INFO 2025-06-26 18:58:20,944 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 18:58:20,944 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission - Maria Fox's algorithm in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 18:58:20,944 process.py process_mission():449 [1] Processing CANON September 2011 mission 2011.286.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:58:20,944 process.py download_process():165 [1] Download and processing steps for 2011.286.00 INFO 2025-06-26 18:58:20,944 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011286/2011.286.00 INFO 2025-06-26 18:58:20,944 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011286/2011.286.00 to /data/auv_data/dorado/missionlogs/2011.286.00 INFO 2025-06-26 18:58:24,825 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.286.00 INFO 2025-06-26 18:58:24,825 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/ctdDriver.log (8803878 bytes) INFO 2025-06-26 18:58:25,463 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/ctdDriver2.log (8803967 bytes) INFO 2025-06-26 18:58:26,112 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/gps.log (185684 bytes) INFO 2025-06-26 18:58:26,140 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/hydroscatlog.log (7705930 bytes) INFO 2025-06-26 18:58:26,954 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/navigation.log (31165078 bytes) INFO 2025-06-26 18:58:29,164 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/isuslog.log (728661 bytes) INFO 2025-06-26 18:58:29,238 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/parosci.log (9328838 bytes) INFO 2025-06-26 18:58:30,032 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/tailCone.log (5508571 bytes) INFO 2025-06-26 18:58:30,717 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/biolume.log (6411722 bytes) INFO 2025-06-26 18:58:31,357 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:58:31,683 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.86 seconds INFO 2025-06-26 18:58:31,684 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.286.00/lopc.bin (94203000 bytes) INFO 2025-06-26 18:58:31,684 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:58:31 2025 INFO 2025-06-26 18:58:31,684 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.286.00/parosci.nc INFO 2025-06-26 18:58:31,684 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:58:31,684 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.286.00/parosci.nc INFO 2025-06-26 18:58:31,688 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1318518694.1, sensor_off_time = 1318541645.2 INFO 2025-06-26 18:58:31,688 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 22951 seconds. Expecting to read 45902 L frames from the lopc.bin file. INFO 2025-06-26 18:58:31,688 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 45902 records from the lopc.bin file. INFO 2025-06-26 18:58:31,971 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-10-13 15:11:34 Z and endTime = 2011-10-13 21:34:05 Z with 45902 records expected to be read from lopc.bin INFO 2025-06-26 18:58:31,971 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.286.00/lopc.bin INFO 2025-06-26 18:58:31,971 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.286.00/lopc.nc INFO 2025-06-26 18:58:31,972 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.286.00/lopc.nc INFO 2025-06-26 18:58:31,972 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.286.00 INFO 2025-06-26 18:58:31,972 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 18:58:31,976 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0441073 WARNING 2025-06-26 18:58:31,977 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 18:58:32,072 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 18:58:32,072 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 18:58:32,072 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 18:58:39,507 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:58:39,508 process.py calibrate():227 [1] Calibration steps for 2011.286.00 INFO 2025-06-26 18:58:39,704 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 18:58:39,706 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:58:40,487 calibrate.py _nudge_pos():1806 [1] 113: 0.180 0.0026351 -0.0018152 8870 29.56 13.218 -11.378 2011-10-13T15:42:58.928181760 INFO 2025-06-26 18:58:41,934 calibrate.py _nudge_pos():1806 [1] 267: 0.180 0.0006833 -0.0008849 4845 16.15 6.275 -10.156 2011-10-13T16:01:40.931319296 INFO 2025-06-26 18:58:42,771 calibrate.py _nudge_pos():1806 [1] 356: 0.190 -0.0002120 -0.0007900 4659 15.53 -2.024 -9.428 2011-10-13T16:18:40.931444480 INFO 2025-06-26 18:58:43,609 calibrate.py _nudge_pos():1806 [1] 446: 0.190 0.0007233 -0.0019550 4834 16.11 6.657 -22.487 2011-10-13T16:36:16.929103616 INFO 2025-06-26 18:58:44,637 calibrate.py _nudge_pos():1806 [1] 554: 0.190 -0.0000299 -0.0016771 4535 15.11 -0.293 -20.563 2011-10-13T16:53:10.929639936 INFO 2025-06-26 18:58:46,372 calibrate.py _nudge_pos():1806 [1] 740: 0.200 -0.0000068 -0.0016467 4414 14.71 -0.069 -20.743 2011-10-13T17:10:58.926477056 INFO 2025-06-26 18:58:47,373 calibrate.py _nudge_pos():1806 [1] 847: 0.200 -0.0003513 -0.0024180 4779 15.93 -3.270 -28.132 2011-10-13T17:28:40.933724416 INFO 2025-06-26 18:58:49,032 calibrate.py _nudge_pos():1806 [1] 1019: 0.010 -0.0000778 -0.0013774 4695 15.65 -0.737 -16.313 2011-10-13T17:47:11.127671040 INFO 2025-06-26 18:58:49,931 calibrate.py _nudge_pos():1806 [1] 1112: 0.200 0.0002130 -0.0017018 4519 15.06 2.097 -20.940 2011-10-13T18:03:46.929453824 INFO 2025-06-26 18:58:51,252 calibrate.py _nudge_pos():1806 [1] 1249: 0.010 0.0009120 -0.0015687 4630 15.43 8.764 -18.838 2011-10-13T18:21:29.126688512 INFO 2025-06-26 18:58:52,267 calibrate.py _nudge_pos():1806 [1] 1356: 0.010 0.0002406 -0.0017358 4600 15.33 2.327 -20.981 2011-10-13T18:38:35.126402560 INFO 2025-06-26 18:58:53,000 calibrate.py _nudge_pos():1806 [1] 1433: 0.010 0.0003587 -0.0020958 4930 16.43 3.238 -23.636 2011-10-13T18:56:17.133650176 INFO 2025-06-26 18:58:54,603 calibrate.py _nudge_pos():1806 [1] 1599: 0.010 -0.0004108 -0.0011879 4515 15.05 -4.048 -14.629 2011-10-13T19:14:05.130487552 INFO 2025-06-26 18:58:55,217 calibrate.py _nudge_pos():1806 [1] 1662: 0.020 0.0000328 -0.0000747 80 0.26 18.444 -52.554 2011-10-13T19:15:23.125144320 INFO 2025-06-26 18:58:55,522 calibrate.py _nudge_pos():1806 [1] 1693: 0.010 0.0004719 -0.0021623 4650 15.50 4.516 -25.856 2011-10-13T19:31:23.129379584 INFO 2025-06-26 18:58:56,251 calibrate.py _nudge_pos():1806 [1] 1768: 0.010 0.0002880 -0.0017248 4700 15.66 2.726 -20.404 2011-10-13T19:48:17.129915648 INFO 2025-06-26 18:58:57,710 calibrate.py _nudge_pos():1806 [1] 1919: 0.020 0.0019032 -0.0014937 4740 15.80 17.864 -17.521 2011-10-13T20:06:35.134697216 INFO 2025-06-26 18:58:59,348 calibrate.py _nudge_pos():1806 [1] 2088: 0.030 0.0012583 -0.0020213 4830 16.10 11.591 -23.269 2011-10-13T20:25:29.127013376 INFO 2025-06-26 18:59:00,191 calibrate.py _nudge_pos():1806 [1] 2174: 0.030 -0.0008815 -0.0014193 4555 15.18 -8.611 -17.325 2011-10-13T20:42:05.128782848 INFO 2025-06-26 18:59:01,111 calibrate.py _nudge_pos():1806 [1] 2269: 0.030 0.0008387 -0.0020066 4840 16.13 7.710 -23.052 2011-10-13T20:59:47.126030848 INFO 2025-06-26 18:59:02,124 calibrate.py _nudge_pos():1806 [1] 2372: 0.020 0.0009707 -0.0019413 4890 16.30 8.833 -22.073 2011-10-13T21:17:47.132045568 INFO 2025-06-26 18:59:03,491 calibrate.py _nudge_pos():1806 [1] 2512: 0.030 0.0003385 -0.0013169 3925 13.08 3.838 -18.657 2011-10-13T21:33:11.128747264 INFO 2025-06-26 18:59:04,020 calibrate.py _nudge_pos():1862 [1] 2529: - - - 0 0.00 - - INFO 2025-06-26 18:59:04,020 calibrate.py _nudge_pos():1868 [1] Points in final series = 114029 WARNING 2025-06-26 18:59:04,172 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:59:04,401 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 21 of 91725 INFO 2025-06-26 18:59:05,093 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:05,939 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:06,610 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:06,613 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.286.00/ctd1.nc INFO 2025-06-26 18:59:06,614 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 18:59:06,615 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 18:59:06,615 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:59:07,413 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 18:59:08,102 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 18:59:08,105 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.286.00/ctd2.nc WARNING 2025-06-26 18:59:08,106 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (4222) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 18:59:08,106 calibrate.py _range_qc_combined_nc():898 [1] Setting 4222 ctd2_salinity values to NaN INFO 2025-06-26 18:59:08,107 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 18:59:08,107 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:59:08,148 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:59:09,395 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 18:59:09,431 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.286.00 ERROR 2025-06-26 18:59:09,431 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.286.00 INFO 2025-06-26 18:59:09,523 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_cal.nc INFO 2025-06-26 18:59:09,676 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 18:59:09,682 process.py align():251 [1] Alignment steps for 2011.286.00 INFO 2025-06-26 18:59:09,723 align.py process_cal():139 [1] Processing dorado_2011.286.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.286.00 INFO 2025-06-26 18:59:09,755 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:59:09,759 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:59:09,835 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:59:09,841 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:59:09,917 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:59:09,923 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:59:09,970 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:59:09,970 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:59:09,999 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:59:10,004 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:59:10,080 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,085 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,151 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,156 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,221 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,226 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,295 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,300 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,367 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,372 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,437 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,442 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,511 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,516 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,584 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,589 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,657 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,661 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,727 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,732 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,799 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,804 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,869 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,874 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:10,940 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:10,945 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,013 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,018 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,086 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,090 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,156 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,161 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,228 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,232 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,299 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,304 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,372 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,377 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,445 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,451 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,525 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,530 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,602 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.286.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:59:11,606 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:59:11,686 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:59:11,742 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:59:11,799 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:59:11,857 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:59:11,916 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:59:12,014 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 18:59:12,591 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:59:12,645 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_align.nc INFO 2025-06-26 18:59:12,805 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 18:59:12,807 process.py resample():273 [1] Resampling steps for 2011.286.00 INFO 2025-06-26 18:59:12,808 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:59:12,853 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_align.nc mission netCDF file INFO 2025-06-26 18:59:12,860 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_align.nc mission netCDF file INFO 2025-06-26 18:59:12,861 resample.py get_mission_start_end():1145 [1] navigation: 2011-10-13T15:12:11.544736256 to 2011-10-13T21:34:05.125048320 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 18:59:12,863 resample.py get_mission_start_end():1145 [1] hs2 : 2011-10-13T15:11:42.676713728 to 2011-10-13T21:34:05.105049600 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 18:59:12,865 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-10-13T15:12:00.365501952 to 2011-10-13T21:34:05.125048320 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 18:59:12,866 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-10-13T15:12:00.715478016 to 2011-10-13T21:34:05.225041408 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:59:12,868 resample.py get_mission_start_end():1145 [1] isus : 2011-10-13T15:12:52.371939072 to 2011-10-13T21:34:05.225041408 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:59:12,869 resample.py get_mission_start_end():1145 [1] biolume : 2011-10-13T15:11:33.287322624 to 2011-10-13T21:34:03.775106304 (0 days 00:00:01.449935104 before mission_end) INFO 2025-06-26 18:59:12,871 resample.py get_mission_start_end():1145 [1] tailcone : 2011-10-13T15:11:35.177227520 to 2011-10-13T21:34:05.175044864 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 18:59:12,871 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_align.nc mission netCDF file INFO 2025-06-26 18:59:12,872 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,124 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,166 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,207 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,248 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,285 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,321 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,356 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,391 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,424 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,456 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,489 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,521 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,554 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,586 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,619 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,651 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,685 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,720 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,755 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,800 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,834 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,869 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,904 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,939 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,958 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,974 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:13,989 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:14,004 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:14,018 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:14,025 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:59:14,025 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:59:14,888 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:59:15,042 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:59:15,123 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:59:15,159 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:59:15,188 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:59:15,188 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:59:15,234 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:59:15,481 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_1S.nc INFO 2025-06-26 18:59:16,807 create_products.py gulper_odv():401 [1] No gulper times found for 2011.286.00 INFO 2025-06-26 18:59:16,807 process.py archive():337 [1] Archiving steps for 2011.286.00 INFO 2025-06-26 18:59:16,807 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00, BASE_PATH = /data/auv_data INFO 2025-06-26 18:59:16,807 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:59:16,809 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.286.00_1S.nc INFO 2025-06-26 18:59:16,836 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:59:16,837 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.286.00_cal.nc INFO 2025-06-26 18:59:17,014 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:59:17,015 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.286.00_align.nc INFO 2025-06-26 18:59:17,269 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:59:17,301 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,328 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,334 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,358 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,446 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,453 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,479 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,503 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,574 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,586 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011286/2011.286.00 done. INFO 2025-06-26 18:59:17,586 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:59:17,587 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.286.00/dorado_2011.286.00_processing.log /Volumes/AUVCTD/surveys/2011/netcdf