INFO 2025-06-26 19:39:10,216 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 19:39:10,216 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Molecular Ecology - August 2013 - North Monterey Bay - ctdToUse = ctd2 INFO 2025-06-26 19:39:10,216 process.py process_mission():449 [1] Processing SIMZ August 2013 mission 2013.228.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:39:10,216 process.py download_process():165 [1] Download and processing steps for 2013.228.00 INFO 2025-06-26 19:39:10,216 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013228/2013.228.00 INFO 2025-06-26 19:39:10,216 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013228/2013.228.00 to /data/auv_data/dorado/missionlogs/2013.228.00 INFO 2025-06-26 19:39:13,948 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.228.00 INFO 2025-06-26 19:39:13,949 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/ctdDriver.log (4102950 bytes) INFO 2025-06-26 19:39:14,241 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/ctdDriver2.log (4109183 bytes) INFO 2025-06-26 19:39:14,524 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.228.00/ctdDriver2.log: [1] INFO 2025-06-26 19:39:14,537 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/gps.log (330044 bytes) INFO 2025-06-26 19:39:14,579 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/hydroscatlog.log (3601438 bytes) INFO 2025-06-26 19:39:14,954 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/navigation.log (14539894 bytes) INFO 2025-06-26 19:39:15,959 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/isuslog.log (317077 bytes) INFO 2025-06-26 19:39:15,993 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.228.00/isuslog.log: [1] INFO 2025-06-26 19:39:15,994 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/parosci.log (5064662 bytes) INFO 2025-06-26 19:39:16,426 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.228.00/parosci.log: [89872 89873 89874 89875 89877 89878] INFO 2025-06-26 19:39:16,438 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/tailCone.log (2574331 bytes) INFO 2025-06-26 19:39:16,755 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/biolume.log (2998042 bytes) INFO 2025-06-26 19:39:17,048 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:39:17,200 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.25 seconds INFO 2025-06-26 19:39:17,200 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.228.00/lopc.bin (38099011 bytes) INFO 2025-06-26 19:39:17,201 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:39:17 2025 INFO 2025-06-26 19:39:17,201 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.228.00/parosci.nc INFO 2025-06-26 19:39:17,201 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:39:17,201 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.228.00/parosci.nc INFO 2025-06-26 19:39:17,204 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1376664467.7, sensor_off_time = 1376675192.4 INFO 2025-06-26 19:39:17,204 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10724 seconds. Expecting to read 21448 L frames from the lopc.bin file. INFO 2025-06-26 19:39:17,204 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21448 records from the lopc.bin file. INFO 2025-06-26 19:39:17,333 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-08-16 14:47:47 Z and endTime = 2013-08-16 17:46:32 Z with 21448 records expected to be read from lopc.bin INFO 2025-06-26 19:39:17,333 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.228.00/lopc.bin INFO 2025-06-26 19:39:17,333 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.228.00/lopc.nc INFO 2025-06-26 19:39:17,334 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.228.00/lopc.nc INFO 2025-06-26 19:39:17,335 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.228.00 INFO 2025-06-26 19:39:17,335 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:39:17,444 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:39:17,445 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:39:17,445 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:39:17,490 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:39:17,491 process.py calibrate():227 [1] Calibration steps for 2013.228.00 INFO 2025-06-26 19:39:17,618 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 19:39:17,620 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:39:18,202 calibrate.py _nudge_pos():1806 [1] 93: 0.170 0.0001895 -0.0000946 470 1.56 17.951 -11.211 2013-08-16T14:50:51.888678144 INFO 2025-06-26 19:39:18,212 calibrate.py _nudge_pos():1806 [1] 94: 0.170 -0.0000113 -0.0000956 30 0.10 -17.272 -183.319 2013-08-16T14:50:57.888267008 INFO 2025-06-26 19:39:18,497 calibrate.py _nudge_pos():1806 [1] 125: 0.170 0.0000056 -0.0000468 95 0.31 2.645 -27.670 2013-08-16T14:51:46.884910592 INFO 2025-06-26 19:39:18,516 calibrate.py _nudge_pos():1806 [1] 127: 0.180 0.0087654 -0.0056518 9140 30.46 42.622 -34.379 2013-08-16T15:22:15.879615744 INFO 2025-06-26 19:39:19,043 calibrate.py _nudge_pos():1806 [1] 184: 0.180 0.0060896 -0.0080593 9860 32.86 27.454 -45.443 2013-08-16T15:56:03.880688128 INFO 2025-06-26 19:39:19,552 calibrate.py _nudge_pos():1806 [1] 239: 0.180 0.0028669 -0.0060540 7410 24.70 17.201 -45.424 2013-08-16T16:21:39.885464576 INFO 2025-06-26 19:39:19,902 calibrate.py _nudge_pos():1806 [1] 277: 0.180 0.0007114 -0.0028927 3805 12.68 8.313 -42.272 2013-08-16T16:34:57.880798208 INFO 2025-06-26 19:40:00,320 calibrate.py _nudge_pos():1862 [1] 4535: - - - 2 0.00 - - INFO 2025-06-26 19:40:00,320 calibrate.py _nudge_pos():1868 [1] Points in final series = 53099 INFO 2025-06-26 19:40:02,431 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:40:02,843 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:40:03,171 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:40:03,173 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.228.00/ctd1.nc INFO 2025-06-26 19:40:03,175 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:40:03,175 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 19:40:03,175 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:40:05,562 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:40:05,882 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:40:05,884 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.228.00/ctd2.nc INFO 2025-06-26 19:40:05,886 calibrate.py _range_qc_combined_nc():898 [1] Setting 40 ctd2_salinity values to NaN INFO 2025-06-26 19:40:05,886 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 19:40:05,886 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:40:06,360 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:40:06,806 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] INFO 2025-06-26 19:40:06,901 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:40:16,586 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.228.00 ERROR 2025-06-26 19:40:16,586 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.228.00 INFO 2025-06-26 19:40:16,630 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_cal.nc INFO 2025-06-26 19:40:18,700 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 19:40:18,705 process.py align():251 [1] Alignment steps for 2013.228.00 INFO 2025-06-26 19:40:18,737 align.py process_cal():139 [1] Processing dorado_2013.228.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.228.00 INFO 2025-06-26 19:40:18,755 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:40:18,757 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:40:18,797 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:40:18,800 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:40:18,839 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:40:18,842 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:40:18,866 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:40:18,866 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:40:18,881 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:40:18,884 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:40:18,924 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:18,927 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:18,961 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:18,964 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:18,999 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,002 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,037 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,040 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,076 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,079 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,114 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,117 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,153 