INFO 2025-06-26 19:45:33,680 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 19:45:33,680 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:45:33,680 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.261.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:45:33,681 process.py download_process():165 [1] Download and processing steps for 2013.261.01 INFO 2025-06-26 19:45:33,681 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013261/2013.261.01 INFO 2025-06-26 19:45:33,681 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013261/2013.261.01 to /data/auv_data/dorado/missionlogs/2013.261.01 INFO 2025-06-26 19:45:36,549 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.261.01 INFO 2025-06-26 19:45:36,549 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/ctdDriver.log (5520294 bytes) INFO 2025-06-26 19:45:36,939 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/ctdDriver2.log (5520191 bytes) INFO 2025-06-26 19:45:37,375 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/gps.log (37580 bytes) INFO 2025-06-26 19:45:37,387 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/hydroscatlog.log (4834138 bytes) INFO 2025-06-26 19:45:37,937 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/navigation.log (19541430 bytes) INFO 2025-06-26 19:45:39,338 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/isuslog.log (429909 bytes) INFO 2025-06-26 19:45:39,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/parosci.log (6785222 bytes) INFO 2025-06-26 19:45:39,964 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/tailCone.log (3456667 bytes) INFO 2025-06-26 19:45:40,406 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/biolume.log (4024418 bytes) INFO 2025-06-26 19:45:40,800 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:45:41,007 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.46 seconds INFO 2025-06-26 19:45:41,008 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.261.01/lopc.bin (34559792 bytes) INFO 2025-06-26 19:45:41,008 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:45:41 2025 INFO 2025-06-26 19:45:41,008 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.261.01/parosci.nc INFO 2025-06-26 19:45:41,008 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:45:41,008 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.261.01/parosci.nc INFO 2025-06-26 19:45:41,011 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1379529908.0, sensor_off_time = 1379544308.7 INFO 2025-06-26 19:45:41,012 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14400 seconds. Expecting to read 28800 L frames from the lopc.bin file. INFO 2025-06-26 19:45:41,012 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 28800 records from the lopc.bin file. INFO 2025-06-26 19:45:41,182 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-18 18:45:07 Z and endTime = 2013-09-18 22:45:08 Z with 28800 records expected to be read from lopc.bin INFO 2025-06-26 19:45:41,182 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.261.01/lopc.bin INFO 2025-06-26 19:45:41,182 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.261.01/lopc.nc INFO 2025-06-26 19:45:41,183 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.261.01/lopc.nc INFO 2025-06-26 19:45:41,183 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.261.01 INFO 2025-06-26 19:45:41,184 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:45:41,186 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0379012 WARNING 2025-06-26 19:45:41,187 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:45:41,282 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:45:41,282 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:45:41,282 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:45:41,591 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:45:41,592 process.py calibrate():227 [1] Calibration steps for 2013.261.01 INFO 2025-06-26 19:45:41,748 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 19:45:41,750 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:45:42,546 calibrate.py _nudge_pos():1806 [1] 112: 0.200 0.0075273 -0.0041967 13599 45.33 24.661 -17.156 2013-09-18T19:32:16.481323520 INFO 2025-06-26 19:45:42,556 calibrate.py _nudge_pos():1806 [1] 113: 0.010 0.0000689 -0.0000215 100 0.33 31.010 -12.077 2013-09-18T19:32:36.679939840 INFO 2025-06-26 19:45:43,699 calibrate.py _nudge_pos():1806 [1] 234: 0.020 0.0034063 -0.0039798 14090 46.96 10.767 -15.703 2013-09-18T20:21:34.678673152 INFO 2025-06-26 19:45:44,480 calibrate.py _nudge_pos():1806 [1] 317: 0.010 0.0000312 0.0000126 35 0.11 40.873 20.508 2013-09-18T20:23:03.682575872 INFO 2025-06-26 19:45:44,501 calibrate.py _nudge_pos():1806 [1] 319: 0.020 0.0009447 -0.0050219 13800 46.00 3.048 -20.231 2013-09-18T21:09:04.673434880 INFO 2025-06-26 19:45:44,544 calibrate.py _nudge_pos():1806 [1] 323: 0.020 0.0000097 -0.0000858 190 0.63 2.289 -25.240 2013-09-18T21:09:45.680625920 INFO 2025-06-26 19:45:45,513 calibrate.py _nudge_pos():1806 [1] 425: 0.030 0.0017303 -0.0038892 13840 46.13 5.564 -15.623 2013-09-18T21:57:34.674086400 INFO 2025-06-26 19:45:46,184 calibrate.py _nudge_pos():1806 [1] 496: 0.030 0.0025557 -0.0027770 13850 46.16 8.210 -11.147 2013-09-18T22:44:54.679532800 INFO 2025-06-26 19:45:46,314 calibrate.py _nudge_pos():1862 [1] 474: - - - 5 0.01 - - INFO 2025-06-26 19:45:46,314 calibrate.py _nudge_pos():1868 [1] Points in final series = 71792 INFO 2025-06-26 19:45:47,016 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:45:47,572 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:45:48,000 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:45:48,002 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.261.01/ctd1.nc INFO 2025-06-26 19:45:48,003 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:45:48,004 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 19:45:48,004 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:45:48,520 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:45:48,947 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:45:48,949 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.261.01/ctd2.nc INFO 2025-06-26 19:45:48,950 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 19:45:48,951 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 19:45:48,951 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:45:48,978 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:45:49,579 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92] INFO 2025-06-26 19:45:49,705 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:46:02,678 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.261.01 ERROR 2025-06-26 19:46:02,678 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.261.01 INFO 2025-06-26 19:46:02,737 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_cal.nc INFO 2025-06-26 19:46:02,853 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 19:46:02,859 process.py align():251 [1] Alignment steps for 2013.261.01 INFO 2025-06-26 19:46:02,894 align.py process_cal():139 [1] Processing dorado_2013.261.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.261.01 INFO 2025-06-26 19:46:02,916 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:02,920 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:02,971 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:02,975 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:03,028 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:03,032 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:03,062 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:46:03,062 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:46:03,082 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:03,086 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:03,137 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,140 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,185 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,189 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,235 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,238 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,283 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,287 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,333 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,337 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,381 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,385 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,432 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,435 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,479 