INFO 2025-06-26 19:34:20,610 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 19:34:20,611 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Molecular Ecology - August 2013 - North Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:34:20,611 process.py process_mission():449 [1] Processing SIMZ August 2013 mission 2013.225.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:34:20,611 process.py download_process():165 [1] Download and processing steps for 2013.225.01 INFO 2025-06-26 19:34:20,611 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013225/2013.225.01 INFO 2025-06-26 19:34:20,611 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013225/2013.225.01 to /data/auv_data/dorado/missionlogs/2013.225.01 INFO 2025-06-26 19:34:23,892 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.225.01 INFO 2025-06-26 19:34:23,892 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/ctdDriver.log (3978438 bytes) INFO 2025-06-26 19:34:24,174 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/ctdDriver2.log (3978143 bytes) INFO 2025-06-26 19:34:24,460 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/gps.log (33548 bytes) INFO 2025-06-26 19:34:24,471 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/hydroscatlog.log (3489802 bytes) INFO 2025-06-26 19:34:24,825 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/navigation.log (14089190 bytes) INFO 2025-06-26 19:34:25,809 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/isuslog.log (307605 bytes) INFO 2025-06-26 19:34:25,841 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.225.01/isuslog.log: [2] INFO 2025-06-26 19:34:25,842 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/parosci.log (4900358 bytes) INFO 2025-06-26 19:34:26,235 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.225.01/parosci.log: [56176 56177 84261] INFO 2025-06-26 19:34:26,247 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/tailCone.log (2494651 bytes) INFO 2025-06-26 19:34:26,551 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/biolume.log (2905458 bytes) INFO 2025-06-26 19:34:26,833 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:34:26,980 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.09 seconds INFO 2025-06-26 19:34:26,980 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.01/lopc.bin (35630111 bytes) INFO 2025-06-26 19:34:26,980 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:34:26 2025 INFO 2025-06-26 19:34:26,980 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.225.01/parosci.nc INFO 2025-06-26 19:34:26,980 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:34:26,980 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.225.01/parosci.nc INFO 2025-06-26 19:34:26,983 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1376421362.0, sensor_off_time = 1376431755.0 INFO 2025-06-26 19:34:26,984 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10393 seconds. Expecting to read 20786 L frames from the lopc.bin file. INFO 2025-06-26 19:34:26,984 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 20786 records from the lopc.bin file. INFO 2025-06-26 19:34:27,106 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-08-13 19:16:01 Z and endTime = 2013-08-13 22:09:15 Z with 20786 records expected to be read from lopc.bin INFO 2025-06-26 19:34:27,106 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.225.01/lopc.bin INFO 2025-06-26 19:34:27,106 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.225.01/lopc.nc INFO 2025-06-26 19:34:27,107 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.225.01/lopc.nc INFO 2025-06-26 19:34:27,107 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.225.01 INFO 2025-06-26 19:34:27,107 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:34:27,177 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:34:27,177 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:34:27,177 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:34:27,246 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:34:27,247 process.py calibrate():227 [1] Calibration steps for 2013.225.01 INFO 2025-06-26 19:34:27,375 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 19:34:27,377 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:34:27,962 calibrate.py _nudge_pos():1806 [1] 94: 0.170 0.0020517 0.0001963 4240 14.13 21.519 2.574 2013-08-13T19:31:40.004413952 INFO 2025-06-26 19:34:28,303 calibrate.py _nudge_pos():1806 [1] 131: 0.170 -0.0024584 -0.0017205 7710 25.70 -14.181 -12.407 2013-08-13T19:57:58.006313216 INFO 2025-06-26 19:34:28,844 calibrate.py _nudge_pos():1806 [1] 189: 0.180 -0.0033952 -0.0035073 8115 27.05 -18.612 -24.029 2013-08-13T20:25:58.001225728 INFO 2025-06-26 19:34:29,278 calibrate.py _nudge_pos():1806 [1] 236: 0.180 0.0012574 -0.0006007 2440 8.13 22.930 -13.690 2013-08-13T20:34:52.004643840 INFO 2025-06-26 19:34:29,704 calibrate.py _nudge_pos():1806 [1] 282: 0.180 0.0047621 -0.0055260 6885 22.95 30.764 -44.624 2013-08-13T20:58:34.007229952 INFO 2025-06-26 19:34:30,149 calibrate.py _nudge_pos():1806 [1] 330: 0.190 0.0056449 -0.0030187 7565 25.21 33.183 -22.185 2013-08-13T21:24:34.000363264 INFO 2025-06-26 19:34:30,563 calibrate.py _nudge_pos():1806 [1] 375: 0.190 0.0057002 -0.0037590 7430 24.76 34.112 -28.128 2013-08-13T21:50:04.005550592 INFO 2025-06-26 19:34:31,024 calibrate.py _nudge_pos():1806 [1] 425: 0.190 0.0036548 -0.0018312 5365 17.88 30.287 -18.978 2013-08-13T22:08:46.008688128 INFO 2025-06-26 19:34:31,288 calibrate.py _nudge_pos():1862 [1] 416: - - - 5 0.01 - - INFO 2025-06-26 19:34:31,288 calibrate.py _nudge_pos():1868 [1] Points in final series = 51777 INFO 2025-06-26 19:34:33,074 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 9 of 41533 INFO 2025-06-26 19:34:33,395 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:34:33,792 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:34:34,098 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:34:34,099 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.225.01/ctd1.nc INFO 2025-06-26 19:34:34,101 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:34:34,101 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 19:34:34,101 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:34:34,474 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:34:34,782 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:34:34,784 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.225.01/ctd2.nc INFO 2025-06-26 19:34:34,785 calibrate.py _range_qc_combined_nc():898 [1] Setting 10 ctd2_salinity values to NaN INFO 2025-06-26 19:34:34,785 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 19:34:34,786 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:34:35,249 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:34:35,682 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62] INFO 2025-06-26 19:34:35,776 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:34:45,205 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.225.01 ERROR 2025-06-26 19:34:45,205 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.225.01 INFO 2025-06-26 19:34:45,248 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_cal.nc INFO 2025-06-26 19:34:45,343 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 19:34:45,349 process.py align():251 [1] Alignment steps for 2013.225.01 INFO 2025-06-26 19:34:45,381 align.py process_cal():139 [1] Processing dorado_2013.225.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.225.01 INFO 2025-06-26 19:34:45,399 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:45,402 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:45,441 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:45,445 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:45,483 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:45,487 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:45,510 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:34:45,510 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:34:45,525 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:45,528 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:45,567 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,570 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,604 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,607 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,641 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,645 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,681 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,684 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,719 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,722 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,756 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,760 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,795 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,798 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,832 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,835 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,870 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,873 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,908 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,911 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,946 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,950 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:45,984 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:45,988 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,023 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,027 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,061 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,064 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,100 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,103 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,138 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,142 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,178 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,182 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,217 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,220 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,256 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,259 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,295 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,298 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,333 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,337 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,373 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:46,378 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:46,424 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:46,459 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:46,493 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:46,527 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:34:46,563 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:34:46,617 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:34:46,889 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:46,918 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_align.nc INFO 2025-06-26 19:34:47,018 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 19:34:47,020 process.py resample():273 [1] Resampling steps for 2013.225.01 INFO 2025-06-26 19:34:47,021 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:34:47,050 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_align.nc mission netCDF file INFO 2025-06-26 19:34:47,056 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_align.nc mission netCDF file INFO 2025-06-26 19:34:47,057 resample.py get_mission_start_end():1145 [1] navigation: 2013-08-13T19:16:37.216259072 to 2013-08-13T22:09:15.006701824 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 19:34:47,058 resample.py get_mission_start_end():1145 [1] hs2 : 2013-08-13T19:16:07.598288128 to 2013-08-13T22:09:14.926707200 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 19:34:47,060 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-08-13T19:16:36.476309760 to 2013-08-13T22:09:14.986703104 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:34:47,061 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-08-13T19:16:37.586233600 to 2013-08-13T22:09:15.096695552 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:34:47,062 resample.py get_mission_start_end():1145 [1] isus : 2013-08-13T19:16:59.974700032 to 2013-08-13T22:09:12.506872832 (0 days 00:00:02.589822720 before mission_end) INFO 2025-06-26 19:34:47,064 resample.py get_mission_start_end():1145 [1] biolume : 2013-08-13T19:16:01.218690816 to 2013-08-13T22:09:14.416708096 (0 days 00:00:00.679987456 before mission_end) INFO 2025-06-26 19:34:47,065 resample.py get_mission_start_end():1145 [1] tailcone : 2013-08-13T19:16:02.558633216 to 2013-08-13T22:09:15.046699008 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 19:34:47,066 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_align.nc mission netCDF file INFO 2025-06-26 19:34:47,066 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,193 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,217 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,239 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,263 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,284 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,305 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,325 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,345 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,363 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,382 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,400 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,418 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,437 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,457 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,476 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,495 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,514 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,535 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,556 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,577 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,598 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,618 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,638 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,658 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,671 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,683 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,694 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,704 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,714 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:47,717 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:34:47,717 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:34:48,092 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:34:48,160 resample.py add_biolume_proxies():633 [1] Zero flow values found: 3 of 10394 - replaced with 350 ml/s INFO 2025-06-26 19:34:48,161 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:34:48,200 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:34:48,218 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:34:48,234 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:34:48,234 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:34:48,262 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:48,432 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_1S.nc INFO 2025-06-26 19:34:50,342 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:34:59,157 create_products.py gulper_odv():522 [1] Wrote 8 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.225.01/dorado_2013.225.01_1S_Gulper.txt INFO 2025-06-26 19:34:59,157 process.py archive():337 [1] Archiving steps for 2013.225.01 INFO 2025-06-26 19:34:59,157 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:34:59,159 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:34:59,159 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.01_1S.nc INFO 2025-06-26 19:34:59,175 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:59,176 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.01_cal.nc INFO 2025-06-26 19:34:59,251 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:59,252 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.01_align.nc INFO 2025-06-26 19:34:59,353 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:59,371 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,386 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,391 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,404 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,443 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,448 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,465 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,477 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,508 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,513 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.01 done. INFO 2025-06-26 19:34:59,513 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:34:59,514 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.225.01_1S_Gulper.txt INFO 2025-06-26 19:34:59,519 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.225.01/dorado_2013.225.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:34:59,519 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.01/dorado_2013.225.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf