INFO 2025-06-26 20:25:56,510 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 20:25:56,510 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Summer 2014 in Bodega Bay - ctdToUse = ctd2 INFO 2025-06-26 20:25:56,510 process.py process_mission():449 [1] Processing SIMZ July 2014 mission 2014.211.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:25:56,510 process.py download_process():165 [1] Download and processing steps for 2014.211.03 INFO 2025-06-26 20:25:56,510 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014211/2014.211.03 INFO 2025-06-26 20:25:56,510 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014211/2014.211.03 to /data/auv_data/dorado/missionlogs/2014.211.03 INFO 2025-06-26 20:26:00,249 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.211.03 INFO 2025-06-26 20:26:00,249 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/ctdDriver.log (4190886 bytes) INFO 2025-06-26 20:26:00,545 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/ctdDriver2.log (4190591 bytes) INFO 2025-06-26 20:26:00,842 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/gps.log (44564 bytes) INFO 2025-06-26 20:26:00,856 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/hydroscatlog.log (3671578 bytes) INFO 2025-06-26 20:26:01,230 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/navigation.log (15688098 bytes) INFO 2025-06-26 20:26:02,361 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/isuslog.log (270581 bytes) INFO 2025-06-26 20:26:02,391 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/parosci.log (5156342 bytes) INFO 2025-06-26 20:26:02,824 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/tailCone.log (2625883 bytes) INFO 2025-06-26 20:26:03,147 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/biolume.log (3057966 bytes) INFO 2025-06-26 20:26:03,456 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:26:03,608 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.36 seconds INFO 2025-06-26 20:26:03,608 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.211.03/lopc.bin (30950185 bytes) INFO 2025-06-26 20:26:03,608 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:26:03 2025 INFO 2025-06-26 20:26:03,608 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.211.03/parosci.nc INFO 2025-06-26 20:26:03,608 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:26:03,609 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.211.03/parosci.nc INFO 2025-06-26 20:26:03,612 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1406743454.1, sensor_off_time = 1406754392.4 INFO 2025-06-26 20:26:03,612 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10938 seconds. Expecting to read 21876 L frames from the lopc.bin file. INFO 2025-06-26 20:26:03,612 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21876 records from the lopc.bin file. INFO 2025-06-26 20:26:03,742 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-07-30 18:04:14 Z and endTime = 2014-07-30 21:06:32 Z with 21876 records expected to be read from lopc.bin INFO 2025-06-26 20:26:03,742 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.211.03/lopc.bin INFO 2025-06-26 20:26:03,742 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.211.03/lopc.nc INFO 2025-06-26 20:26:03,743 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.211.03/lopc.nc INFO 2025-06-26 20:26:03,744 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.211.03 INFO 2025-06-26 20:26:03,744 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:26:03,747 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:26:03,807 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:26:03,808 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:26:03,808 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:26:14,253 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:26:14,254 process.py calibrate():227 [1] Calibration steps for 2014.211.03 INFO 2025-06-26 20:26:14,387 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 20:26:14,389 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:26:15,107 calibrate.py _nudge_pos():1806 [1] 115: 0.150 -0.0000649 -0.0000396 770 2.56 -3.679 -2.866 2014-07-30T18:08:40.283745280 INFO 2025-06-26 20:26:15,545 calibrate.py _nudge_pos():1806 [1] 162: 0.150 -0.0001901 0.0000564 2800 9.33 -2.963 1.121 2014-07-30T18:18:46.282231552 INFO 2025-06-26 20:26:16,206 calibrate.py _nudge_pos():1806 [1] 234: 0.150 0.0024626 0.0057657 10265 34.21 10.464 31.227 2014-07-30T18:54:10.286727424 INFO 2025-06-26 20:26:16,216 calibrate.py _nudge_pos():1806 [1] 235: 0.150 0.0000234 0.0000122 30 0.10 35.163 23.348 2014-07-30T18:54:16.286316288 INFO 2025-06-26 20:26:16,660 calibrate.py _nudge_pos():1806 [1] 283: 0.170 -0.0024332 0.0018677 12665 42.21 -8.382 8.199 2014-07-30T19:37:16.279574528 INFO 2025-06-26 20:26:17,248 calibrate.py _nudge_pos():1806 [1] 346: 0.170 -0.0050511 0.0020841 9770 32.56 -22.556 11.859 2014-07-30T20:10:52.281469184 INFO 2025-06-26 20:26:17,875 calibrate.py _nudge_pos():1806 [1] 414: 0.170 -0.0019819 0.0005570 3835 12.78 -22.551 8.076 2014-07-30T20:24:46.284336128 INFO 2025-06-26 20:26:18,390 calibrate.py _nudge_pos():1806 [1] 470: 0.170 -0.0005031 0.0003172 2485 8.28 -8.837 7.099 2014-07-30T20:33:58.286521088 INFO 2025-06-26 20:26:18,445 calibrate.py _nudge_pos():1806 [1] 476: 0.170 -0.0000149 0.0000135 70 0.23 -9.414 10.891 2014-07-30T20:34:17.285219840 INFO 2025-06-26 20:26:18,964 calibrate.py _nudge_pos():1806 [1] 532: 0.170 0.0016068 0.0012497 3165 10.55 22.154 21.956 2014-07-30T20:45:46.288019968 INFO 2025-06-26 20:26:19,002 calibrate.py _nudge_pos():1806 [1] 536: 0.160 -0.0000271 0.0000000 85 0.28 -14.053 0.013 2014-07-30T20:46:06.286649856 INFO 2025-06-26 20:26:19,529 calibrate.py _nudge_pos():1806 [1] 593: 0.170 -0.0000130 0.0000246 25 0.08 -23.664 57.020 2014-07-30T20:47:07.282471424 INFO 2025-06-26 20:26:19,655 calibrate.py _nudge_pos():1862 [1] 560: - - - 5760 19.20 - - INFO 2025-06-26 20:26:19,655 calibrate.py _nudge_pos():1868 [1] Points in final series = 54464 INFO 2025-06-26 20:26:20,148 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:26:20,568 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:26:20,892 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:26:20,894 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.211.03/ctd1.nc INFO 2025-06-26 20:26:20,895 calibrate.py _range_qc_combined_nc():898 [1] Setting 79 ctd1_salinity values to NaN INFO 2025-06-26 20:26:20,895 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 20:26:20,895 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:26:21,291 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:26:21,614 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:26:21,616 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.211.03/ctd2.nc INFO 2025-06-26 20:26:21,617 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:26:21,617 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 20:26:21,618 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:26:21,638 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:26:22,172 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66] INFO 2025-06-26 20:26:22,268 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:26:32,067 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.211.03 ERROR 2025-06-26 20:26:32,067 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.211.03 INFO 2025-06-26 20:26:32,112 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_cal.nc INFO 2025-06-26 20:26:32,212 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 20:26:32,218 process.py align():251 [1] Alignment steps for 2014.211.03 INFO 2025-06-26 20:26:32,250 align.py process_cal():139 [1] Processing dorado_2014.211.