INFO 2025-06-26 20:45:27,771 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:45:27,772 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2014 Northern Monterey Bay gulper missions - ctdToUse = ctd2 INFO 2025-06-26 20:45:27,772 process.py process_mission():449 [1] Processing SIMZ October 2014 mission 2014.295.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:45:27,772 process.py download_process():165 [1] Download and processing steps for 2014.295.00 INFO 2025-06-26 20:45:27,772 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014295/2014.295.00 INFO 2025-06-26 20:45:27,772 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014295/2014.295.00 to /data/auv_data/dorado/missionlogs/2014.295.00 INFO 2025-06-26 20:45:31,987 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.295.00 INFO 2025-06-26 20:45:31,988 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/ctdDriver.log (7225926 bytes) INFO 2025-06-26 20:45:32,753 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/ctdDriver2.log (7232447 bytes) INFO 2025-06-26 20:45:33,336 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/gps.log (104180 bytes) INFO 2025-06-26 20:45:33,372 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/hydroscatlog.log (6332446 bytes) INFO 2025-06-26 20:45:34,334 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/navigation.log (27093762 bytes) INFO 2025-06-26 20:45:36,516 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/isuslog.log (467413 bytes) INFO 2025-06-26 20:45:36,568 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.295.00/isuslog.log: [1 2 3] INFO 2025-06-26 20:45:36,570 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/parosci.log (8897990 bytes) INFO 2025-06-26 20:45:37,419 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/tailCone.log (4526635 bytes) INFO 2025-06-26 20:45:38,108 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/biolume.log (5269474 bytes) INFO 2025-06-26 20:45:38,654 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:45:38,922 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.93 seconds INFO 2025-06-26 20:45:38,923 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.295.00/lopc.bin (24246649 bytes) INFO 2025-06-26 20:45:38,923 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:45:38 2025 INFO 2025-06-26 20:45:38,923 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.295.00/parosci.nc INFO 2025-06-26 20:45:38,923 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:45:38,923 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.295.00/parosci.nc INFO 2025-06-26 20:45:38,927 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1413991498.7, sensor_off_time = 1414010356.0 INFO 2025-06-26 20:45:38,927 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 18857 seconds. Expecting to read 37714 L frames from the lopc.bin file. INFO 2025-06-26 20:45:38,927 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 37714 records from the lopc.bin file. INFO 2025-06-26 20:45:39,154 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-22 15:24:58 Z and endTime = 2014-10-22 20:39:15 Z with 37714 records expected to be read from lopc.bin INFO 2025-06-26 20:45:39,155 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.295.00/lopc.bin INFO 2025-06-26 20:45:39,155 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.295.00/lopc.nc INFO 2025-06-26 20:45:39,155 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.295.00/lopc.nc INFO 2025-06-26 20:45:39,156 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.295.00 INFO 2025-06-26 20:45:39,156 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:45:39,208 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:45:39,208 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:45:39,208 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 20:45:48,224 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10000 20455 0 0 0 0 0 9.1 seconds, last L Frame: 37714 ERROR 2025-06-26 20:45:48,233 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:45:48,234 process.py calibrate():227 [1] Calibration steps for 2014.295.00 INFO 2025-06-26 20:45:48,449 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:45:48,451 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:45:49,497 calibrate.py _nudge_pos():1806 [1] 128: 0.020 -0.0003310 0.0000822 1895 6.31 -7.764 2.413 2014-10-22T15:33:21.098404096 INFO 2025-06-26 20:45:50,384 calibrate.py _nudge_pos():1806 [1] 215: 0.030 0.0002470 -0.0000211 8480 28.26 1.294 -0.138 2014-10-22T16:03:03.096328704 INFO 2025-06-26 20:45:51,109 calibrate.py _nudge_pos():1806 [1] 290: 0.040 0.0004600 0.0002980 8120 27.06 2.518 2.041 2014-10-22T16:31:21.090008320 INFO 2025-06-26 20:45:51,603 calibrate.py _nudge_pos():1806 [1] 338: 0.040 0.0005727 0.0003403 6845 22.81 3.720 2.764 2014-10-22T16:54:57.093005312 INFO 2025-06-26 20:45:52,277 calibrate.py _nudge_pos():1806 [1] 405: 0.040 0.0008262 0.0001529 4080 13.60 9.005 2.084 2014-10-22T17:09:39.092584448 INFO 2025-06-26 20:45:53,485 calibrate.py _nudge_pos():1806 [1] 513: 0.040 -0.0021173 0.0003417 6245 20.81 -15.076 3.042 2014-10-22T17:32:15.099691264 INFO 2025-06-26 20:45:53,572 calibrate.py _nudge_pos():1806 [1] 522: 0.040 0.0000016 -0.0000543 200 0.66 0.367 -15.177 2014-10-22T17:33:03.096403712 INFO 2025-06-26 20:45:54,530 calibrate.py _nudge_pos():1806 [1] 605: 0.050 -0.0027810 0.0001230 6425 21.41 -19.250 1.064 2014-10-22T17:55:51.092689152 INFO 2025-06-26 20:45:54,747 calibrate.py _nudge_pos():1806 [1] 622: 0.040 -0.0038206 0.0001339 7690 25.63 -22.100 0.968 2014-10-22T18:21:45.096232960 INFO 2025-06-26 20:45:55,356 calibrate.py _nudge_pos():1806 [1] 673: 0.040 -0.0008088 -0.0006312 1760 5.86 -20.450 -19.948 2014-10-22T18:28:27.098693888 INFO 2025-06-26 20:45:55,890 calibrate.py _nudge_pos():1806 [1] 727: 0.050 -0.0000156 -0.0000205 20 0.06 -36.632 -59.868 2014-10-22T18:29:24.094789376 INFO 2025-06-26 20:45:55,994 calibrate.py _nudge_pos():1806 [1] 737: 0.050 0.0007802 0.0000495 3480 11.60 9.974 0.791 2014-10-22T18:41:09.096493312 INFO 2025-06-26 20:45:56,669 calibrate.py _nudge_pos():1806 [1] 802: 0.050 -0.0001621 -0.0002006 3460 11.53 -2.084 -3.224 2014-10-22T18:53:45.094703872 INFO 2025-06-26 20:45:56,738 calibrate.py _nudge_pos():1806 [1] 809: 0.050 0.0000465 -0.0000908 240 0.80 8.645 -21.121 2014-10-22T18:54:40.090936320 INFO 2025-06-26 20:45:57,208 calibrate.py _nudge_pos():1806 [1] 855: 0.050 -0.0005721 -0.0007555 5950 19.83 -4.276 -7.060 2014-10-22T19:15:15.096332800 INFO 2025-06-26 20:45:57,242 calibrate.py _nudge_pos():1806 [1] 858: 0.050 0.0000370 0.0000068 270 0.90 6.110 1.411 2014-10-22T19:16:11.092496640 INFO 2025-06-26 20:45:57,924 calibrate.py _nudge_pos():1806 [1] 918: 0.050 -0.0003946 -0.0011313 6535 21.78 -2.685 -9.625 2014-10-22T19:38:57.098918912 INFO 2025-06-26 20:45:58,521 calibrate.py _nudge_pos():1806 [1] 978: 0.060 -0.0005093 -0.0011801 7445 24.81 -3.041 -8.813 2014-10-22T20:04:45.092873984 INFO 2025-06-26 20:45:59,244 calibrate.py _nudge_pos():1806 [1] 1034: 0.060 -0.0001041 -0.0006200 4945 16.48 -0.936 -6.972 2014-10-22T20:22:09.091355392 INFO 2025-06-26 20:45:59,879 calibrate.py _nudge_pos():1806 [1] 1098: 0.070 0.0001104 -0.0000888 3135 10.45 1.566 -1.575 2014-10-22T20:33:39.094086912 INFO 2025-06-26 20:46:03,635 calibrate.py _nudge_pos():1862 [1] 1388: - - - 4 0.01 - - INFO 2025-06-26 20:46:03,635 calibrate.py _nudge_pos():1868 [1] Points in final series = 94067 INFO 2025-06-26 20:46:04,680 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:46:05,609 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:46:06,426 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:46:06,429 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.295.00/ctd1.nc INFO 2025-06-26 20:46:06,431 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:46:06,432 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:46:06,432 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:46:07,348 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:46:08,069 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:46:08,072 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.295.00/ctd2.nc INFO 2025-06-26 20:46:08,073 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:46:08,073 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:46:08,073 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:46:09,114 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:46:10,247 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] INFO 2025-06-26 20:46:10,540 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:46:32,827 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.295.00 ERROR 2025-06-26 20:46:32,828 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.295.00 INFO 2025-06-26 20:46:32,903 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_cal.nc INFO 2025-06-26 20:46:33,084 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:46:33,090 process.py align():251 [1] Alignment steps for 2014.295.00 INFO 2025-06-26 20:46:33,132 align.py process_cal():139 [1] Processing dorado_2014.295.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.295.00 INFO 2025-06-26 20:46:33,163 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:46:33,167 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:46:33,237 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:46:33,242 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:46:33,327 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:46:33,334 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:46:33,383 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:46:33,383 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:46:33,420 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:46:33,427 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:46:33,522 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,529 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:33,611 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,616 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:33,683 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,690 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:33,779 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,785 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:33,871 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,878 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:33,957 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:33,962 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,034 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,041 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,124 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,129 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,219 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,226 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,301 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,309 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,374 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,379 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,438 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,443 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,506 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,510 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,570 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,574 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,636 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,641 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,715 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,722 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,822 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,829 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,923 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,929 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:34,994 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:34,999 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:35,063 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:35,068 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:35,132 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:35,137 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:35,200 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:46:35,205 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:46:35,281 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:46:35,336 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:46:35,393 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:46:35,453 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:46:35,527 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:46:35,662 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:46:36,154 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:46:36,224 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_align.nc INFO 2025-06-26 20:46:36,388 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:46:36,392 process.py resample():273 [1] Resampling steps for 2014.295.00 INFO 2025-06-26 20:46:36,393 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:46:36,430 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_align.nc mission netCDF file INFO 2025-06-26 20:46:36,436 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_align.nc mission netCDF file INFO 2025-06-26 20:46:36,438 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-22T15:25:42.709805824 to 2014-10-22T20:39:15.891014656 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:46:36,440 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-22T15:25:03.602484992 to 2014-10-22T20:39:15.931011840 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 20:46:36,442 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-22T15:25:40.319969536 to 2014-10-22T20:39:15.901013760 (0 days 00:00:00.139990784 before mission_end) INFO 2025-06-26 20:46:36,443 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-22T15:25:23.951090688 to 2014-10-22T20:39:16.021005568 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 20:46:36,445 resample.py get_mission_start_end():1145 [1] isus : 2014-10-22T15:25:55.548926464 to 2014-10-22T20:39:15.201061888 (0 days 00:00:00.839942656 before mission_end) INFO 2025-06-26 20:46:36,446 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-22T15:24:56.182958848 to 2014-10-22T20:39:14.551072000 (0 days 00:00:01.489932544 before mission_end) INFO 2025-06-26 20:46:36,448 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-22T15:24:57.172925184 to 2014-10-22T20:39:16.041004544 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:46:36,449 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_align.nc mission netCDF file INFO 2025-06-26 20:46:36,449 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,729 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,767 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,804 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,841 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,878 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,914 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,955 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:36,998 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,038 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,072 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,102 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,132 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,163 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,193 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,228 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,261 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,290 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,323 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,364 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,408 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,455 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,495 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,527 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,570 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,593 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,615 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,637 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,658 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,677 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:37,683 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:46:37,683 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:46:38,462 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:46:38,624 resample.py add_biolume_proxies():633 [1] Zero flow values found: 18859 of 18859 - replaced with 350 ml/s INFO 2025-06-26 20:46:38,624 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:46:38,710 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:46:38,755 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:46:38,797 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:46:38,797 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:46:38,849 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:46:39,101 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_1S.nc INFO 2025-06-26 20:46:41,108 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 20:47:04,370 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.295.00/dorado_2014.295.00_1S_Gulper.txt INFO 2025-06-26 20:47:04,370 process.py archive():337 [1] Archiving steps for 2014.295.00 INFO 2025-06-26 20:47:04,370 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:47:04,372 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:47:04,373 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.295.00_1S.nc INFO 2025-06-26 20:47:04,393 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:47:04,394 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.295.00_cal.nc INFO 2025-06-26 20:47:04,516 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:47:04,517 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.295.00_align.nc INFO 2025-06-26 20:47:04,688 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:47:04,714 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,737 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,741 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,762 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,832 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,839 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,864 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,884 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,937 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,957 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014295/2014.295.00 done. INFO 2025-06-26 20:47:04,958 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:47:04,959 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.295.00_1S_Gulper.txt INFO 2025-06-26 20:47:04,963 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.295.00/dorado_2014.295.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:47:04,964 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.295.00/dorado_2014.295.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf