INFO 2025-06-26 14:15:10,475 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 14:15:10,475 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Rob McEwen's software with gulper trigger at 2e-3 Chlor - ctdToUse = ctd1 INFO 2025-06-26 14:15:10,476 process.py process_mission():449 [1] Processing AUVCTD mission 2008.281.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:15:10,476 process.py download_process():165 [1] Download and processing steps for 2008.281.03 INFO 2025-06-26 14:15:10,476 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008281/2008.281.03 INFO 2025-06-26 14:15:10,476 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008281/2008.281.03 to /data/auv_data/dorado/missionlogs/2008.281.03 INFO 2025-06-26 14:15:13,652 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.281.03 INFO 2025-06-26 14:15:13,652 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/ctdDriver.log (5937404 bytes) INFO 2025-06-26 14:15:14,112 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/ctdDriver2.log (5937397 bytes) INFO 2025-06-26 14:15:14,543 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.281.03/ctdDriver2.log: [22084] INFO 2025-06-26 14:15:14,565 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/gps.log (60980 bytes) INFO 2025-06-26 14:15:14,580 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/hydroscatlog.log (5679178 bytes) INFO 2025-06-26 14:15:15,180 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/navigation.log (19922774 bytes) INFO 2025-06-26 14:15:16,632 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/isuslog.log (395669 bytes) INFO 2025-06-26 14:15:16,672 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.281.03/isuslog.log: [1 2 3 4 5 6 7 8] INFO 2025-06-26 14:15:16,674 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/parosci.log (7049846 bytes) INFO 2025-06-26 14:15:17,287 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/tailCone.log (820891 bytes) INFO 2025-06-26 14:15:17,396 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.74 seconds INFO 2025-06-26 14:15:17,396 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.281.03/lopc.bin (12085413 bytes) INFO 2025-06-26 14:15:17,396 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:15:17 2025 INFO 2025-06-26 14:15:17,396 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.281.03/parosci.nc INFO 2025-06-26 14:15:17,397 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:15:17,397 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.281.03/parosci.nc INFO 2025-06-26 14:15:17,400 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1223392257.5, sensor_off_time = 1223409168.1 INFO 2025-06-26 14:15:17,400 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 16910 seconds. Expecting to read 33820 L frames from the lopc.bin file. INFO 2025-06-26 14:15:17,400 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 33820 records from the lopc.bin file. INFO 2025-06-26 14:15:17,598 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-10-07 15:10:57 Z and endTime = 2008-10-07 19:52:48 Z with 33820 records expected to be read from lopc.bin INFO 2025-06-26 14:15:17,598 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.281.03/lopc.bin INFO 2025-06-26 14:15:17,598 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.281.03/lopc.nc INFO 2025-06-26 14:15:17,599 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.281.03/lopc.nc INFO 2025-06-26 14:15:17,599 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.281.03 INFO 2025-06-26 14:15:17,599 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:15:17,677 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:15:17,677 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:15:17,677 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:15:17,808 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 14:15:17,808 process.py calibrate():227 [1] Calibration steps for 2008.281.03 INFO 2025-06-26 14:15:17,954 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 14:15:17,956 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:15:18,697 calibrate.py _nudge_pos():1806 [1] 104: 0.090 -0.0025937 0.0001080 2795 9.31 -41.307 2.148 2008-10-07T15:21:54.149792000 INFO 2025-06-26 14:15:18,961 calibrate.py _nudge_pos():1806 [1] 132: 0.090 0.0000650 0.0000422 105 0.35 27.807 22.551 2008-10-07T15:22:42.146503936 INFO 2025-06-26 14:15:18,999 calibrate.py _nudge_pos():1806 [1] 136: 0.090 0.0000436 0.0000463 75 0.25 26.194 34.771 2008-10-07T15:23:00.145271040 INFO 2025-06-26 14:15:19,330 calibrate.py _nudge_pos():1806 [1] 171: 0.110 -0.0003228 0.0001281 4954 16.51 -2.900 1.437 2008-10-07T15:40:06.144985088 INFO 2025-06-26 14:15:19,436 calibrate.py _nudge_pos():1806 [1] 182: 0.110 0.0000310 0.0000131 70 0.23 19.985 10.525 2008-10-07T15:40:30.143341312 INFO 2025-06-26 14:15:19,613 calibrate.py _nudge_pos():1806 [1] 201: 0.100 -0.0000110 0.0000748 60 0.20 -8.328 70.449 2008-10-07T15:41:00.151285504 INFO 2025-06-26 14:15:19,660 calibrate.py _nudge_pos():1806 [1] 206: 0.090 -0.0000491 0.0000365 2140 7.13 -1.021 0.947 2008-10-07T15:48:12.151691520 INFO 2025-06-26 14:15:20,016 calibrate.py _nudge_pos():1806 [1] 244: 0.100 0.0000512 0.0003645 3955 13.18 0.576 5.124 2008-10-07T16:02:00.144969984 INFO 2025-06-26 14:15:20,196 calibrate.py _nudge_pos():1806 [1] 263: 0.100 0.0000716 -0.0000140 60 0.20 53.997 -13.163 2008-10-07T16:02:30.142915072 INFO 2025-06-26 14:15:20,384 calibrate.py _nudge_pos():1806 [1] 283: 0.100 -0.0000710 -0.0000113 2095 6.98 -1.509 -0.300 2008-10-07T16:09:48.142909952 INFO 2025-06-26 14:15:20,837 calibrate.py _nudge_pos():1806 [1] 331: 0.100 0.0000370 -0.0000096 4295 14.31 0.383 -0.124 2008-10-07T16:24:54.150844160 INFO 2025-06-26 14:15:21,236 calibrate.py _nudge_pos():1806 [1] 373: 0.100 0.0000202 -0.0000567 9215 30.71 0.098 -0.342 2008-10-07T16:56:18.151781376 INFO 2025-06-26 14:15:21,698 calibrate.py _nudge_pos():1806 [1] 422: 0.100 0.0000885 -0.0000356 9207 30.70 0.427 -0.215 2008-10-07T17:27:48.152307200 INFO 2025-06-26 14:15:22,039 calibrate.py _nudge_pos():1806 [1] 458: 0.120 0.0001711 -0.0000411 9515 31.71 0.800 -0.240 2008-10-07T18:00:06.149545472 INFO 2025-06-26 14:15:22,537 calibrate.py _nudge_pos():1806 [1] 510: 0.120 0.0002156 0.0000741 9255 30.85 1.035 0.445 2008-10-07T18:31:48.149249536 INFO 2025-06-26 14:15:22,625 calibrate.py _nudge_pos():1806 [1] 519: 0.130 0.0000104 -0.0000092 55 0.18 8.570 -9.488 2008-10-07T18:32:07.147948032 INFO 2025-06-26 14:15:22,826 calibrate.py _nudge_pos():1806 [1] 540: 0.130 0.0000009 0.0000175 20 0.06 2.025 51.076 2008-10-07T18:32:31.146304256 INFO 2025-06-26 14:15:23,084 calibrate.py _nudge_pos():1806 [1] 567: 0.140 0.0000710 -0.0000312 5835 19.45 0.541 -0.298 2008-10-07T18:52:24.144578048 INFO 2025-06-26 14:15:23,537 calibrate.py _nudge_pos():1806 [1] 614: 0.140 -0.0000027 0.0002841 4270 14.23 -0.029 3.700 2008-10-07T19:07:24.142924032 INFO 2025-06-26 14:15:23,871 calibrate.py _nudge_pos():1806 [1] 649: 0.130 0.0010502 0.0000792 2319 7.73 20.134 1.900 2008-10-07T19:15:42.148808192 INFO 2025-06-26 14:15:24,300 calibrate.py _nudge_pos():1806 [1] 693: 0.140 0.0000934 0.0000337 4555 15.18 0.911 0.412 2008-10-07T19:31:36.143454976 INFO 2025-06-26 14:15:24,773 calibrate.py _nudge_pos():1806 [1] 742: 0.130 0.0009990 0.0000636 2070 6.90 21.458 1.708 2008-10-07T19:39:18.151805440 INFO 2025-06-26 14:15:25,151 calibrate.py _nudge_pos():1806 [1] 781: 0.140 0.0000455 0.0001516 3585 11.95 0.564 2.351 2008-10-07T19:51:54.150016000 INFO 2025-06-26 14:15:25,670 calibrate.py _nudge_pos():1862 [1] 802: - - - 4 0.01 - - INFO 2025-06-26 14:15:25,670 calibrate.py _nudge_pos():1868 [1] Points in final series = 84409 INFO 2025-06-26 14:15:25,783 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=30) for self.args.mission=2008.281.03 INFO 2025-06-26 14:15:25,786 calibrate.py _depth_process():2175 [1] Setting 30 depths values to NaN WARNING 2025-06-26 14:15:25,789 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:15:25,911 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 67597 INFO 2025-06-26 14:15:26,419 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:15:27,051 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:15:27,549 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:15:27,551 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.281.03/ctd1.nc INFO 2025-06-26 14:15:27,552 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:15:27,552 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 14:15:27,552 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:15:31,287 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:15:31,799 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:15:31,801 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.281.03/ctd2.nc INFO 2025-06-26 14:15:31,802 calibrate.py _range_qc_combined_nc():898 [1] Setting 119 ctd2_salinity values to NaN INFO 2025-06-26 14:15:31,803 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 14:15:31,803 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 14:15:32,389 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.281.03 ERROR 2025-06-26 14:15:32,390 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2008.281.03 ERROR 2025-06-26 14:15:32,391 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.281.03 INFO 2025-06-26 14:15:32,484 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_cal.nc INFO 2025-06-26 14:15:34,627 calibrate.py write_netcdf():3512 [1] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 14:15:34,632 process.py align():251 [1] Alignment steps for 2008.281.03 INFO 2025-06-26 14:15:34,657 align.py process_cal():139 [1] Processing dorado_2008.281.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.281.03 INFO 2025-06-26 14:15:34,683 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:15:34,686 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:15:34,745 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:15:34,749 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:15:34,807 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:15:34,811 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:15:34,846 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:15:34,846 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:15:34,869 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:15:34,873 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:15:34,930 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:34,934 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:15:34,985 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:34,989 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:15:35,042 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,047 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:15:35,099 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,103 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,156 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,161 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,211 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,215 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,267 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,271 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,322 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,326 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,378 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,382 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,434 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,438 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,490 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,494 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,545 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,550 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,602 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,605 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,656 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,660 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,712 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,716 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,768 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,772 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,825 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,830 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,882 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,886 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,939 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,944 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:35,995 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.281.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:15:35,999 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 14:15:36,063 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:15:36,107 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:15:36,150 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:15:36,194 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:15:36,211 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_align.nc INFO 2025-06-26 14:15:36,277 align.py write_netcdf():342 [1] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 14:15:36,279 process.py resample():273 [1] Resampling steps for 2008.281.03 INFO 2025-06-26 14:15:36,280 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:15:36,301 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_align.nc mission netCDF file INFO 2025-06-26 14:15:36,306 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_align.nc mission netCDF file INFO 2025-06-26 14:15:36,307 resample.py get_mission_start_end():1145 [1] navigation: 2008-10-07T15:11:25.272872960 to 2008-10-07T19:52:47.946330624 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 14:15:36,309 resample.py get_mission_start_end():1145 [1] hs2 : 2008-10-07T15:11:01.284516352 to 2008-10-07T19:52:47.966329344 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:15:36,311 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-10-07T15:11:20.233218304 to 2008-10-07T19:52:47.896334080 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 14:15:36,312 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-10-07T15:11:20.013233408 to 2008-10-07T19:52:47.906333440 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 14:15:36,314 resample.py get_mission_start_end():1145 [1] isus : 2008-10-07T15:11:53.620931072 to 2008-10-07T19:52:46.946399232 (0 days 00:00:01.019930112 before mission_end) INFO 2025-06-26 14:15:36,315 resample.py get_mission_start_end():1145 [1] tailcone : 2008-10-07T15:10:56.614836224 to 2008-10-07T19:52:47.916332800 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 14:15:36,316 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_align.nc mission netCDF file INFO 2025-06-26 14:15:36,316 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,513 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,548 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,581 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,619 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,649 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,678 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,706 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,733 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,761 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,787 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,814 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,840 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,866 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,893 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,919 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,946 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:36,976 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,004 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,034 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,062 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,090 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,118 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,133 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,147 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,159 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,173 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:15:37,360 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_1S.nc INFO 2025-06-26 14:15:39,133 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 14:15:49,479 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.281.03/dorado_2008.281.03_1S_Gulper.txt INFO 2025-06-26 14:15:49,480 process.py archive():337 [1] Archiving steps for 2008.281.03 INFO 2025-06-26 14:15:49,480 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03, BASE_PATH = /data/auv_data INFO 2025-06-26 14:15:49,480 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:15:49,481 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.281.03_1S.nc INFO 2025-06-26 14:15:49,496 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:15:49,497 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.281.03_cal.nc INFO 2025-06-26 14:15:49,567 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:15:49,569 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.281.03_align.nc INFO 2025-06-26 14:15:49,627 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:15:49,647 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,668 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,672 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,689 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,744 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,751 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,772 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,780 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,786 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008281/2008.281.03 done. INFO 2025-06-26 14:15:49,786 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:15:49,787 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.281.03_1S_Gulper.txt INFO 2025-06-26 14:15:49,792 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.281.03/dorado_2008.281.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 14:15:49,792 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.281.03/dorado_2008.281.03_processing.log /Volumes/AUVCTD/surveys/2008/netcdf