INFO 2025-06-26 19:36:22,340 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 19:36:22,341 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Molecular Ecology - August 2013 - North Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:36:22,341 process.py process_mission():449 [1] Processing SIMZ August 2013 mission 2013.226.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:36:22,341 process.py download_process():165 [1] Download and processing steps for 2013.226.03 INFO 2025-06-26 19:36:22,341 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013226/2013.226.03 INFO 2025-06-26 19:36:22,341 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013226/2013.226.03 to /data/auv_data/dorado/missionlogs/2013.226.03 INFO 2025-06-26 19:36:25,908 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.226.03 INFO 2025-06-26 19:36:25,908 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/ctdDriver.log (4755462 bytes) INFO 2025-06-26 19:36:26,254 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/ctdDriver2.log (4755551 bytes) INFO 2025-06-26 19:36:26,611 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/gps.log (50540 bytes) INFO 2025-06-26 19:36:26,624 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/hydroscatlog.log (4164154 bytes) INFO 2025-06-26 19:36:27,069 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/navigation.log (16817622 bytes) INFO 2025-06-26 19:36:28,230 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/isuslog.log (367957 bytes) INFO 2025-06-26 19:36:28,268 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.226.03/isuslog.log: [ 1 2 3 5 6 7 8 9 10 11 12 13 14 16 17 18 19] INFO 2025-06-26 19:36:28,270 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/parosci.log (5848406 bytes) INFO 2025-06-26 19:36:28,766 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/tailCone.log (2976715 bytes) INFO 2025-06-26 19:36:29,142 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/biolume.log (3466642 bytes) INFO 2025-06-26 19:36:29,497 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:36:29,670 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.76 seconds INFO 2025-06-26 19:36:29,670 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.03/lopc.bin (43406786 bytes) INFO 2025-06-26 19:36:29,671 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:36:29 2025 INFO 2025-06-26 19:36:29,671 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.226.03/parosci.nc INFO 2025-06-26 19:36:29,671 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:36:29,671 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.226.03/parosci.nc INFO 2025-06-26 19:36:29,674 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1376507326.0, sensor_off_time = 1376519726.8 INFO 2025-06-26 19:36:29,674 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 12400 seconds. Expecting to read 24800 L frames from the lopc.bin file. INFO 2025-06-26 19:36:29,674 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 24800 records from the lopc.bin file. INFO 2025-06-26 19:36:29,818 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-08-14 19:08:45 Z and endTime = 2013-08-14 22:35:26 Z with 24800 records expected to be read from lopc.bin INFO 2025-06-26 19:36:29,818 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.226.03/lopc.bin INFO 2025-06-26 19:36:29,818 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.226.03/lopc.nc INFO 2025-06-26 19:36:29,819 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.226.03/lopc.nc INFO 2025-06-26 19:36:29,819 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.226.03 INFO 2025-06-26 19:36:29,819 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:36:29,823 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:36:29,932 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:36:29,932 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:36:29,932 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:36:29,984 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:36:29,984 process.py calibrate():227 [1] Calibration steps for 2013.226.03 INFO 2025-06-26 19:36:30,126 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 19:36:30,128 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:36:30,680 calibrate.py _nudge_pos():1806 [1] 90: 0.200 -0.0031615 -0.0027899 7839 26.13 -17.934 -19.787 2013-08-14T19:36:20.976319232 INFO 2025-06-26 19:36:31,154 calibrate.py _nudge_pos():1806 [1] 141: 0.010 -0.0033932 -0.0037285 6940 23.13 -21.746 -29.870 2013-08-14T20:00:19.167796480 INFO 2025-06-26 19:36:31,536 calibrate.py _nudge_pos():1806 [1] 182: 0.010 -0.0032282 -0.0042721 6765 22.55 -21.228 -35.110 2013-08-14T20:23:33.172300544 INFO 2025-06-26 19:36:31,620 calibrate.py _nudge_pos():1806 [1] 191: 0.010 0.0000118 -0.0000081 60 0.20 8.872 -7.633 2013-08-14T20:23:53.170930688 INFO 2025-06-26 19:36:32,012 calibrate.py _nudge_pos():1806 [1] 233: 0.010 0.0014867 -0.0014706 2155 7.18 30.699 -37.954 2013-08-14T20:31:45.168596480 INFO 2025-06-26 19:36:32,041 calibrate.py _nudge_pos():1806 [1] 236: 0.010 0.0000021 -0.0000054 75 0.25 1.241 -4.088 2013-08-14T20:32:02.167432192 INFO 2025-06-26 19:36:32,498 calibrate.py _nudge_pos():1806 [1] 285: 0.010 0.0034669 -0.0028004 3665 12.21 42.089 -42.487 2013-08-14T20:45:03.173929472 INFO 2025-06-26 19:36:32,768 calibrate.py _nudge_pos():1806 [1] 314: 0.020 0.0033690 -0.0020096 4570 15.23 32.795 -24.450 2013-08-14T21:00:45.169398272 INFO 2025-06-26 19:36:32,835 calibrate.py _nudge_pos():1806 [1] 321: 0.200 -0.0000067 0.0000864 144 0.48 -2.084 33.562 2013-08-14T21:01:19.977013760 INFO 2025-06-26 19:36:33,175 calibrate.py _nudge_pos():1806 [1] 356: 0.020 0.0046552 -0.0039279 5625 18.75 36.811 -38.825 2013-08-14T21:20:39.167603968 INFO 2025-06-26 19:36:33,483 calibrate.py _nudge_pos():1806 [1] 389: 0.020 0.0055731 -0.0037423 6710 22.36 36.936 -31.009 2013-08-14T21:43:33.173478144 INFO 2025-06-26 19:36:33,976 calibrate.py _nudge_pos():1806 [1] 441: 0.020 0.0058586 -0.0037386 6825 22.75 38.168 -30.456 2013-08-14T22:07:09.176475392 INFO 2025-06-26 19:36:34,376 calibrate.py _nudge_pos():1806 [1] 483: 0.030 0.0039059 -0.0018535 4775 15.91 36.368 -21.583 2013-08-14T22:23:45.168244992 INFO 2025-06-26 19:36:34,923 calibrate.py _nudge_pos():1806 [1] 540: 0.030 0.0017660 -0.0005411 2480 8.26 31.663 -12.133 2013-08-14T22:32:57.170430464 INFO 2025-06-26 19:36:36,340 calibrate.py _nudge_pos():1862 [1] 652: - - - 3 0.01 - - INFO 2025-06-26 19:36:36,340 calibrate.py _nudge_pos():1868 [1] Points in final series = 61706 INFO 2025-06-26 19:36:36,525 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 2 of 49561 INFO 2025-06-26 19:36:36,908 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:37,377 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:37,742 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:37,744 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.226.03/ctd1.nc INFO 2025-06-26 19:36:37,745 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:36:37,746 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 19:36:37,746 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:36:38,186 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:38,549 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:38,551 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.226.03/ctd2.nc INFO 2025-06-26 19:36:38,552 calibrate.py _range_qc_combined_nc():898 [1] Setting 102 ctd2_salinity values to NaN INFO 2025-06-26 19:36:38,552 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 19:36:38,552 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:36:39,098 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:36:39,698 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 19:36:39,810 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:36:50,988 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.226.03 ERROR 2025-06-26 19:36:50,988 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.226.03 INFO 2025-06-26 19:36:51,039 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_cal.nc INFO 2025-06-26 19:36:51,143 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 19:36:51,149 process.py align():251 [1] Alignment steps for 2013.226.03 INFO 2025-06-26 19:36:51,183 align.py process_cal():139 [1] Processing dorado_2013.226.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.226.03 INFO 2025-06-26 19:36:51,203 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:51,206 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:51,252 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:51,257 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:51,302 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:51,307 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:51,333 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:36:51,333 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:36:51,351 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:51,355 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:51,400 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,403 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,443 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,447 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,488 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,491 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,531 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,534 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,577 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,580 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,620 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,624 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,665 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,669 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,708 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,712 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,752 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,756 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,796 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,800 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,841 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,844 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,884 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,888 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,928 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,932 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:51,972 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:51,976 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,018 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,022 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,062 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,066 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,109 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,113 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,154 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,158 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,200 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,204 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,243 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,248 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,289 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,293 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,334 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:52,338 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:52,390 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:52,428 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:52,467 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:52,508 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:36:52,548 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:36:52,610 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:36:52,925 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:52,959 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_align.nc INFO 2025-06-26 19:36:53,066 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 19:36:53,068 process.py resample():273 [1] Resampling steps for 2013.226.03 INFO 2025-06-26 19:36:53,069 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:36:53,100 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_align.nc mission netCDF file INFO 2025-06-26 19:36:53,106 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_align.nc mission netCDF file INFO 2025-06-26 19:36:53,107 resample.py get_mission_start_end():1145 [1] navigation: 2013-08-14T19:09:22.787172864 to 2013-08-14T22:35:26.770182144 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:36:53,109 resample.py get_mission_start_end():1145 [1] hs2 : 2013-08-14T19:08:50.089412864 to 2013-08-14T22:35:26.710186240 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 19:36:53,110 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-08-14T19:09:04.398432768 to 2013-08-14T22:35:26.610192896 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 19:36:53,112 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-08-14T19:09:04.198446336 to 2013-08-14T22:35:26.650190336 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 19:36:53,113 resample.py get_mission_start_end():1145 [1] isus : 2013-08-14T19:09:44.745668608 to 2013-08-14T22:35:26.580195072 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 19:36:53,114 resample.py get_mission_start_end():1145 [1] biolume : 2013-08-14T19:08:42.959866880 to 2013-08-14T22:35:25.930205440 (0 days 00:00:00.839976704 before mission_end) INFO 2025-06-26 19:36:53,116 resample.py get_mission_start_end():1145 [1] tailcone : 2013-08-14T19:08:45.709712896 to 2013-08-14T22:35:26.660189696 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:36:53,116 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_align.nc mission netCDF file INFO 2025-06-26 19:36:53,117 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,264 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,290 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,317 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,343 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,367 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,390 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,413 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,435 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,457 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,478 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,500 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,521 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,543 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,564 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,585 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,607 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,628 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,651 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,674 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,697 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,719 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,741 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,763 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,785 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,799 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,811 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,824 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,834 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,845 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:53,849 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:36:53,849 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:36:54,290 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:36:54,370 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:36:54,416 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:36:54,436 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:36:54,454 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:36:54,454 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:36:54,485 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:54,664 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_1S.nc INFO 2025-06-26 19:36:56,791 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:37:07,640 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.226.03/dorado_2013.226.03_1S_Gulper.txt INFO 2025-06-26 19:37:07,640 process.py archive():337 [1] Archiving steps for 2013.226.03 INFO 2025-06-26 19:37:07,640 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03, BASE_PATH = /data/auv_data INFO 2025-06-26 19:37:07,641 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:37:07,642 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.03_1S.nc INFO 2025-06-26 19:37:07,657 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:37:07,657 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.03_cal.nc INFO 2025-06-26 19:37:07,742 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:37:07,743 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.03_align.nc INFO 2025-06-26 19:37:07,871 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:37:07,890 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,907 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,912 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,927 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,970 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,976 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:07,996 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:08,011 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:08,046 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:08,052 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.03 done. INFO 2025-06-26 19:37:08,052 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:37:08,053 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.226.03_1S_Gulper.txt INFO 2025-06-26 19:37:08,058 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.226.03/dorado_2013.226.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:37:08,059 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.03/dorado_2013.226.03_processing.log /Volumes/AUVCTD/surveys/2013/netcdf