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,483 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,529 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,533 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,578 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,582 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,628 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,632 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,676 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,680 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,726 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,730 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,775 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,779 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,826 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,830 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,875 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,879 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,926 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,930 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:03,975 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:03,979 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:04,027 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:04,031 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:04,076 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:04,080 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:04,127 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:04,131 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:04,176 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.261.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:04,180 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:04,236 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.94 INFO 2025-06-26 19:46:04,278 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.94 INFO 2025-06-26 19:46:04,320 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.94 INFO 2025-06-26 19:46:04,363 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:46:04,406 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:46:04,477 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:46:04,846 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:04,883 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_align.nc INFO 2025-06-26 19:46:05,001 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 19:46:05,003 process.py resample():273 [1] Resampling steps for 2013.261.01 INFO 2025-06-26 19:46:05,004 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:46:05,038 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_align.nc mission netCDF file INFO 2025-06-26 19:46:05,043 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_align.nc mission netCDF file INFO 2025-06-26 19:46:05,045 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-18T18:45:41.882766592 to 2013-09-18T22:45:08.678573568 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 19:46:05,046 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-18T18:45:17.544433920 to 2013-09-18T22:45:08.528583936 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 19:46:05,048 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-18T18:45:35.243221504 to 2013-09-18T22:45:08.688572928 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:46:05,049 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-18T18:45:35.353213696 to 2013-09-18T22:45:08.538583296 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 19:46:05,051 resample.py get_mission_start_end():1145 [1] isus : 2013-09-18T18:46:24.439851264 to 2013-09-18T22:45:07.848630528 (0 days 00:00:00.839942400 before mission_end) INFO 2025-06-26 19:46:05,052 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-18T18:45:06.915127808 to 2013-09-18T22:45:07.228638720 (0 days 00:00:01.459934208 before mission_end) INFO 2025-06-26 19:46:05,053 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-18T18:45:07.955090688 to 2013-09-18T22:45:08.528583936 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 19:46:05,054 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_align.nc mission netCDF file INFO 2025-06-26 19:46:05,055 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,219 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,249 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,278 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,307 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,333 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,359 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,384 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,409 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,433 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,456 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,480 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,503 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,526 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,549 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,572 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,595 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,618 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,643 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,667 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,691 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,714 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,738 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,763 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,787 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,800 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,814 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,826 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,837 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,849 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:05,853 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:46:05,853 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:46:06,372 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:46:06,467 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:46:06,518 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:46:06,540 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:46:06,560 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:46:06,560 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:46:06,592 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:06,783 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_1S.nc INFO 2025-06-26 19:46:08,382 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:46:19,861 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.261.01/dorado_2013.261.01_1S_Gulper.txt INFO 2025-06-26 19:46:19,862 process.py archive():337 [1] Archiving steps for 2013.261.01 INFO 2025-06-26 19:46:19,862 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:46:19,862 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:46:19,863 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.261.01_1S.nc INFO 2025-06-26 19:46:19,881 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:19,882 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.261.01_cal.nc INFO 2025-06-26 19:46:19,986 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:19,987 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.261.01_align.nc INFO 2025-06-26 19:46:20,124 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:20,144 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,162 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,166 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,184 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,237 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,244 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,265 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,281 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,323 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,329 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013261/2013.261.01 done. INFO 2025-06-26 19:46:20,329 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:46:20,330 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.261.01_1S_Gulper.txt INFO 2025-06-26 19:46:20,335 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.261.01/dorado_2013.261.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:46:20,336 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.261.01/dorado_2013.261.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf