INFO 2025-06-26 18:26:27,329 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 18:26:27,329 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission - Following SIO_WWL_1 for September 2011 CANON - ctdToUse = ctd1 INFO 2025-06-26 18:26:27,330 process.py process_mission():449 [1] Processing CANON September 2011 mission 2011.256.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:26:27,330 process.py download_process():165 [1] Download and processing steps for 2011.256.02 INFO 2025-06-26 18:26:27,330 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011256/2011.256.02 INFO 2025-06-26 18:26:27,330 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011256/2011.256.02 to /data/auv_data/dorado/missionlogs/2011.256.02 INFO 2025-06-26 18:26:28,930 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.256.02 INFO 2025-06-26 18:26:28,930 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/ctdDriver.log (697830 bytes) INFO 2025-06-26 18:26:28,988 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/ctdDriver2.log (697823 bytes) INFO 2025-06-26 18:26:29,045 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/gps.log (28220 bytes) INFO 2025-06-26 18:26:29,056 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/hydroscatlog.log (617506 bytes) INFO 2025-06-26 18:26:29,128 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/navigation.log (2463366 bytes) INFO 2025-06-26 18:26:29,312 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/isuslog.log (56309 bytes) INFO 2025-06-26 18:26:29,322 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/parosci.log (749750 bytes) INFO 2025-06-26 18:26:29,388 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/tailCone.log (442843 bytes) INFO 2025-06-26 18:26:29,449 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/biolume.log (518154 bytes) INFO 2025-06-26 18:26:29,503 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:26:29,532 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.60 seconds INFO 2025-06-26 18:26:29,533 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.02/lopc.bin (10356000 bytes) INFO 2025-06-26 18:26:29,533 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:26:29 2025 INFO 2025-06-26 18:26:29,533 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc INFO 2025-06-26 18:26:29,533 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:26:29,534 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc INFO 2025-06-26 18:26:29,535 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1315951939.7, sensor_off_time = 1315953783.5 INFO 2025-06-26 18:26:29,535 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 1843 seconds. Expecting to read 3686 L frames from the lopc.bin file. INFO 2025-06-26 18:26:29,536 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 3686 records from the lopc.bin file. INFO 2025-06-26 18:26:29,559 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-09-13 22:12:19 Z and endTime = 2011-09-13 22:43:03 Z with 3686 records expected to be read from lopc.bin INFO 2025-06-26 18:26:29,559 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.256.02/lopc.bin INFO 2025-06-26 18:26:29,559 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.256.02/lopc.nc INFO 2025-06-26 18:26:29,560 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.256.02/lopc.nc INFO 2025-06-26 18:26:29,561 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.256.02 INFO 2025-06-26 18:26:29,561 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 18:26:29,572 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:26:29,573 process.py calibrate():227 [1] Calibration steps for 2011.256.02 INFO 2025-06-26 18:26:29,668 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 18:26:29,670 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:26:29,923 calibrate.py _nudge_pos():1806 [1] 56: 0.200 0.0000033 0.0000307 34 0.11 4.469 51.695 2011-09-13T22:13:19.326705920 INFO 2025-06-26 18:26:32,456 calibrate.py _nudge_pos():1806 [1] 325: 0.210 0.0036709 -0.0028250 7289 24.29 22.413 -21.548 2011-09-13T22:42:05.318467584 INFO 2025-06-26 18:26:32,575 calibrate.py _nudge_pos():1806 [1] 338: 0.200 0.0000072 0.0000039 19 0.06 17.879 12.108 2011-09-13T22:42:21.327371008 INFO 2025-06-26 18:26:32,991 calibrate.py _nudge_pos():1862 [1] 344: - - - 4 0.01 - - INFO 2025-06-26 18:26:32,991 calibrate.py _nudge_pos():1868 [1] Points in final series = 8922 WARNING 2025-06-26 18:26:33,007 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:26:33,091 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:26:33,181 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:26:33,239 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:26:33,240 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.256.02/ctd1.nc INFO 2025-06-26 18:26:33,242 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 18:26:33,242 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 18:26:33,242 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:26:33,322 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 18:26:33,381 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 18:26:33,383 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.256.02/ctd2.nc INFO 2025-06-26 18:26:33,384 calibrate.py _range_qc_combined_nc():898 [1] Setting 95 ctd2_salinity values to NaN INFO 2025-06-26 18:26:33,385 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 18:26:33,385 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:26:33,395 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:26:33,473 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 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152] INFO 2025-06-26 18:26:33,493 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 1 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 18:26:35,186 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.256.02 ERROR 2025-06-26 18:26:35,187 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.256.02 INFO 2025-06-26 18:26:35,198 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_cal.nc INFO 2025-06-26 18:26:35,261 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 18:26:35,270 process.py align():251 [1] Alignment steps for 2011.256.02 INFO 2025-06-26 18:26:35,302 align.py process_cal():139 [1] Processing dorado_2011.256.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.256.02 INFO 2025-06-26 18:26:35,309 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:26:35,311 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:26:35,327 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:26:35,330 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:26:35,344 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:26:35,347 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:26:35,356 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:26:35,356 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:26:35,362 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:26:35,364 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:26:35,380 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,383 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,397 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,400 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,414 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,416 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,431 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,433 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,448 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,451 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,465 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,468 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,484 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,486 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,505 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,520 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,522 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,538 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,541 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,555 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,557 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,572 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,574 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,589 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,592 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,610 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,612 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,630 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,633 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,652 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,655 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,672 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,675 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,692 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,695 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,711 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,714 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,729 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,732 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,748 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,750 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,765 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:26:35,768 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:26:35,787 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:26:35,805 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:26:35,823 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:26:35,842 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:26:35,862 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:26:35,884 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 18:26:35,967 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:26:35,987 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc INFO 2025-06-26 18:26:36,052 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 18:26:36,055 process.py resample():273 [1] Resampling steps for 2011.256.02 INFO 2025-06-26 18:26:36,056 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:26:36,087 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-06-26 18:26:36,092 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-06-26 18:26:36,093 resample.py get_mission_start_end():1145 [1] navigation: 2011-09-13T22:12:53.938445312 to 2011-09-13T22:43:03.324493824 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 18:26:36,095 resample.py get_mission_start_end():1145 [1] hs2 : 2011-09-13T22:12:27.820234496 to 2011-09-13T22:43:03.334493184 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 18:26:36,096 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-09-13T22:12:48.368826880 to 2011-09-13T22:43:03.434486272 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 18:26:36,098 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-09-13T22:12:48.378826240 to 2011-09-13T22:43:03.494482176 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:26:36,099 resample.py get_mission_start_end():1145 [1] isus : 2011-09-13T22:13:43.215069440 to 2011-09-13T22:43:03.264497920 (0 days 00:00:00.229984256 before mission_end) INFO 2025-06-26 18:26:36,101 resample.py get_mission_start_end():1145 [1] biolume : 2011-09-13T22:12:20.740685312 to 2011-09-13T22:43:02.984482816 (0 days 00:00:00.509999360 before mission_end) INFO 2025-06-26 18:26:36,102 resample.py get_mission_start_end():1145 [1] tailcone : 2011-09-13T22:12:19.040835840 to 2011-09-13T22:43:03.354491648 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 18:26:36,103 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-06-26 18:26:36,104 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,155 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,168 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,181 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,193 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,207 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,219 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,232 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,245 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,256 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,267 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,278 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,289 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,300 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,311 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,322 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,333 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,343 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,357 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,369 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,381 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,393 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,404 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,416 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,428 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,440 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,451 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,461 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,471 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,479 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,483 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:26:36,483 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:26:36,556 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:26:36,574 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:26:36,585 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:26:36,591 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:26:36,599 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:26:36,599 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:26:36,617 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:26:36,762 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_1S.nc INFO 2025-06-26 18:26:40,112 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 18:26:40,460 create_products.py gulper_odv():522 [1] Wrote 2 Gulper data lines to /data/auv_data/dorado/missionodvs/2011.256.02/dorado_2011.256.02_1S_Gulper.txt INFO 2025-06-26 18:26:40,460 process.py archive():337 [1] Archiving steps for 2011.256.02 INFO 2025-06-26 18:26:40,460 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02, BASE_PATH = /data/auv_data INFO 2025-06-26 18:26:40,461 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:26:40,462 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.02_1S.nc INFO 2025-06-26 18:26:40,470 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:26:40,470 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.02_cal.nc INFO 2025-06-26 18:26:40,490 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:26:40,492 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.02_align.nc INFO 2025-06-26 18:26:40,517 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:26:40,526 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,540 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,548 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,560 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,565 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,580 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,591 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,596 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-06-26 18:26:40,596 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:26:40,597 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2011/odv/dorado_2011.256.02_1S_Gulper.txt INFO 2025-06-26 18:26:40,602 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2011.256.02/dorado_2011.256.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2011/odv done. INFO 2025-06-26 18:26:40,602 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_processing.log /Volumes/AUVCTD/surveys/2011/netcdf