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,156 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,191 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,194 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,230 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,233 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,268 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,271 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,306 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,309 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,344 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,348 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,383 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,387 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,422 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,425 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,461 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,465 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,501 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,504 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,540 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,543 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,579 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,582 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,618 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,621 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,656 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,660 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,702 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,706 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,741 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.228.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:40:19,744 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:40:19,789 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:40:19,822 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:40:19,856 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:40:19,890 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:40:19,927 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:40:19,982 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:40:20,263 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:40:20,294 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_align.nc INFO 2025-06-26 19:40:20,476 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 19:40:20,479 process.py resample():273 [1] Resampling steps for 2013.228.00 INFO 2025-06-26 19:40:20,479 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:40:20,510 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_align.nc mission netCDF file INFO 2025-06-26 19:40:20,516 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_align.nc mission netCDF file INFO 2025-06-26 19:40:20,517 resample.py get_mission_start_end():1145 [1] navigation: 2013-08-16T14:48:23.098870784 to 2013-08-16T17:46:32.286611200 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-26 19:40:20,518 resample.py get_mission_start_end():1145 [1] hs2 : 2013-08-16T14:47:52.190988032 to 2013-08-16T17:46:32.266612480 (0 days 00:00:00.189987328 before mission_end) INFO 2025-06-26 19:40:20,520 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-08-16T14:48:29.948401408 to 2013-08-16T17:46:32.456599808 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:40:20,521 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-08-16T14:48:13.749511168 to 2013-08-16T17:46:32.436600832 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 19:40:20,523 resample.py get_mission_start_end():1145 [1] isus : 2013-08-16T14:48:46.497267968 to 2013-08-16T17:46:31.836642048 (0 days 00:00:00.619957760 before mission_end) INFO 2025-06-26 19:40:20,524 resample.py get_mission_start_end():1145 [1] biolume : 2013-08-16T14:47:46.471345664 to 2013-08-16T17:46:31.096658432 (0 days 00:00:01.359941376 before mission_end) INFO 2025-06-26 19:40:20,526 resample.py get_mission_start_end():1145 [1] tailcone : 2013-08-16T14:47:47.701295616 to 2013-08-16T17:46:32.296610560 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 19:40:20,526 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_align.nc mission netCDF file INFO 2025-06-26 19:40:20,527 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,656 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,679 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,702 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,725 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,746 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,767 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,787 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,807 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,825 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,844 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,863 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,881 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,901 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,920 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,939 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,959 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,978 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:20,999 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,021 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,043 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,063 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,084 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,104 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,125 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,138 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,149 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,161 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,171 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,180 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,184 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:40:21,184 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:40:21,589 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:40:21,657 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:40:21,697 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:40:21,715 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:40:21,731 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:40:21,731 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:40:21,760 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:40:21,930 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_1S.nc INFO 2025-06-26 19:40:23,886 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 19:40:34,884 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.228.00/dorado_2013.228.00_1S_Gulper.txt INFO 2025-06-26 19:40:34,884 process.py archive():337 [1] Archiving steps for 2013.228.00 INFO 2025-06-26 19:40:34,884 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:40:34,886 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:40:34,886 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.228.00_1S.nc INFO 2025-06-26 19:40:34,902 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:40:34,903 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.228.00_cal.nc INFO 2025-06-26 19:40:34,976 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:40:34,977 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.228.00_align.nc INFO 2025-06-26 19:40:35,086 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:40:35,105 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,121 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,126 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,141 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,181 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,187 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,205 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,218 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,249 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,255 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013228/2013.228.00 done. INFO 2025-06-26 19:40:35,255 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:40:35,257 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.228.00_1S_Gulper.txt INFO 2025-06-26 19:40:35,261 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.228.00/dorado_2013.228.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:40:35,262 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.228.00/dorado_2013.228.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf