INFO 2025-06-26 14:08:15,394 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 14:08:15,394 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Ryan - ESP inner northern shelf (something hit AUV just before midnight) - ctdToUse = ctd1 INFO 2025-06-26 14:08:15,394 process.py process_mission():449 [1] Processing AUVCTD mission 2008.161.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:08:15,394 process.py download_process():165 [1] Download and processing steps for 2008.161.02 INFO 2025-06-26 14:08:15,394 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008161/2008.161.02 INFO 2025-06-26 14:08:15,395 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008161/2008.161.02 to /data/auv_data/dorado/missionlogs/2008.161.02 INFO 2025-06-26 14:08:20,207 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.161.02 INFO 2025-06-26 14:08:20,208 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/ctdDriver.log (11215556 bytes) INFO 2025-06-26 14:08:21,015 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.161.02/ctdDriver.log: [46538] INFO 2025-06-26 14:08:21,048 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/ctdDriver2.log (11215373 bytes) INFO 2025-06-26 14:08:21,840 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.161.02/ctdDriver2.log: [56956] INFO 2025-06-26 14:08:21,881 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/gps.log (86468 bytes) INFO 2025-06-26 14:08:21,898 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/hydroscatlog.log (7652834 bytes) INFO 2025-06-26 14:08:22,871 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.161.02/hydroscatlog.log: [18504 18505] INFO 2025-06-26 14:08:22,895 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/navigation.log (37610030 bytes) INFO 2025-06-26 14:08:25,600 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/isuslog.log (795157 bytes) INFO 2025-06-26 14:08:25,677 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.161.02/isuslog.log: [ 1 2 3 4 5 6 7 8 10] INFO 2025-06-26 14:08:25,679 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/parosci.log (13414646 bytes) INFO 2025-06-26 14:08:26,822 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/tailCone.log (1545403 bytes) INFO 2025-06-26 14:08:27,021 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/biolume.log (8681564 bytes) INFO 2025-06-26 14:08:27,841 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:08:28,295 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.09 seconds INFO 2025-06-26 14:08:28,295 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.161.02/lopc.bin (22300579 bytes) INFO 2025-06-26 14:08:28,296 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:08:28 2025 INFO 2025-06-26 14:08:28,296 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.161.02/parosci.nc INFO 2025-06-26 14:08:28,296 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:08:28,296 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.161.02/parosci.nc INFO 2025-06-26 14:08:28,299 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1213048884.4, sensor_off_time = 1213080784.6 INFO 2025-06-26 14:08:28,299 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 31900 seconds. Expecting to read 63800 L frames from the lopc.bin file. INFO 2025-06-26 14:08:28,299 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 63800 records from the lopc.bin file. INFO 2025-06-26 14:08:28,675 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-06-09 22:01:24 Z and endTime = 2008-06-10 06:53:04 Z with 63800 records expected to be read from lopc.bin INFO 2025-06-26 14:08:28,675 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.161.02/lopc.bin INFO 2025-06-26 14:08:28,675 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.161.02/lopc.nc INFO 2025-06-26 14:08:28,676 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.161.02/lopc.nc INFO 2025-06-26 14:08:28,676 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.161.02 INFO 2025-06-26 14:08:28,676 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 14:08:28,697 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 14:08:28,698 process.py calibrate():227 [1] Calibration steps for 2008.161.02 INFO 2025-06-26 14:08:28,941 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 14:08:28,943 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:08:29,447 calibrate.py _nudge_pos():1806 [1] 76: 0.010 -0.0000621 -0.0000335 15 0.05 -197.522 -132.833 2008-06-09T22:02:40.857955840 INFO 2025-06-26 14:08:29,495 calibrate.py _nudge_pos():1806 [1] 81: 0.010 -0.0000333 0.0002606 6315 21.05 -0.234 2.294 2008-06-09T22:23:47.861160192 INFO 2025-06-26 14:08:30,256 calibrate.py _nudge_pos():1806 [1] 160: 0.010 0.0000583 -0.0001309 5430 18.10 0.478 -1.340 2008-06-09T22:43:11.851421696 INFO 2025-06-26 14:08:30,403 calibrate.py _nudge_pos():1806 [1] 175: 0.010 0.0000092 -0.0000092 20 0.06 21.531 -26.840 2008-06-09T22:43:29.860187648 INFO 2025-06-26 14:08:30,739 calibrate.py _nudge_pos():1806 [1] 210: 0.020 0.0000393 -0.0000296 2620 8.73 0.667 -0.629 2008-06-09T22:52:47.851962880 INFO 2025-06-26 14:08:31,162 calibrate.py _nudge_pos():1806 [1] 254: 0.010 0.0001325 0.0000850 4580 15.26 1.288 1.032 2008-06-09T23:08:47.856198144 INFO 2025-06-26 14:08:31,498 calibrate.py _nudge_pos():1806 [1] 289: 0.020 0.0000000 0.0000146 20 0.06 0.041 42.722 2008-06-09T23:09:25.853595136 INFO 2025-06-26 14:08:31,527 calibrate.py _nudge_pos():1806 [1] 292: 0.010 0.0000676 -0.0000379 2739 9.13 1.098 -0.769 2008-06-09T23:18:35.855917312 INFO 2025-06-26 14:08:31,827 calibrate.py _nudge_pos():1806 [1] 323: 0.020 0.0000144 -0.0001686 5280 17.60 0.121 -1.775 2008-06-09T23:36:41.851521536 INFO 2025-06-26 14:08:32,621 calibrate.py _nudge_pos():1806 [1] 405: 0.020 0.0002112 -0.0000653 9525 31.75 0.986 -0.381 2008-06-10T00:09:47.855470848 INFO 2025-06-26 14:08:33,022 calibrate.py _nudge_pos():1806 [1] 446: 0.020 0.0001985 -0.0000566 9545 31.81 0.925 -0.330 2008-06-10T00:42:17.851887104 INFO 2025-06-26 14:08:33,711 calibrate.py _nudge_pos():1806 [1] 517: 0.020 0.0001724 -0.0000442 9664 32.21 0.793 -0.254 2008-06-10T01:15:41.854603264 INFO 2025-06-26 14:08:34,234 calibrate.py _nudge_pos():1806 [1] 570: 0.020 0.0003541 0.0000113 9460 31.53 1.664 0.067 2008-06-10T01:48:05.851430400 INFO 2025-06-26 14:08:34,691 calibrate.py _nudge_pos():1806 [1] 617: 0.020 0.0000123 -0.0000106 15 0.05 38.906 -42.075 2008-06-10T01:48:54.858073344 INFO 2025-06-26 14:08:34,769 calibrate.py _nudge_pos():1806 [1] 625: 0.020 0.0001473 0.0001811 10550 35.16 0.621 0.955 2008-06-10T02:24:11.853049344 INFO 2025-06-26 14:08:35,112 calibrate.py _nudge_pos():1806 [1] 659: 0.020 -0.0000226 -0.0000651 6045 20.15 -0.166 -0.598 2008-06-10T02:44:53.857965824 INFO 2025-06-26 14:08:35,588 calibrate.py _nudge_pos():1806 [1] 706: 0.020 0.0010022 -0.0000128 2290 7.63 19.457 -0.311 2008-06-10T02:53:17.853440000 INFO 2025-06-26 14:08:35,598 calibrate.py _nudge_pos():1806 [1] 707: 0.020 -0.0000230 0.0000017 50 0.16 -20.882 1.974 2008-06-10T02:53:27.852754944 INFO 2025-06-26 14:08:35,981 calibrate.py _nudge_pos():1806 [1] 745: 0.020 0.0001469 0.0000160 4955 16.51 1.318 0.179 2008-06-10T03:10:35.852332032 INFO 2025-06-26 14:08:36,023 calibrate.py _nudge_pos():1806 [1] 749: 0.010 0.0000141 0.0000322 70 0.23 9.099 25.893 2008-06-10T03:10:52.861166848 INFO 2025-06-26 14:08:36,457 calibrate.py _nudge_pos():1806 [1] 792: 0.020 0.0008977 0.0000177 2285 7.61 17.467 0.431 2008-06-10T03:19:11.856983296 INFO 2025-06-26 14:08:36,926 calibrate.py _nudge_pos():1806 [1] 838: 0.020 0.0000333 0.0001380 4545 15.15 0.325 1.689 2008-06-10T03:35:05.851630336 INFO 2025-06-26 14:08:37,346 calibrate.py _nudge_pos():1806 [1] 879: 0.020 0.0031155 0.0015541 9940 33.13 13.934 8.692 2008-06-10T04:08:53.852702976 INFO 2025-06-26 14:08:38,081 calibrate.py _nudge_pos():1806 [1] 951: 0.020 0.0043470 0.0017032 12515 41.71 15.446 7.566 2008-06-10T04:51:47.856371456 INFO 2025-06-26 14:08:38,507 calibrate.py _nudge_pos():1806 [1] 993: 0.020 0.0044083 0.0017591 13415 44.71 14.618 7.290 2008-06-10T05:37:11.859764224 INFO 2025-06-26 14:08:39,099 calibrate.py _nudge_pos():1806 [1] 1050: 0.020 0.0041427 0.0018558 13100 43.66 14.071 7.876 2008-06-10T06:21:47.856445952 INFO 2025-06-26 14:08:39,428 calibrate.py _nudge_pos():1806 [1] 1082: 0.020 -0.0000093 0.0000077 20 0.06 -21.838 22.637 2008-06-10T06:22:22.854048512 INFO 2025-06-26 14:08:39,510 calibrate.py _nudge_pos():1806 [1] 1090: 0.030 0.0013464 0.0004249 3780 12.60 15.854 6.251 2008-06-10T06:35:05.851779584 INFO 2025-06-26 14:08:40,068 calibrate.py _nudge_pos():1806 [1] 1143: 0.030 0.0001001 -0.0002099 4870 16.23 0.914 -2.397 2008-06-10T06:52:11.851493888 INFO 2025-06-26 14:08:40,545 calibrate.py _nudge_pos():1862 [1] 1159: - - - 39 0.13 - - INFO 2025-06-26 14:08:40,546 calibrate.py _nudge_pos():1868 [1] Points in final series = 159344 WARNING 2025-06-26 14:08:40,766 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 14:08:56,879 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 11 of 127530 INFO 2025-06-26 14:08:57,861 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 0 seconds, d_end_time_diff: -3 seconds INFO 2025-06-26 14:09:06,951 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -3 seconds INFO 2025-06-26 14:09:07,922 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -3 seconds INFO 2025-06-26 14:09:07,925 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.161.02/ctd1.nc INFO 2025-06-26 14:09:07,926 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:09:07,926 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 14:09:07,926 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:09:14,980 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: -3 seconds INFO 2025-06-26 14:09:15,981 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: -3 seconds INFO 2025-06-26 14:09:15,983 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.161.02/ctd2.nc INFO 2025-06-26 14:09:15,985 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 14:09:15,985 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 14:09:15,985 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:09:17,192 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:09:18,636 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 9840 27600 72420 72421 72422 94620 114300 114301 114302 124080 124081 138000 161460 161461 161462 161463 171180 171181 171182 186000 186001 186002 201780 203040 204300 205560 315480 315481 403560 403561 403562 403563 413520 413521 413522 413523 705600 705601 842160 842161 842162 842163 876600 878580 882840 1104660 1108980 1453740 1453741 1611660 1611661 1667160 1712340] INFO 2025-06-26 14:09:18,916 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -3 seconds ERROR 2025-06-26 14:09:18,922 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 14:09:18,922 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2008.161.02 ERROR 2025-06-26 14:09:18,922 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.161.02 INFO 2025-06-26 14:09:18,950 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_cal.nc INFO 2025-06-26 14:09:28,748 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, 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 14:09:28,753 process.py align():251 [1] Alignment steps for 2008.161.02 INFO 2025-06-26 14:09:28,783 align.py process_cal():139 [1] Processing dorado_2008.161.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.161.02 INFO 2025-06-26 14:09:28,826 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:09:28,831 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:09:28,931 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:09:28,938 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:09:29,036 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:09:29,043 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:09:29,106 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:09:29,106 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:09:29,146 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:09:29,152 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:09:29,251 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,257 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,344 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,350 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,441 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,446 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,538 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,629 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,635 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,721 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,727 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,816 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,821 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:29,908 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:29,914 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,003 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,009 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,096 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,102 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,189 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,195 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,280 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,286 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,372 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,377 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,464 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,470 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,559 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,565 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,652 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,658 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,749 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,755 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,843 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,850 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:30,937 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:30,943 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:31,033 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.161.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:09:31,039 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:09:31,146 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:09:31,216 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:09:31,288 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:09:31,362 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:09:31,436 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:09:31,460 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_align.nc INFO 2025-06-26 14:09:31,552 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, 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 14:09:31,555 process.py resample():273 [1] Resampling steps for 2008.161.02 INFO 2025-06-26 14:09:31,555 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:09:31,581 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_align.nc mission netCDF file INFO 2025-06-26 14:09:31,587 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_align.nc mission netCDF file INFO 2025-06-26 14:09:31,589 resample.py get_mission_start_end():1145 [1] navigation: 2008-06-09T22:01:52.751251456 to 2008-06-10T06:53:04.657876480 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:09:31,591 resample.py get_mission_start_end():1145 [1] hs2 : 2008-06-09T22:01:25.163141376 to 2008-06-10T06:53:02.368033280 (0 days 00:00:02.289843200 before mission_end) INFO 2025-06-26 14:09:31,592 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-06-09T22:01:47.171633664 to 2008-06-10T06:53:02.218043648 (0 days 00:00:02.439832832 before mission_end) INFO 2025-06-26 14:09:31,594 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-06-09T22:01:47.151635200 to 2008-06-10T06:53:02.398031360 (0 days 00:00:02.259845120 before mission_end) INFO 2025-06-26 14:09:31,596 resample.py get_mission_start_end():1145 [1] isus : 2008-06-09T22:02:20.579345152 to 2008-06-10T06:53:02.028056576 (0 days 00:00:02.629819904 before mission_end) INFO 2025-06-26 14:09:31,597 resample.py get_mission_start_end():1145 [1] biolume : 2008-06-09T22:01:19.023527936 to 2008-06-10T06:53:01.478060032 (0 days 00:00:03.179816448 before mission_end) INFO 2025-06-26 14:09:31,598 resample.py get_mission_start_end():1145 [1] tailcone : 2008-06-09T22:01:24.023219712 to 2008-06-10T06:53:04.217906432 (0 days 00:00:00.439970048 before mission_end) INFO 2025-06-26 14:09:31,599 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_align.nc mission netCDF file INFO 2025-06-26 14:09:31,599 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:31,935 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:31,991 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,046 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,101 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,148 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,195 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,241 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,287 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,330 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,372 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,416 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,459 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,502 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,545 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,588 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,631 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,677 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,722 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,766 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,809 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,853 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,899 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,920 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,939 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,956 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,976 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:32,996 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:09:33,266 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_1S.nc INFO 2025-06-26 14:09:35,949 create_products.py gulper_odv():401 [1] No gulper times found for 2008.161.02 INFO 2025-06-26 14:09:35,949 process.py archive():337 [1] Archiving steps for 2008.161.02 INFO 2025-06-26 14:09:35,949 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02, BASE_PATH = /data/auv_data INFO 2025-06-26 14:09:35,951 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:09:35,953 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.161.02_1S.nc INFO 2025-06-26 14:09:35,979 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:09:35,980 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.161.02_cal.nc INFO 2025-06-26 14:09:36,111 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:09:36,113 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.161.02_align.nc INFO 2025-06-26 14:09:36,223 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:09:36,256 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,289 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,294 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,318 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,428 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,436 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,473 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,483 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,578 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008161/2008.161.02 done. INFO 2025-06-26 14:09:36,578 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:09:36,578 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.161.02/dorado_2008.161.02_processing.log /Volumes/AUVCTD/surveys/2008/netcdf