INFO 2025-06-26 19:47:56,908 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 19:47:56,908 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:47:56,908 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.268.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:47:56,908 process.py download_process():165 [1] Download and processing steps for 2013.268.00 INFO 2025-06-26 19:47:56,908 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013268/2013.268.00 INFO 2025-06-26 19:47:56,908 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013268/2013.268.00 to /data/auv_data/dorado/missionlogs/2013.268.00 INFO 2025-06-26 19:48:01,297 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.268.00 INFO 2025-06-26 19:48:01,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/ctdDriver.log (9396006 bytes) INFO 2025-06-26 19:48:01,974 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/ctdDriver2.log (9402431 bytes) INFO 2025-06-26 19:48:02,644 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/gps.log (93596 bytes) INFO 2025-06-26 19:48:02,662 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/hydroscatlog.log (8230342 bytes) INFO 2025-06-26 19:48:03,507 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/navigation.log (33283958 bytes) INFO 2025-06-26 19:48:05,845 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/isuslog.log (749589 bytes) INFO 2025-06-26 19:48:05,919 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/parosci.log (11549654 bytes) INFO 2025-06-26 19:48:06,887 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/tailCone.log (5882395 bytes) INFO 2025-06-26 19:48:07,601 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/biolume.log (6847094 bytes) INFO 2025-06-26 19:48:08,267 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:48:08,601 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.30 seconds INFO 2025-06-26 19:48:08,602 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.268.00/lopc.bin (54572144 bytes) INFO 2025-06-26 19:48:08,602 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:48:08 2025 INFO 2025-06-26 19:48:08,602 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.268.00/parosci.nc INFO 2025-06-26 19:48:08,602 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:48:08,602 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.268.00/parosci.nc INFO 2025-06-26 19:48:08,605 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1380123380.2, sensor_off_time = 1380147888.8 INFO 2025-06-26 19:48:08,605 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 24508 seconds. Expecting to read 49016 L frames from the lopc.bin file. INFO 2025-06-26 19:48:08,606 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 49016 records from the lopc.bin file. INFO 2025-06-26 19:48:08,896 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-25 15:36:20 Z and endTime = 2013-09-25 22:24:48 Z with 49016 records expected to be read from lopc.bin INFO 2025-06-26 19:48:08,896 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.268.00/lopc.bin INFO 2025-06-26 19:48:08,896 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.268.00/lopc.nc INFO 2025-06-26 19:48:08,897 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.268.00/lopc.nc INFO 2025-06-26 19:48:08,897 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.268.00 INFO 2025-06-26 19:48:08,898 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:48:08,952 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:48:08,952 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:48:08,952 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:48:10,457 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:48:10,458 process.py calibrate():227 [1] Calibration steps for 2013.268.00 INFO 2025-06-26 19:48:10,665 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 19:48:10,667 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:48:11,407 calibrate.py _nudge_pos():1806 [1] 107: 0.150 -0.0000103 -0.0000142 15 0.05 -32.840 -56.315 2013-09-25T15:38:07.289270528 INFO 2025-06-26 19:48:11,570 calibrate.py _nudge_pos():1806 [1] 124: 0.150 0.0000522 -0.0000221 1520 5.06 1.532 -0.809 2013-09-25T15:43:27.287349248 INFO 2025-06-26 19:48:12,441 calibrate.py _nudge_pos():1806 [1] 216: 0.150 -0.0001934 -0.0002462 2035 6.78 -4.241 -6.728 2013-09-25T15:51:45.293233408 INFO 2025-06-26 19:48:12,611 calibrate.py _nudge_pos():1806 [1] 234: 0.160 -0.0009924 -0.0010906 8853 29.51 -4.998 -6.848 2013-09-25T16:21:33.290747136 INFO 2025-06-26 19:48:13,063 calibrate.py _nudge_pos():1806 [1] 281: 0.160 -0.0000203 -0.0000098 15 0.05 -64.748 -38.726 2013-09-25T16:22:22.287390720 INFO 2025-06-26 19:48:13,609 calibrate.py _nudge_pos():1806 [1] 338: 0.170 -0.0015474 -0.0006194 15005 50.01 -4.598 -2.295 2013-09-25T17:13:19.287972096 INFO 2025-06-26 19:48:14,400 calibrate.py _nudge_pos():1806 [1] 421: 0.160 -0.0000017 0.0000110 60 0.20 -1.315 10.332 2013-09-25T17:14:53.291532288 INFO 2025-06-26 19:48:14,439 calibrate.py _nudge_pos():1806 [1] 425: 0.170 -0.0016765 -0.0012406 9915 33.05 -7.536 -6.957 2013-09-25T17:47:59.285482240 INFO 2025-06-26 19:48:15,483 calibrate.py _nudge_pos():1806 [1] 534: 0.170 -0.0020883 -0.0012267 13520 45.06 -6.882 -5.044 2013-09-25T18:34:51.292846592 INFO 2025-06-26 19:48:16,201 calibrate.py _nudge_pos():1806 [1] 609: 0.180 -0.0018303 -0.0001841 18110 60.36 -4.500 -0.565 2013-09-25T19:36:27.289653504 INFO 2025-06-26 19:48:17,000 calibrate.py _nudge_pos():1806 [1] 692: 0.180 -0.0008806 0.0002771 5200 17.33 -7.540 2.963 2013-09-25T19:55:09.292790784 INFO 2025-06-26 19:48:17,793 calibrate.py _nudge_pos():1806 [1] 774: 0.200 -0.0028555 -0.0008988 10425 34.75 -12.190 -4.793 2013-09-25T20:31:15.284410368 INFO 2025-06-26 19:48:18,634 calibrate.py _nudge_pos():1806 [1] 861: 0.200 -0.0020024 -0.0008497 9889 32.96 -9.008 -4.777 2013-09-25T21:05:39.293016320 INFO 2025-06-26 19:48:19,501 calibrate.py _nudge_pos():1806 [1] 950: 0.010 -0.0016529 -0.0007489 8650 28.83 -8.498 -4.813 2013-09-25T21:35:57.488461312 INFO 2025-06-26 19:48:20,494 calibrate.py _nudge_pos():1806 [1] 1051: 0.010 -0.0019658 -0.0011748 8370 27.90 -10.442 -7.804 2013-09-25T22:05:33.486796800 INFO 2025-06-26 19:48:20,564 calibrate.py _nudge_pos():1806 [1] 1058: 0.010 0.0000212 -0.0000057 95 0.31 10.003 -3.365 2013-09-25T22:05:58.485084416 INFO 2025-06-26 19:48:20,614 calibrate.py _nudge_pos():1806 [1] 1063: 0.010 -0.0000344 -0.0000025 25 0.08 -63.688 -5.812 2013-09-25T22:06:07.484467968 INFO 2025-06-26 19:48:21,332 calibrate.py _nudge_pos():1806 [1] 1135: 0.010 0.0000120 0.0000040 15 0.05 38.092 15.974 2013-09-25T22:07:21.489398272 INFO 2025-06-26 19:48:21,500 calibrate.py _nudge_pos():1806 [1] 1152: 0.010 -0.0011717 -0.0004097 4480 14.93 -11.627 -5.084 2013-09-25T22:22:33.486922240 INFO 2025-06-26 19:48:22,844 calibrate.py _nudge_pos():1862 [1] 1250: - - - 2 0.00 - - INFO 2025-06-26 19:48:22,844 calibrate.py _nudge_pos():1868 [1] Points in final series = 122188 INFO 2025-06-26 19:48:23,999 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:48:24,914 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:48:25,635 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:48:25,638 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.268.00/ctd1.nc INFO 2025-06-26 19:48:25,639 calibrate.py _range_qc_combined_nc():898 [1] Setting 309 ctd1_salinity values to NaN INFO 2025-06-26 19:48:25,639 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 19:48:25,639 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:48:26,505 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:48:27,223 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:48:27,226 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.268.00/ctd2.nc INFO 2025-06-26 19:48:27,227 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd2_salinity values to NaN INFO 2025-06-26 19:48:27,227 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 19:48:27,227 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:48:27,269 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:48:28,367 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61] INFO 2025-06-26 19:48:28,577 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:48:50,853 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.268.00 ERROR 2025-06-26 19:48:50,854 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.268.00 INFO 2025-06-26 19:48:50,950 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_cal.nc INFO 2025-06-26 19:48:51,112 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 19:48:51,119 process.py align():251 [1] Alignment steps for 2013.268.00 INFO 2025-06-26 19:48:51,161 align.py process_cal():139 [1] Processing dorado_2013.268.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.268.00 INFO 2025-06-26 19:48:51,197 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:48:51,202 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:48:51,288 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:48:51,295 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:48:51,375 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:48:51,381 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:48:51,429 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:48:51,429 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:48:51,460 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:48:51,466 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:48:51,545 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,550 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,621 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,626 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,696 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,701 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,769 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,774 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,850 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,919 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,924 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:51,994 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:51,999 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,073 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,078 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,148 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,153 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,222 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,228 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,298 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,303 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,371 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,376 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,447 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,452 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,522 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,527 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,599 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,603 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,674 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,680 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,752 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,757 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,826 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,832 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,904 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,909 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:52,978 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:52,984 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:53,055 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:53,060 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:53,131 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.268.