INFO 2025-06-26 17:14:35,064 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 17:14:35,064 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Out and back from M1 - ctdToUse = ctd1 INFO 2025-06-26 17:14:35,064 process.py process_mission():449 [1] Processing AUVCTD mission 2010.341.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 17:14:35,064 process.py download_process():165 [1] Download and processing steps for 2010.341.01 INFO 2025-06-26 17:14:35,064 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010341/2010.341.01 INFO 2025-06-26 17:14:35,065 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010341/2010.341.01 to /data/auv_data/dorado/missionlogs/2010.341.01 INFO 2025-06-26 17:14:37,912 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.341.01 INFO 2025-06-26 17:14:37,912 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/ctdDriver.log (4015595 bytes) INFO 2025-06-26 17:14:38,182 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.341.01/ctdDriver.log: [ 6 74 78 288 526 733 772 852 1043 1089 1322 1371 1515 1598 1749 2158 2441 2665 2962 4722 5218 5330 5614 6534 7090 9811 10779 12311 12457 14591 17705 22734 29000 30202 36288 36882 39649 40114] INFO 2025-06-26 17:14:38,193 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/ctdDriver2.log (4016351 bytes) INFO 2025-06-26 17:14:38,470 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.341.01/ctdDriver2.log: [ 71 74 285 732 771 852 1044 1089 1513 1670 2157 2441 2960 4596 5216 6533 6891 7091 7925 8540 9230 9814 10684 12463 14599 17713 22743 26083 29005 30206 35516 36890] INFO 2025-06-26 17:14:38,485 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/gps.log (51476 bytes) INFO 2025-06-26 17:14:38,499 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/hydroscatlog.log (3526762 bytes) INFO 2025-06-26 17:14:38,861 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.341.01/hydroscatlog.log: [ 81 152 309 369 463 550 586 627 698 709 774 776 861 907 917 919 1073 1138 1184 1228 1462 1468 1613 1696 1698 1773 1850 2151 2156 2263 2330 2462 2549 2773 2862 3069 3171 3176 3201 3628 3817 3836 4464 4580 4581 4713 4806 4838 5334 5447 5651 5970 6194 6542 6654 6838 7212 8046 9353 9807 9939 10222 10732 10812 10910 11588 12038 12039 12182 12592 13846 13847 13915 14325 14729 14863 15299 15354 16233 17529 17844 19410 19570 19697 22439 23986 25929 26219 26516 26697 27207 27369 27759 32221 33814 34710 35733 36435 39253 39798 40936 41028] INFO 2025-06-26 17:14:38,872 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/navigation.log (12284398 bytes) INFO 2025-06-26 17:14:39,745 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/isuslog.log (260053 bytes) INFO 2025-06-26 17:14:39,774 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/parosci.log (4581446 bytes) INFO 2025-06-26 17:14:40,176 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/tailCone.log (2503819 bytes) INFO 2025-06-26 17:14:40,487 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/biolume.log (2937834 bytes) INFO 2025-06-26 17:14:40,772 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 17:14:40,928 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.02 seconds INFO 2025-06-26 17:14:40,928 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.341.01/lopc.bin (16137000 bytes) INFO 2025-06-26 17:14:40,928 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 17:14:40 2025 INFO 2025-06-26 17:14:40,929 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.341.01/parosci.nc INFO 2025-06-26 17:14:40,929 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 17:14:40,929 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.341.01/parosci.nc INFO 2025-06-26 17:14:40,932 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1291750742.0, sensor_off_time = 1291761247.0 INFO 2025-06-26 17:14:40,932 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10504 seconds. Expecting to read 21008 L frames from the lopc.bin file. INFO 2025-06-26 17:14:40,932 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21008 records from the lopc.bin file. INFO 2025-06-26 17:14:41,054 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-12-07 19:39:02 Z and endTime = 2010-12-07 22:34:06 Z with 21008 records expected to be read from lopc.bin INFO 2025-06-26 17:14:41,054 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.341.01/lopc.bin INFO 2025-06-26 17:14:41,054 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.341.01/lopc.nc INFO 2025-06-26 17:14:41,055 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.341.01/lopc.nc INFO 2025-06-26 17:14:41,055 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.341.01 INFO 2025-06-26 17:14:41,055 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 17:14:41,058 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0274400 WARNING 2025-06-26 17:14:41,058 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 17:14:41,111 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 17:14:41,111 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 17:14:41,111 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 17:14:49,533 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 34963 22182 1 0 0 0 0 8.5 seconds, last L Frame: 21008 ERROR 2025-06-26 17:15:00,218 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 17:15:00,219 process.py calibrate():227 [1] Calibration steps for 2010.341.01 INFO 2025-06-26 17:15:00,438 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 17:15:00,440 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 17:15:01,239 calibrate.py _nudge_pos():1806 [1] 127: 0.010 0.0009110 -0.0002909 1388 4.76 28.383 -11.316 2010-12-07T19:45:46.204733696 INFO 2025-06-26 17:15:02,330 calibrate.py _nudge_pos():1806 [1] 245: 0.010 -0.0033488 -0.0163015 13895 46.65 -10.657 -64.756 2010-12-07T20:34:22.204973824 INFO 2025-06-26 17:15:03,305 calibrate.py _nudge_pos():1806 [1] 349: 0.010 0.0006776 -0.0163806 13065 43.68 2.303 -69.490 2010-12-07T21:19:46.208366848 INFO 2025-06-26 17:15:04,259 calibrate.py _nudge_pos():1806 [1] 451: 0.020 0.0082451 -0.0119367 13145 43.91 27.870 -50.369 2010-12-07T22:05:22.200938496 INFO 2025-06-26 17:15:05,200 calibrate.py _nudge_pos():1806 [1] 550: 0.020 -0.0029924 -0.0037869 7351 24.56 -18.081 -28.567 2010-12-07T22:31:34.203248896 INFO 2025-06-26 17:15:06,647 calibrate.py _nudge_pos():1862 [1] 650: - - - 3 0.01 - - INFO 2025-06-26 17:15:06,647 calibrate.py _nudge_pos():1868 [1] Points in final series = 51986 WARNING 2025-06-26 17:15:06,727 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 17:15:12,309 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:15:15,337 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:15:15,650 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:15:15,652 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.341.01/ctd1.nc INFO 2025-06-26 17:15:15,653 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 17:15:15,654 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 17:15:15,654 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 17:15:17,978 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:15:18,327 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:15:18,329 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.341.01/ctd2.nc INFO 2025-06-26 17:15:18,331 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 17:15:18,331 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 17:15:18,331 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 17:15:18,352 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 17:15:18,798 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 617589 617590 617591] INFO 2025-06-26 17:15:18,892 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 17:15:28,482 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.341.01 ERROR 2025-06-26 17:15:28,483 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.341.01 INFO 2025-06-26 17:15:28,525 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_cal.nc INFO 2025-06-26 17:15:33,158 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 17:15:33,165 process.py align():251 [1] Alignment steps for 2010.341.01 INFO 2025-06-26 17:15:33,197 align.py process_cal():139 [1] Processing dorado_2010.341.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.341.01 INFO 2025-06-26 17:15:33,215 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:15:33,218 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 17:15:33,259 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:15:33,263 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 17:15:33,304 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:15:33,307 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 17:15:33,331 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 17:15:33,332 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 17:15:33,347 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:15:33,350 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 17:15:33,391 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,394 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,430 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,433 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,469 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,472 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,508 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,512 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,549 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,552 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,587 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,591 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,627 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,630 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,666 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,670 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,707 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,710 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,746 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,749 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,786 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,789 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,824 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,828 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,864 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,867 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,903 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,906 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,943 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,946 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:33,982 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:33,985 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,024 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,028 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,064 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,068 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,106 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,112 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,172 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,178 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,238 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,244 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,283 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.341.