INFO 2025-06-26 18:11:19,964 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 18:11:19,964 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission - first of Sept 2011 CANON aborted due to software - ctdToUse = ctd1 INFO 2025-06-26 18:11:19,964 process.py process_mission():449 [1] Processing CANON September 2011 mission 2011.249.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:11:19,965 process.py download_process():165 [1] Download and processing steps for 2011.249.00 INFO 2025-06-26 18:11:19,965 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011249/2011.249.00 INFO 2025-06-26 18:11:19,965 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011249/2011.249.00 to /data/auv_data/dorado/missionlogs/2011.249.00 INFO 2025-06-26 18:11:23,736 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.249.00 INFO 2025-06-26 18:11:23,736 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/ctdDriver.log (7038054 bytes) INFO 2025-06-26 18:11:24,246 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/ctdDriver2.log (7038239 bytes) INFO 2025-06-26 18:11:24,786 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/gps.log (102884 bytes) INFO 2025-06-26 18:11:24,806 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/hydroscatlog.log (6165706 bytes) INFO 2025-06-26 18:11:25,505 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/navigation.log (24929206 bytes) INFO 2025-06-26 18:11:27,342 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/isuslog.log (582485 bytes) INFO 2025-06-26 18:11:27,402 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/parosci.log (7470182 bytes) INFO 2025-06-26 18:11:28,065 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/tailCone.log (4407307 bytes) INFO 2025-06-26 18:11:28,615 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/biolume.log (5130598 bytes) INFO 2025-06-26 18:11:29,119 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:11:29,389 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.65 seconds INFO 2025-06-26 18:11:29,389 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.249.00/lopc.bin (89358355 bytes) INFO 2025-06-26 18:11:29,389 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:11:29 2025 INFO 2025-06-26 18:11:29,390 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.249.00/parosci.nc INFO 2025-06-26 18:11:29,390 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:11:29,390 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.249.00/parosci.nc INFO 2025-06-26 18:11:29,393 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1315344520.0, sensor_off_time = 1315362883.2 INFO 2025-06-26 18:11:29,394 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 18363 seconds. Expecting to read 36726 L frames from the lopc.bin file. INFO 2025-06-26 18:11:29,394 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 36726 records from the lopc.bin file. INFO 2025-06-26 18:11:29,611 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-09-06 21:28:39 Z and endTime = 2011-09-07 02:34:43 Z with 36726 records expected to be read from lopc.bin INFO 2025-06-26 18:11:29,612 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.249.00/lopc.bin INFO 2025-06-26 18:11:29,612 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.249.00/lopc.nc INFO 2025-06-26 18:11:29,612 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.249.00/lopc.nc INFO 2025-06-26 18:11:29,613 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.249.00 INFO 2025-06-26 18:11:29,613 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 18:11:29,689 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 18:11:29,689 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 18:11:29,689 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 18:11:30,529 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:11:30,530 process.py calibrate():227 [1] Calibration steps for 2011.249.00 INFO 2025-06-26 18:11:30,704 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 18:11:30,706 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:11:33,841 calibrate.py _nudge_pos():1806 [1] 363: 0.010 0.0062739 -0.0046076 8760 29.20 31.862 -29.243 2011-09-06T22:03:53.174961408 INFO 2025-06-26 18:11:35,175 calibrate.py _nudge_pos():1806 [1] 504: 0.030 0.0067513 -0.0053425 9140 30.46 32.869 -32.497 2011-09-06T22:36:41.170144512 INFO 2025-06-26 18:11:35,233 calibrate.py _nudge_pos():1806 [1] 510: 0.030 -0.0000048 -0.0000121 15 0.05 -15.225 -48.055 2011-09-06T22:36:49.169596416 INFO 2025-06-26 18:11:35,272 calibrate.py _nudge_pos():1806 [1] 514: 0.030 -0.0000026 -0.0000845 35 0.11 -3.443 -138.211 2011-09-06T22:36:59.168911360 INFO 2025-06-26 18:11:36,365 calibrate.py _nudge_pos():1806 [1] 627: 0.020 0.0066845 -0.0056388 9085 30.28 32.748 -34.507 2011-09-06T23:09:08.176765440 INFO 2025-06-26 18:11:36,761 calibrate.py _nudge_pos():1806 [1] 668: 0.030 0.0000289 -0.0000141 15 0.05 91.884 -56.027 2011-09-06T23:09:51.173819904 INFO 2025-06-26 18:11:36,820 calibrate.py _nudge_pos():1806 [1] 674: 0.030 -0.0000032 -0.0000068 65 0.21 -2.247 -5.948 2011-09-06T23:10:09.172587008 INFO 2025-06-26 18:11:37,491 calibrate.py _nudge_pos():1806 [1] 744: 0.030 0.0072158 -0.0064227 9205 30.68 34.899 -38.792 2011-09-06T23:41:59.171742976 INFO 2025-06-26 18:11:38,558 calibrate.py _nudge_pos():1806 [1] 855: 0.030 -0.0000139 -0.0000275 15 0.05 -44.064 -109.031 2011-09-06T23:43:52.174001920 INFO 2025-06-26 18:11:38,664 calibrate.py _nudge_pos():1806 [1] 866: 0.040 0.0085357 -0.0082040 9525 31.75 39.906 -47.885 2011-09-07T00:15:47.172815360 INFO 2025-06-26 18:11:39,634 calibrate.py _nudge_pos():1806 [1] 965: 0.040 0.0063694 -0.0079277 9345 31.15 30.358 -47.164 2011-09-07T00:48:35.167998464 INFO 2025-06-26 18:11:40,038 calibrate.py _nudge_pos():1806 [1] 1006: 0.040 0.0000074 0.0000046 20 0.06 17.457 13.331 2011-09-07T00:49:19.174983680 INFO 2025-06-26 18:11:40,955 calibrate.py _nudge_pos():1806 [1] 1093: 0.040 0.0044063 -0.0063861 9530 31.76 20.598 -37.255 2011-09-07T01:22:31.168522752 INFO 2025-06-26 18:11:41,831 calibrate.py _nudge_pos():1806 [1] 1183: 0.040 -0.0000051 -0.0000138 15 0.05 -16.324 -54.763 2011-09-07T01:24:03.172220160 INFO 2025-06-26 18:11:41,974 calibrate.py _nudge_pos():1806 [1] 1198: 0.040 0.0014716 -0.0053542 9120 30.40 7.189 -32.640 2011-09-07T01:54:41.176308480 INFO 2025-06-26 18:11:41,985 calibrate.py _nudge_pos():1806 [1] 1199: 0.050 -0.0000054 -0.0000056 75 0.25 -3.227 -4.212 2011-09-07T01:54:56.175280896 INFO 2025-06-26 18:11:42,842 calibrate.py _nudge_pos():1806 [1] 1288: 0.040 -0.0000533 -0.0000212 55 0.18 -44.005 -21.819 2011-09-07T01:56:37.168362496 INFO 2025-06-26 18:11:42,958 calibrate.py _nudge_pos():1806 [1] 1300: 0.050 -0.0003486 -0.0045150 9225 30.75 -1.684 -27.210 2011-09-07T02:27:35.171080448 INFO 2025-06-26 18:11:44,065 calibrate.py _nudge_pos():1806 [1] 1414: 0.050 -0.0000672 0.0000203 25 0.08 -124.826 47.093 2011-09-07T02:29:33.172996864 INFO 2025-06-26 18:11:44,091 calibrate.py _nudge_pos():1862 [1] 1382: - - - 1535 5.11 - - INFO 2025-06-26 18:11:44,091 calibrate.py _nudge_pos():1868 [1] Points in final series = 91643 WARNING 2025-06-26 18:11:44,214 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:11:44,341 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 12 of 73389 INFO 2025-06-26 18:11:44,895 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:11:45,581 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 37 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:11:46,123 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 37 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:11:46,125 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.249.00/ctd1.nc INFO 2025-06-26 18:11:46,126 calibrate.py _range_qc_combined_nc():898 [1] Setting 15 ctd1_salinity values to NaN INFO 2025-06-26 18:11:46,127 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 18:11:46,127 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:11:46,774 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:11:47,330 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:11:47,332 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.249.00/ctd2.nc INFO 2025-06-26 18:11:47,333 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 18:11:47,334 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 18:11:47,334 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:11:47,368 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:11:48,212 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63] INFO 2025-06-26 18:11:48,400 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 18:12:05,037 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.249.00 ERROR 2025-06-26 18:12:05,038 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.249.00 INFO 2025-06-26 18:12:05,111 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_cal.nc INFO 2025-06-26 18:12:05,246 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 18:12:05,251 process.py align():251 [1] Alignment steps for 2011.249.00 INFO 2025-06-26 18:12:05,290 align.py process_cal():139 [1] Processing dorado_2011.249.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.249.00 INFO 2025-06-26 18:12:05,317 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:12:05,321 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:12:05,383 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:12:05,388 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:12:05,452 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:12:05,458 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:12:05,495 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:12:05,495 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:12:05,520 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:12:05,524 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:12:05,587 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,592 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,645 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,650 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,707 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,711 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,766 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,770 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,827 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,832 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,887 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,891 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:05,948 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:05,953 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,008 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,012 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,068 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,072 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,126 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,131 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,187 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,191 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,245 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,249 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,305 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,309 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,363 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,367 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,423 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,428 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,482 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,487 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,543 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,548 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,604 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,608 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,666 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,670 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,725 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,730 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,787 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,791 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,848 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:12:06,852 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:12:06,919 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:12:06,967 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:12:07,015 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:12:07,065 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:12:07,115 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:12:07,192 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 18:12:07,658 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:12:07,705 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_align.nc INFO 2025-06-26 18:12:07,844 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 18:12:07,847 process.py resample():273 [1] Resampling steps for 2011.249.00 INFO 2025-06-26 18:12:07,847 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:12:07,883 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_align.nc mission netCDF file INFO 2025-06-26 18:12:07,889 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_align.nc mission netCDF file INFO 2025-06-26 18:12:07,890 resample.py get_mission_start_end():1145 [1] navigation: 2011-09-06T21:29:14.787340544 to 2011-09-07T02:34:43.171760384 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:12:07,892 resample.py get_mission_start_end():1145 [1] hs2 : 2011-09-06T21:28:47.179232000 to 2011-09-07T02:34:42.981773312 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 18:12:07,893 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-09-06T21:29:17.207174912 to 2011-09-07T02:34:43.041769216 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 18:12:07,895 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-09-06T21:29:16.777204480 to 2011-09-07T02:34:43.101765120 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 18:12:07,896 resample.py get_mission_start_end():1145 [1] isus : 2011-09-06T21:30:01.764122368 to 2011-09-07T02:34:42.811784960 (0 days 00:00:00.359975424 before mission_end) INFO 2025-06-26 18:12:07,898 resample.py get_mission_start_end():1145 [1] biolume : 2011-09-06T21:28:39.709709312 to 2011-09-07T02:34:41.901812992 (0 days 00:00:01.269947392 before mission_end) INFO 2025-06-26 18:12:07,899 resample.py get_mission_start_end():1145 [1] tailcone : 2011-09-06T21:28:41.709606656 to 2011-09-07T02:34:43.161761024 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 18:12:07,900 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_align.nc mission netCDF file INFO 2025-06-26 18:12:07,900 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,105 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,142 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,178 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,214 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,246 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,276 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,306 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,335 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,363 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,393 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,422 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,450 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,477 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,505 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,532 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,560 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,587 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,616 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,645 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,673 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,702 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,731 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,760 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,789 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,805 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,820 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,834 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,847 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,861 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:08,865 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:12:08,866 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:12:09,543 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:12:09,674 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:12:09,740 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:12:09,770 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:12:09,794 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:12:09,794 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:12:09,835 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:12:10,052 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_1S.nc INFO 2025-06-26 18:12:13,492 create_products.py gulper_odv():401 [1] No gulper times found for 2011.249.00 INFO 2025-06-26 18:12:13,492 process.py archive():337 [1] Archiving steps for 2011.249.00 INFO 2025-06-26 18:12:13,492 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00, BASE_PATH = /data/auv_data INFO 2025-06-26 18:12:13,492 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:12:13,494 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.249.00_1S.nc INFO 2025-06-26 18:12:13,515 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:12:13,516 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.249.00_cal.nc INFO 2025-06-26 18:12:13,635 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:12:13,636 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.249.00_align.nc INFO 2025-06-26 18:12:13,806 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:12:13,830 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,851 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,855 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,875 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,946 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,953 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,975 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:13,994 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:14,042 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:14,050 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011249/2011.249.00 done. INFO 2025-06-26 18:12:14,050 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:12:14,050 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.249.00/dorado_2011.249.00_processing.log /Volumes/AUVCTD/surveys/2011/netcdf