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.211.03 INFO 2025-06-26 20:26:32,269 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:26:32,272 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:26:32,314 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:26:32,317 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:26:32,359 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:26:32,363 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:26:32,387 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:26:32,387 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:26:32,403 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:26:32,406 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:26:32,448 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,452 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,489 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,492 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,530 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,533 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,571 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,574 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,615 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,652 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,655 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,693 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,696 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,732 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,736 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,773 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,777 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,813 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,817 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,854 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,858 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,894 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,897 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,934 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,938 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:32,975 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:32,978 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,016 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,020 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,057 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,060 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,098 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,102 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,139 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,143 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,181 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,184 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,220 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,224 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,261 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,265 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,301 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.211.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:26:33,305 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:26:33,351 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:26:33,386 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:26:33,420 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:26:33,457 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:26:33,494 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:26:33,550 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:26:33,838 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:26:33,869 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_align.nc INFO 2025-06-26 20:26:33,975 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 20:26:33,978 process.py resample():273 [1] Resampling steps for 2014.211.03 INFO 2025-06-26 20:26:33,978 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:26:34,010 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_align.nc mission netCDF file INFO 2025-06-26 20:26:34,015 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_align.nc mission netCDF file INFO 2025-06-26 20:26:34,016 resample.py get_mission_start_end():1145 [1] navigation: 2014-07-30T18:04:59.698856704 to 2014-07-30T21:06:32.282663424 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:26:34,018 resample.py get_mission_start_end():1145 [1] hs2 : 2014-07-30T18:04:23.061366272 to 2014-07-30T21:06:32.272664064 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 20:26:34,020 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-07-30T18:04:40.860146944 to 2014-07-30T21:06:32.282663424 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:26:34,021 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-07-30T18:04:40.580166400 to 2014-07-30T21:06:32.322660608 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 20:26:34,022 resample.py get_mission_start_end():1145 [1] isus : 2014-07-30T18:05:28.506882816 to 2014-07-30T21:06:32.432653312 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:26:34,024 resample.py get_mission_start_end():1145 [1] biolume : 2014-07-30T18:04:12.442059520 to 2014-07-30T21:06:31.532680448 (0 days 00:00:00.899972864 before mission_end) INFO 2025-06-26 20:26:34,025 resample.py get_mission_start_end():1145 [1] tailcone : 2014-07-30T18:04:13.482022400 to 2014-07-30T21:06:32.262664704 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-26 20:26:34,026 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_align.nc mission netCDF file INFO 2025-06-26 20:26:34,026 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,162 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,186 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,210 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,233 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,255 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,276 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,296 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,317 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,336 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,356 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,375 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,394 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,413 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,432 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,451 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,470 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,489 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,514 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,535 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,555 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,576 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,596 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,616 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,638 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,650 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,663 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,674 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,685 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,695 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:34,699 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:26:34,699 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:26:35,119 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:26:35,188 resample.py add_biolume_proxies():633 [1] Zero flow values found: 10940 of 10940 - replaced with 350 ml/s INFO 2025-06-26 20:26:35,189 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:26:35,228 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:26:35,245 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:26:35,260 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:26:35,261 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:26:35,289 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:26:35,459 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_1S.nc INFO 2025-06-26 20:26:39,122 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 20:26:53,462 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.211.03/dorado_2014.211.03_1S_Gulper.txt INFO 2025-06-26 20:26:53,463 process.py archive():337 [1] Archiving steps for 2014.211.03 INFO 2025-06-26 20:26:53,463 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03, BASE_PATH = /data/auv_data INFO 2025-06-26 20:26:53,464 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:26:53,465 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.211.03_1S.nc INFO 2025-06-26 20:26:53,482 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:26:53,483 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.211.03_cal.nc INFO 2025-06-26 20:26:53,750 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:26:53,751 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.211.03_align.nc INFO 2025-06-26 20:26:53,867 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:26:53,883 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,898 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,902 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,916 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,957 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,962 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,980 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:53,994 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:54,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:54,038 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014211/2014.211.03 done. INFO 2025-06-26 20:26:54,038 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:26:54,039 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.211.03_1S_Gulper.txt INFO 2025-06-26 20:26:54,044 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.211.03/dorado_2014.211.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:26:54,044 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.211.03/dorado_2014.211.03_processing.log /Volumes/AUVCTD/surveys/2014/netcdf