ctd1 : 2015-05-28T15:43:06.562777344 to 2015-05-28T22:19:33.063290368 (0 days 00:00:00 before mission_end) INFO 2025-06-26 21:33:48,171 resample.py get_mission_start_end():1145 [1] ctd2 : 2015-05-28T15:43:07.042744320 to 2015-05-28T22:19:33.023292928 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 21:33:48,172 resample.py get_mission_start_end():1145 [1] isus : 2015-05-28T15:43:56.719341312 to 2015-05-28T22:19:31.793377280 (0 days 00:00:01.269913088 before mission_end) INFO 2025-06-26 21:33:48,174 resample.py get_mission_start_end():1145 [1] biolume : 2015-05-28T15:42:38.194686464 to 2015-05-28T22:19:31.603356160 (0 days 00:00:01.459934208 before mission_end) INFO 2025-06-26 21:33:48,175 resample.py get_mission_start_end():1145 [1] tailcone : 2015-05-28T15:42:39.924602112 to 2015-05-28T22:19:32.913300480 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 21:33:48,176 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_align.nc mission netCDF file INFO 2025-06-26 21:33:48,176 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,428 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,473 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,516 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,559 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,597 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,635 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,677 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,717 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,752 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,786 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,818 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,850 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,883 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,915 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,947 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:48,980 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,015 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,054 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,091 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,239 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,273 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,307 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,340 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,374 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,390 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,406 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,420 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,435 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,448 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:49,453 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 21:33:49,453 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 21:33:50,246 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 21:33:50,424 resample.py add_biolume_proxies():633 [1] Zero flow values found: 23814 of 23814 - replaced with 350 ml/s INFO 2025-06-26 21:33:50,425 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 21:33:50,519 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 21:33:50,555 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 21:33:50,585 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 21:33:50,585 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 21:33:50,635 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 21:33:50,880 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_1S.nc INFO 2025-06-26 21:33:52,926 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 21:34:12,936 create_products.py gulper_odv():522 [1] Wrote 18 Gulper data lines to /data/auv_data/dorado/missionodvs/2015.148.01/dorado_2015.148.01_1S_Gulper.txt INFO 2025-06-26 21:34:12,937 process.py archive():337 [1] Archiving steps for 2015.148.01 INFO 2025-06-26 21:34:12,937 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01, BASE_PATH = /data/auv_data INFO 2025-06-26 21:34:12,938 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01 files to /Volumes/AUVCTD/surveys/2015/netcdf INFO 2025-06-26 21:34:12,939 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.148.01_1S.nc INFO 2025-06-26 21:34:12,963 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_1S.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:34:12,964 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.148.01_cal.nc INFO 2025-06-26 21:34:13,138 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_cal.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:34:13,139 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.148.01_align.nc INFO 2025-06-26 21:34:13,378 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_align.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:34:13,409 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,437 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,442 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,468 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,568 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,576 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,610 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,635 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,708 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,715 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015148/2015.148.01 done. INFO 2025-06-26 21:34:13,715 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 21:34:13,716 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2015/odv/dorado_2015.148.01_1S_Gulper.txt INFO 2025-06-26 21:34:13,721 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2015.148.01/dorado_2015.148.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2015/odv done. INFO 2025-06-26 21:34:13,721 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.148.01/dorado_2015.148.01_processing.log /Volumes/AUVCTD/surveys/2015/netcdf