INFO 2025-06-26 16:54:31,264 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 16:54:31,264 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey twelfth - Daytime short misison around LatMix - ctdToUse = ctd1 INFO 2025-06-26 16:54:31,264 process.py process_mission():449 [1] Processing AUVCTD mission 2010.294.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:54:31,264 process.py download_process():165 [1] Download and processing steps for 2010.294.01 INFO 2025-06-26 16:54:31,264 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010294/2010.294.01 INFO 2025-06-26 16:54:31,264 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010294/2010.294.01 to /data/auv_data/dorado/missionlogs/2010.294.01 INFO 2025-06-26 16:54:33,758 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.294.01 INFO 2025-06-26 16:54:33,758 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/ctdDriver.log (3113771 bytes) INFO 2025-06-26 16:54:33,968 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.294.01/ctdDriver.log: [ 20 21 166 300 377 399 913 930 1024 1403 1475 1613 1661 2043 2307 2561 2583 2960 3294 3368 3557 3920 4476 5063 5914 7603 8210 9918 10221 10457 10634 11403 13562 14571 15380 23794 25151 25886 27404 28679] INFO 2025-06-26 16:54:33,976 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/ctdDriver2.log (3123935 bytes) INFO 2025-06-26 16:54:34,195 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.294.01/ctdDriver2.log: [ 63 129 273 407 485 507 1021 1024 1038 1120 1134 1513 1584 1769 1930 2151 2414 2623 3166 3285 3398 3472 3660 3756 4024 4580 4691 5167 5308 5523 6018 6979 7644 8311 10557 11082 14673 19202 23897 25255 28976] INFO 2025-06-26 16:54:34,208 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/gps.log (52340 bytes) INFO 2025-06-26 16:54:34,221 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/hydroscatlog.log (2744470 bytes) INFO 2025-06-26 16:54:34,506 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.294.01/hydroscatlog.log: [ 5 84 94 115 150 154 220 296 366 374 463 502 580 610 650 782 814 828 1072 1175 1274 1467 1562 1604 1863 2256 2447 2811 3175 3398 3512 3870 4089 4139 5642 6138 7008 7017 7102 7901 8434 8435 9200 10143 10446 10860 11158 11851 11940 13790 15607 15870 16672 17331 18385 19331 21634 25382 26118 27223 28910 29632 29720 30644] INFO 2025-06-26 16:54:34,516 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/navigation.log (9555294 bytes) INFO 2025-06-26 16:54:35,207 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/isuslog.log (201589 bytes) INFO 2025-06-26 16:54:35,232 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.294.01/isuslog.log: [ 1 2 3 4 6 7 8 9 10 11 12 13] INFO 2025-06-26 16:54:35,233 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/parosci.log (3555974 bytes) INFO 2025-06-26 16:54:35,538 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/tailCone.log (1947931 bytes) INFO 2025-06-26 16:54:35,789 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/biolume.log (2286906 bytes) INFO 2025-06-26 16:54:36,012 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:54:36,126 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.294.01/biolume.log: [1] INFO 2025-06-26 16:54:36,137 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.38 seconds INFO 2025-06-26 16:54:36,137 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.294.01/lopc.bin (8234000 bytes) INFO 2025-06-26 16:54:36,137 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:54:36 2025 INFO 2025-06-26 16:54:36,137 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.294.01/parosci.nc INFO 2025-06-26 16:54:36,137 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:54:36,137 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.294.01/parosci.nc INFO 2025-06-26 16:54:36,140 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1287688709.1, sensor_off_time = 1287696887.3 INFO 2025-06-26 16:54:36,141 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8178 seconds. Expecting to read 16356 L frames from the lopc.bin file. INFO 2025-06-26 16:54:36,141 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 16356 records from the lopc.bin file. INFO 2025-06-26 16:54:36,235 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-21 19:18:29 Z and endTime = 2010-10-21 21:34:47 Z with 16356 records expected to be read from lopc.bin INFO 2025-06-26 16:54:36,236 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.294.01/lopc.bin INFO 2025-06-26 16:54:36,236 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.294.01/lopc.nc INFO 2025-06-26 16:54:36,236 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.294.01/lopc.nc INFO 2025-06-26 16:54:36,236 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.294.01 INFO 2025-06-26 16:54:36,237 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 16:54:36,240 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A031292 WARNING 2025-06-26 16:54:36,240 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 16:54:36,280 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:54:36,280 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:54:36,280 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:54:37,670 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 16:54:37,671 process.py calibrate():227 [1] Calibration steps for 2010.294.01 INFO 2025-06-26 16:54:37,872 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 16:54:37,874 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:54:38,709 calibrate.py _nudge_pos():1806 [1] 126: 0.090 0.0004342 -0.0002237 1060 3.65 17.641 -11.365 2010-10-21T19:24:12.366060032 INFO 2025-06-26 16:54:39,376 calibrate.py _nudge_pos():1806 [1] 196: 0.100 0.0012322 -0.0004395 6319 21.25 8.591 -3.833 2010-10-21T19:46:36.363989760 INFO 2025-06-26 16:54:40,011 calibrate.py _nudge_pos():1806 [1] 263: 0.110 -0.0002232 0.0000135 2146 7.20 -4.595 0.348 2010-10-21T19:54:54.359874816 INFO 2025-06-26 16:54:40,805 calibrate.py _nudge_pos():1806 [1] 346: 0.110 -0.0020539 -0.0045934 7763 25.93 -11.732 -32.825 2010-10-21T20:22:12.357664256 INFO 2025-06-26 16:54:41,550 calibrate.py _nudge_pos():1806 [1] 424: 0.110 -0.0028807 -0.0040422 7876 26.31 -16.213 -28.465 2010-10-21T20:49:48.364220160 INFO 2025-06-26 16:54:42,227 calibrate.py _nudge_pos():1806 [1] 495: 0.100 -0.0014703 -0.0007443 3934 13.13 -16.582 -10.504 2010-10-21T21:04:06.365443072 INFO 2025-06-26 16:54:43,528 calibrate.py _nudge_pos():1806 [1] 633: 0.120 0.0049445 -0.0007929 6204 20.71 35.358 -7.093 2010-10-21T21:27:06.360906752 INFO 2025-06-26 16:54:44,205 calibrate.py _nudge_pos():1806 [1] 704: 0.120 0.0008182 -0.0008877 1897 6.33 19.147 -25.986 2010-10-21T21:34:36.360079872 INFO 2025-06-26 16:54:44,308 calibrate.py _nudge_pos():1862 [1] 667: - - - 4 0.01 - - INFO 2025-06-26 16:54:44,308 calibrate.py _nudge_pos():1868 [1] Points in final series = 40479 WARNING 2025-06-26 16:54:44,370 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:54:48,708 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:54:51,019 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 59 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:54:51,261 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 59 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:54:51,263 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.294.01/ctd1.nc INFO 2025-06-26 16:54:51,264 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 16:54:51,265 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 16:54:51,265 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:54:53,056 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 32 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:54:53,301 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 32 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:54:53,303 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.294.01/ctd2.nc INFO 2025-06-26 16:54:53,304 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 16:54:53,304 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 16:54:53,304 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:54:53,612 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:54:53,952 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 474300 474301 474302] INFO 2025-06-26 16:54:54,026 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:55:01,664 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.294.01 ERROR 2025-06-26 16:55:01,664 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.294.01 INFO 2025-06-26 16:55:01,698 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_cal.nc INFO 2025-06-26 16:55:05,274 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 16:55:05,279 process.py align():251 [1] Alignment steps for 2010.294.01 INFO 2025-06-26 16:55:05,310 align.py process_cal():139 [1] Processing dorado_2010.294.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.294.01 INFO 2025-06-26 16:55:05,325 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:55:05,328 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:55:05,362 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:55:05,365 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:55:05,399 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:55:05,402 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:55:05,421 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:55:05,421 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:55:05,434 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:55:05,437 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:55:05,471 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,474 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,505 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,508 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,538 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,541 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,571 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,574 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,603 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,606 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,635 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,638 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,668 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,671 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,704 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,734 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,737 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,766 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,769 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,800 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,803 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,833 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,836 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,866 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,869 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,899 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,901 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,933 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,936 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:05,966 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:05,969 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,001 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,005 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,036 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,039 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,070 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,073 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,103 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,106 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,137 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,140 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,171 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.294.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:55:06,174 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:55:06,211 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.77 INFO 2025-06-26 16:55:06,239 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.77 INFO 2025-06-26 16:55:06,268 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.77 INFO 2025-06-26 16:55:06,298 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:55:06,328 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:55:06,368 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.86 INFO 2025-06-26 16:55:06,586 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.96 INFO 2025-06-26 16:55:06,612 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_align.nc INFO 2025-06-26 16:55:06,702 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 16:55:06,705 process.py resample():273 [1] Resampling steps for 2010.294.01 INFO 2025-06-26 16:55:06,705 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:55:06,735 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_align.nc mission netCDF file INFO 2025-06-26 16:55:06,741 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_align.nc mission netCDF file INFO 2025-06-26 16:55:06,742 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-21T19:19:16.706313984 to 2010-10-21T21:34:47.159340032 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 16:55:06,744 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-21T19:18:39.538860288 to 2010-10-21T21:34:47.299330304 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 16:55:06,745 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-21T19:19:28.575501056 to 2010-10-21T21:34:47.149340672 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 16:55:06,747 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-21T19:19:01.237373952 to 2010-10-21T21:34:47.309329664 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:55:06,748 resample.py get_mission_start_end():1145 [1] isus : 2010-10-21T19:19:39.694739456 to 2010-10-21T21:34:46.289399552 (0 days 00:00:01.019930112 before mission_end) INFO 2025-06-26 16:55:06,749 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-21T19:18:30.089473280 to 2010-10-21T21:34:46.519349504 (0 days 00:00:00.789980160 before mission_end) INFO 2025-06-26 16:55:06,751 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-21T19:18:28.179638272 to 2010-10-21T21:34:47.129341952 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 16:55:06,752 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_align.nc mission netCDF file INFO 2025-06-26 16:55:06,752 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,861 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,882 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,901 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,921 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,940 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,958 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,975 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:06,992 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,010 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,026 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,042 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,059 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,075 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,091 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,107 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,123 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,138 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,156 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,174 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,191 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,209 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,226 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,244 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,261 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,274 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,284 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,294 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,304 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,312 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,316 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:55:07,316 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:55:07,625 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:55:07,683 resample.py add_biolume_proxies():633 [1] Zero flow values found: 8177 of 8177 - replaced with 350 ml/s INFO 2025-06-26 16:55:07,683 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:55:07,714 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:55:07,727 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:55:07,739 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:55:07,740 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:55:07,763 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:55:07,918 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_1S.nc INFO 2025-06-26 16:55:09,785 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:55:11,980 create_products.py gulper_odv():522 [1] Wrote 2 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.294.01/dorado_2010.294.01_1S_Gulper.txt INFO 2025-06-26 16:55:11,980 process.py archive():337 [1] Archiving steps for 2010.294.01 INFO 2025-06-26 16:55:11,980 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01, BASE_PATH = /data/auv_data INFO 2025-06-26 16:55:11,980 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:55:11,981 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.294.01_1S.nc INFO 2025-06-26 16:55:12,003 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:55:12,004 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.294.01_cal.nc INFO 2025-06-26 16:55:12,066 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:55:12,067 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.294.01_align.nc INFO 2025-06-26 16:55:12,156 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:55:12,170 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,183 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,187 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,199 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,226 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,232 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,246 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,259 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,284 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,292 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010294/2010.294.01 done. INFO 2025-06-26 16:55:12,292 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:55:12,294 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.294.01_1S_Gulper.txt INFO 2025-06-26 16:55:12,299 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.294.01/dorado_2010.294.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:55:12,299 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.294.01/dorado_2010.294.01_processing.log /Volumes/AUVCTD/surveys/2010/netcdf