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:15:34,286 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 17:15:34,331 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:15:34,365 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:15:34,399 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:15:34,435 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:15:34,472 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:15:34,520 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.86 INFO 2025-06-26 17:15:34,790 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.96 INFO 2025-06-26 17:15:34,820 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_align.nc INFO 2025-06-26 17:15:34,921 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 17:15:34,923 process.py resample():273 [1] Resampling steps for 2010.341.01 INFO 2025-06-26 17:15:34,924 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 17:15:34,955 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_align.nc mission netCDF file INFO 2025-06-26 17:15:34,960 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_align.nc mission netCDF file INFO 2025-06-26 17:15:34,962 resample.py get_mission_start_end():1145 [1] navigation: 2010-12-07T19:39:46.639365376 to 2010-12-07T22:34:06.842792448 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 17:15:34,963 resample.py get_mission_start_end():1145 [1] hs2 : 2010-12-07T19:39:08.961946368 to 2010-12-07T22:34:06.902788352 (0 days 00:00:00 before mission_end) INFO 2025-06-26 17:15:34,965 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-12-07T19:39:27.510675968 to 2010-12-07T22:34:06.782796544 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 17:15:34,966 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-12-07T19:39:28.150631936 to 2010-12-07T22:34:06.892788992 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 17:15:34,968 resample.py get_mission_start_end():1145 [1] isus : 2010-12-07T19:40:13.377533696 to 2010-12-07T22:34:06.262832128 (0 days 00:00:00.639956224 before mission_end) INFO 2025-06-26 17:15:34,969 resample.py get_mission_start_end():1145 [1] biolume : 2010-12-07T19:38:57.322709504 to 2010-12-07T22:34:05.572845312 (0 days 00:00:01.329943040 before mission_end) INFO 2025-06-26 17:15:34,970 resample.py get_mission_start_end():1145 [1] tailcone : 2010-12-07T19:39:00.452529408 to 2010-12-07T22:34:06.882789632 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 17:15:34,971 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_align.nc mission netCDF file INFO 2025-06-26 17:15:34,971 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,101 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,125 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,149 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,173 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,195 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,216 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,237 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,258 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,277 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,296 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,315 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,334 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,353 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,372 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,391 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,410 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,432 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,454 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,475 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,496 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,516 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,537 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,558 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,578 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,590 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,601 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,612 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,622 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,632 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:35,636 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 17:15:35,636 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 17:15:36,007 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 17:15:36,075 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 17:15:36,111 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 17:15:36,128 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 17:15:36,143 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 17:15:36,144 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 17:15:36,171 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 17:15:36,339 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_1S.nc INFO 2025-06-26 17:15:37,915 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 17:15:41,186 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.341.01/dorado_2010.341.01_1S_Gulper.txt INFO 2025-06-26 17:15:41,187 process.py archive():337 [1] Archiving steps for 2010.341.01 INFO 2025-06-26 17:15:41,187 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01, BASE_PATH = /data/auv_data INFO 2025-06-26 17:15:41,188 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 17:15:41,189 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.341.01_1S.nc INFO 2025-06-26 17:15:41,201 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 17:15:41,201 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.341.01_cal.nc INFO 2025-06-26 17:15:41,271 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 17:15:41,271 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.341.01_align.nc INFO 2025-06-26 17:15:41,372 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 17:15:41,389 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,404 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,409 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,422 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,459 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,465 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,480 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,493 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,552 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010341/2010.341.01 done. INFO 2025-06-26 17:15:41,552 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 17:15:41,554 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.341.01_1S_Gulper.txt INFO 2025-06-26 17:15:41,559 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.341.01/dorado_2010.341.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 17:15:41,559 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.341.01/dorado_2010.341.01_processing.log /Volumes/AUVCTD/surveys/2010/netcdf