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:48:53,135 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:48:53,224 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:48:53,287 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:48:53,350 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:48:53,416 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:48:53,483 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:48:53,591 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:48:54,211 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:48:54,269 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_align.nc INFO 2025-06-26 19:48:54,437 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 19:48:54,440 process.py resample():273 [1] Resampling steps for 2013.268.00 INFO 2025-06-26 19:48:54,440 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:48:54,480 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_align.nc mission netCDF file INFO 2025-06-26 19:48:54,486 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_align.nc mission netCDF file INFO 2025-06-26 19:48:54,488 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-25T15:36:56.894093056 to 2013-09-25T22:24:48.887646720 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:48:54,489 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-25T15:36:24.886285824 to 2013-09-25T22:24:48.637663488 (0 days 00:00:00.249983232 before mission_end) INFO 2025-06-26 19:48:54,491 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-25T15:37:02.483709952 to 2013-09-25T22:24:48.707659008 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 19:48:54,493 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-25T15:36:45.814852096 to 2013-09-25T22:24:48.787653376 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 19:48:54,494 resample.py get_mission_start_end():1145 [1] isus : 2013-09-25T15:37:34.861492224 to 2013-09-25T22:24:48.267688960 (0 days 00:00:00.619957760 before mission_end) INFO 2025-06-26 19:48:54,496 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-25T15:36:18.646679040 to 2013-09-25T22:24:48.147663104 (0 days 00:00:00.739983616 before mission_end) INFO 2025-06-26 19:48:54,497 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-25T15:36:21.296531712 to 2013-09-25T22:24:48.887646720 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:48:54,498 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_align.nc mission netCDF file INFO 2025-06-26 19:48:54,499 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,764 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,810 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,855 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,900 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,939 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:54,978 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,017 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,055 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,091 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,129 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,165 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,200 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,234 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,270 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,305 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,340 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,375 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,413 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,451 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,489 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,526 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,565 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,602 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,640 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,659 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,677 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,693 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,708 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,723 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:55,728 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:48:55,728 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:48:56,614 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:48:56,779 resample.py add_biolume_proxies():633 [1] Zero flow values found: 21 of 24511 - replaced with 350 ml/s INFO 2025-06-26 19:48:56,779 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:48:56,867 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:48:56,905 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:48:56,936 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:48:56,937 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:48:56,984 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:48:57,235 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_1S.nc INFO 2025-06-26 19:48:59,105 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:49:09,943 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.268.00/dorado_2013.268.00_1S_Gulper.txt INFO 2025-06-26 19:49:09,943 process.py archive():337 [1] Archiving steps for 2013.268.00 INFO 2025-06-26 19:49:09,944 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:49:09,946 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:49:09,947 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.268.00_1S.nc INFO 2025-06-26 19:49:09,972 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:49:09,973 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.268.00_cal.nc INFO 2025-06-26 19:49:10,136 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:49:10,137 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.268.00_align.nc INFO 2025-06-26 19:49:10,365 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:49:10,394 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,422 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,427 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,451 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,545 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,552 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,585 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,607 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,676 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,684 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013268/2013.268.00 done. INFO 2025-06-26 19:49:10,684 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:49:10,685 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.268.00_1S_Gulper.txt INFO 2025-06-26 19:49:10,690 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.268.00/dorado_2013.268.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:49:10,690 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.268.00/dorado_2013.268.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf