INFO 2025-06-26 11:38:49,129 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 11:38:49,129 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - as part of MB06 - Chavez survey for MB06 to fill in spots where glider's aren't going - ctdToUse = ctd1 INFO 2025-06-26 11:38:49,129 process.py process_mission():449 [1] Processing AUVCTD mission 2006.221.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:38:49,129 process.py download_process():165 [1] Download and processing steps for 2006.221.00 INFO 2025-06-26 11:38:49,129 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006221/2006.221.00 INFO 2025-06-26 11:38:49,130 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006221/2006.221.00 to /data/auv_data/dorado/missionlogs/2006.221.00 INFO 2025-06-26 11:38:55,812 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.221.00 INFO 2025-06-26 11:38:55,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/ctdDriver.log (23184435 bytes) INFO 2025-06-26 11:38:58,369 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.221.00/ctdDriver.log: [ 435 910 1959 2422 3010 3683 8224 15091 18499 20057 31485 33844 53510 73909 109384 124819 137179 139135 141080 150952 159150 164884 174644 185781 208137 220795 234600 262615] INFO 2025-06-26 11:38:58,447 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/ctdDriver2.log (23183197 bytes) INFO 2025-06-26 11:39:00,280 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.221.00/ctdDriver2.log: [ 1075 3012 3685 4596 6971 11260 16001 20059 25090 53506 54752 73896 73975 77823 114691 137169 141069 150774 150941 159137 174632 185769 203994 208125 220783 234586 255809 262601] INFO 2025-06-26 11:39:00,366 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/gps.log (76532 bytes) INFO 2025-06-26 11:39:00,382 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/hydroscatlog.log (15814874 bytes) INFO 2025-06-26 11:39:02,485 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.221.00/hydroscatlog.log: [ 782 2481 2720 4264 5768 7072 18601 19393 20159 35294 46743 49508 64977 74892 92328 109008 109009 110742 118941 120588 122313 134572 135342 135343 137905 163228 174367 182261 204131 212238 212665 236487 241406 256408 260323] INFO 2025-06-26 11:39:02,548 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/navigation.log (77747966 bytes) INFO 2025-06-26 11:39:10,369 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/isuslog.log (1584245 bytes) INFO 2025-06-26 11:39:10,527 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/parosci.log (33866918 bytes) INFO 2025-06-26 11:39:13,265 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.221.00/parosci.log: [ 16 31 84 1381 1998 2314 2319 2748 4112 4944 7310 8482 8483 9232 9244 9885 11434 12706 13180 13840 14703 15457 18610 19749 20752 31049 31120 37880 39839 44381 63966 63968 64128 69989 75385 100634 123613 126701 132300 132411 146747 151421 157371 168681 168682 186828 201061 201062 208457 226915 227470 227471 228237 242864 265531 283082 288444 296272 303620 341702 375824 376645 376647 377807 379768 417835 419516 419517 436864 442295 496557 506896 506897 508665 552316 565900 569335 570182 591632 613287 657591 696882 696883] INFO 2025-06-26 11:39:13,358 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/tailCone.log (15807488 bytes) WARNING 2025-06-26 11:39:14,801 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 4 bytes, b = b'\xff' at record 329311, for rudderAngle in file /data/auv_data/dorado/missionlogs/2006.221.00/tailCone.log INFO 2025-06-26 11:39:14,801 logs2netcdfs.py _read_data():224 [1] bytes read = 15807491 file size = 15807488 INFO 2025-06-26 11:39:14,801 logs2netcdfs.py _read_data():229 [1] Tried to read 4 bytes, but only 3 bytes remaining INFO 2025-06-26 11:39:14,801 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 329311 records WARNING 2025-06-26 11:39:14,950 logs2netcdfs.py _create_variable():536 [1] propPwm: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (329312,) and arg 1 with shape (329311,). INFO 2025-06-26 11:39:14,950 logs2netcdfs.py _create_variable():537 [1] len(data) (329311) does not match shape of propPwm.shape[0] (329312) WARNING 2025-06-26 11:39:14,950 logs2netcdfs.py _create_variable():544 [1] propPwm data is short by one, appending the last value: 0 WARNING 2025-06-26 11:39:14,971 logs2netcdfs.py _create_variable():536 [1] propTemp: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (329312,) and arg 1 with shape (329311,). INFO 2025-06-26 11:39:14,971 logs2netcdfs.py _create_variable():537 [1] len(data) (329311) does not match shape of propTemp.shape[0] (329312) WARNING 2025-06-26 11:39:14,971 logs2netcdfs.py _create_variable():544 [1] propTemp data is short by one, appending the last value: 0 INFO 2025-06-26 11:39:15,393 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.221.00/biolume.log (17937180 bytes) INFO 2025-06-26 11:39:17,108 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:39:18,012 logs2netcdfs.py download_process_logs():807 [1] Time to process: 22.20 seconds WARNING 2025-06-26 11:39:18,012 process.py download_process():196 [1] No lopc.bin file for 2006.221.00 INFO 2025-06-26 11:39:18,012 process.py calibrate():227 [1] Calibration steps for 2006.221.00 INFO 2025-06-26 11:39:18,464 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 11:39:18,466 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:39:19,037 calibrate.py _nudge_pos():1806 [1] 71: 0.100 -0.0015386 -0.0002970 4068 13.61 -16.690 -4.042 2006-08-09T22:41:47.261452800 INFO 2025-06-26 11:39:19,492 calibrate.py _nudge_pos():1806 [1] 116: 0.100 -0.0028242 0.0020993 13063 43.56 -9.576 8.929 2006-08-09T23:26:05.269366784 INFO 2025-06-26 11:39:19,939 calibrate.py _nudge_pos():1806 [1] 159: 0.110 -0.0035595 0.0021213 13490 44.98 -11.692 8.739 2006-08-10T00:11:47.261527296 INFO 2025-06-26 11:39:20,392 calibrate.py _nudge_pos():1806 [1] 203: 0.120 -0.0036930 0.0021920 13370 44.58 -12.243 9.111 2006-08-10T00:57:05.265331200 INFO 2025-06-26 11:39:20,891 calibrate.py _nudge_pos():1806 [1] 251: 0.110 -0.0037528 0.0022438 12752 42.51 -13.049 9.780 2006-08-10T01:40:23.267355904 INFO 2025-06-26 11:39:20,925 calibrate.py _nudge_pos():1806 [1] 254: 0.100 0.0000052 -0.0000063 15 0.05 16.518 -24.854 2006-08-10T01:40:28.267013632 INFO 2025-06-26 11:39:21,316 calibrate.py _nudge_pos():1806 [1] 290: 0.110 0.0000114 -0.0000275 20 0.06 26.546 -80.600 2006-08-10T01:41:09.264205056 INFO 2025-06-26 11:39:21,347 calibrate.py _nudge_pos():1806 [1] 293: 0.110 -0.0028533 0.0018968 10769 35.90 -11.753 9.791 2006-08-10T02:17:05.266508544 INFO 2025-06-26 11:39:21,665 calibrate.py _nudge_pos():1806 [1] 324: 0.120 -0.0030243 -0.0002573 16793 56.00 -7.989 -0.851 2006-08-10T03:13:35.264278016 INFO 2025-06-26 11:39:21,985 calibrate.py _nudge_pos():1806 [1] 355: 0.130 -0.0022931 0.0003988 15290 50.98 -6.656 1.449 2006-08-10T04:05:04.262667008 INFO 2025-06-26 11:39:22,397 calibrate.py _nudge_pos():1806 [1] 394: 0.120 -0.0001829 0.0006704 8611 28.71 -0.943 4.327 2006-08-10T04:34:25.262030336 INFO 2025-06-26 11:39:22,761 calibrate.py _nudge_pos():1806 [1] 428: 0.110 -0.0000296 0.0000023 15 0.05 -94.015 9.025 2006-08-10T04:35:01.269563648 INFO 2025-06-26 11:39:22,772 calibrate.py _nudge_pos():1806 [1] 429: 0.130 -0.0006525 0.0000685 11359 37.86 -2.551 0.335 2006-08-10T05:12:53.263921152 INFO 2025-06-26 11:39:22,794 calibrate.py _nudge_pos():1806 [1] 431: 0.120 0.0000840 -0.0000777 35 0.11 109.768 -127.097 2006-08-10T05:13:01.263373312 INFO 2025-06-26 11:39:23,008 calibrate.py _nudge_pos():1806 [1] 451: 0.120 0.0043811 -0.0007634 14530 48.45 13.391 -2.920 2006-08-10T06:01:47.262928640 INFO 2025-06-26 11:39:23,053 calibrate.py _nudge_pos():1806 [1] 455: 0.130 0.0000563 -0.0000301 50 0.16 51.026 -34.130 2006-08-10T06:02:00.262038272 INFO 2025-06-26 11:39:23,354 calibrate.py _nudge_pos():1806 [1] 483: 0.110 -0.0000554 0.0000012 20 0.06 -129.531 3.462 2006-08-10T06:02:31.269913856 INFO 2025-06-26 11:39:23,376 calibrate.py _nudge_pos():1806 [1] 485: 0.120 0.0031871 -0.0008610 12162 40.55 11.643 -3.935 2006-08-10T06:43:05.263174144 INFO 2025-06-26 11:39:23,703 calibrate.py _nudge_pos():1806 [1] 515: 0.130 -0.0000494 -0.0000314 20 0.06 -115.442 -91.977 2006-08-10T06:43:38.260913664 INFO 2025-06-26 11:39:23,736 calibrate.py _nudge_pos():1806 [1] 518: 0.150 0.0048432 -0.0008864 15211 50.71 14.150 -3.239 2006-08-10T07:34:23.262316800 INFO 2025-06-26 11:39:24,056 calibrate.py _nudge_pos():1806 [1] 548: 0.130 0.0037075 -0.0011305 12291 40.98 13.408 -5.112 2006-08-10T08:15:52.261808384 INFO 2025-06-26 11:39:24,398 calibrate.py _nudge_pos():1806 [1] 580: 0.120 0.0044178 -0.0013956 11818 39.40 16.623 -6.564 2006-08-10T08:55:47.267739392 INFO 2025-06-26 11:39:24,749 calibrate.py _nudge_pos():1806 [1] 613: 0.160 0.0061032 -0.0017977 13668 45.56 19.862 -7.311 2006-08-10T09:41:53.268255232 INFO 2025-06-26 11:39:25,121 calibrate.py _nudge_pos():1806 [1] 647: 0.160 0.0058556 -0.0018904 12041 40.15 21.633 -8.725 2006-08-10T10:22:35.260967168 INFO 2025-06-26 11:39:25,502 calibrate.py _nudge_pos():1806 [1] 682: 0.130 0.0058279 -0.0025661 12099 40.33 21.439 -11.790 2006-08-10T11:03:29.262856704 INFO 2025-06-26 11:39:25,810 calibrate.py _nudge_pos():1806 [1] 710: 0.120 0.0024595 -0.0020817 6222 20.75 17.591 -18.593 2006-08-10T11:24:41.265718528 INFO 2025-06-26 11:39:26,109 calibrate.py _nudge_pos():1806 [1] 737: 0.140 -0.0000224 0.0000147 20 0.06 -52.370 43.074 2006-08-10T11:25:11.263663616 INFO 2025-06-26 11:39:26,132 calibrate.py _nudge_pos():1806 [1] 739: 0.130 0.0026787 -0.0024727 6825 22.76 17.464 -20.128 2006-08-10T11:47:58.270017024 INFO 2025-06-26 11:39:26,593 calibrate.py _nudge_pos():1806 [1] 781: 0.150 0.0046861 -0.0019066 17827 59.43 11.698 -5.945 2006-08-10T12:48:05.262921216 INFO 2025-06-26 11:39:27,058 calibrate.py _nudge_pos():1806 [1] 823: 0.140 0.0030585 -0.0026572 11882 39.61 11.452 -12.430 2006-08-10T13:28:23.267276544 INFO 2025-06-26 11:39:27,461 calibrate.py _nudge_pos():1806 [1] 859: 0.150 0.0036993 -0.0032466 18066 60.23 9.107 -9.988 2006-08-10T14:29:12.267302912 INFO 2025-06-26 11:39:27,969 calibrate.py _nudge_pos():1806 [1] 905: 0.150 -0.0004951 -0.0003930 11138 37.13 -1.976 -1.961 2006-08-10T15:07:05.261592064 INFO 2025-06-26 11:39:28,391 calibrate.py _nudge_pos():1806 [1] 943: 0.140 -0.0031319 0.0022252 14477 48.26 -9.616 8.543 2006-08-10T15:55:59.270598912 INFO 2025-06-26 11:39:28,934 calibrate.py _nudge_pos():1806 [1] 992: 0.140 -0.0009146 0.0012350 6959 23.20 -5.841 9.866 2006-08-10T16:19:59.261952512 INFO 2025-06-26 11:39:29,506 calibrate.py _nudge_pos():1806 [1] 1042: 0.140 -0.0014526 0.0011781 7462 24.88 -8.649 8.774 2006-08-10T16:45:41.266318080 INFO 2025-06-26 11:39:29,604 calibrate.py _nudge_pos():1862 [1] 1030: - - - 2 0.00 - - INFO 2025-06-26 11:39:29,604 calibrate.py _nudge_pos():1868 [1] Points in final series = 329432 WARNING 2025-06-26 11:39:41,098 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:40:15,915 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:40:34,425 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:40:36,373 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:40:36,376 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.221.00/ctd1.nc INFO 2025-06-26 11:40:36,378 calibrate.py _range_qc_combined_nc():898 [1] Setting 38 ctd1_salinity values to NaN INFO 2025-06-26 11:40:36,378 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 11:40:36,378 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:40:50,756 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:40:52,711 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:40:52,715 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.221.00/ctd2.nc INFO 2025-06-26 11:40:52,717 calibrate.py _range_qc_combined_nc():898 [1] Setting 26 ctd2_salinity values to NaN INFO 2025-06-26 11:40:52,717 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 11:40:52,717 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:40:52,812 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:40:55,876 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3879194 3889380 3945540] INFO 2025-06-26 11:40:56,559 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:40:56,566 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 11:40:56,567 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.221.00 ERROR 2025-06-26 11:40:56,567 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.221.00 INFO 2025-06-26 11:40:56,901 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_cal.nc INFO 2025-06-26 11:41:17,554 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 11:41:17,558 process.py align():251 [1] Alignment steps for 2006.221.00 INFO 2025-06-26 11:41:17,602 align.py process_cal():139 [1] Processing dorado_2006.221.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.221.00 INFO 2025-06-26 11:41:17,684 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:41:17,693 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:41:17,895 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:41:17,906 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:41:18,113 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:41:18,124 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:41:18,248 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:41:18,248 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:41:18,329 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:41:18,340 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:41:18,534 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:41:18,544 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:18,717 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:41:18,727 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:18,899 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:41:18,908 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,082 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:19,092 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,265 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:19,275 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:19,456 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,627 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:19,637 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,810 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:19,819 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:19,994 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,005 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:20,180 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,189 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:20,365 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,375 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:20,554 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,563 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:20,738 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,746 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:20,919 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:20,928 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:21,103 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:21,113 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:21,287 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:21,299 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:21,475 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:21,484 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:21,657 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:21,667 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:21,841 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:21,851 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:22,024 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.221.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:41:22,033 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:41:22,257 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:41:22,400 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:41:22,547 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:41:22,696 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:41:22,853 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 11:41:22,988 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_align.nc INFO 2025-06-26 11:41:23,144 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 11:41:23,147 process.py resample():273 [1] Resampling steps for 2006.221.00 INFO 2025-06-26 11:41:23,148 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:41:23,181 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_align.nc mission netCDF file INFO 2025-06-26 11:41:23,191 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_align.nc mission netCDF file INFO 2025-06-26 11:41:23,193 resample.py get_mission_start_end():1145 [1] navigation: 2006-08-09T22:27:22.030725120 to 2006-08-10T16:45:49.665742592 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 11:41:23,196 resample.py get_mission_start_end():1145 [1] hs2 : 2006-08-09T22:27:06.061818880 to 2006-08-10T16:45:49.475755776 (0 days 00:00:00.219984896 before mission_end) INFO 2025-06-26 11:41:23,198 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-08-09T22:27:30.520143616 to 2006-08-10T16:45:49.695740672 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:41:23,201 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-08-09T22:27:30.480146176 to 2006-08-10T16:45:49.695740672 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:41:23,203 resample.py get_mission_start_end():1145 [1] isus : 2006-08-09T22:28:25.006410752 to 2006-08-10T16:45:48.425827840 (0 days 00:00:01.269912832 before mission_end) INFO 2025-06-26 11:41:23,205 resample.py get_mission_start_end():1145 [1] biolume : 2006-08-09T22:27:01.512096512 to 2006-08-10T16:45:48.245805824 (0 days 00:00:01.449934848 before mission_end) INFO 2025-06-26 11:41:23,207 resample.py get_mission_start_end():1145 [1] tailcone : 2006-08-09T22:26:59.982235392 to 2006-08-10T16:45:49.405760512 (0 days 00:00:00.289980160 before mission_end) INFO 2025-06-26 11:41:23,208 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_align.nc mission netCDF file INFO 2025-06-26 11:41:23,209 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:23,866 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:23,973 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,079 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,188 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,278 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,368 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,457 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,545 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,626 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,707 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,788 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,868 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:24,949 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,037 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,119 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,199 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,283 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,373 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,459 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,546 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,634 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,720 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,758 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,785 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,811 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,842 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:25,937 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:41:26,413 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_1S.nc INFO 2025-06-26 11:41:29,043 create_products.py gulper_odv():401 [1] No gulper times found for 2006.221.00 INFO 2025-06-26 11:41:29,043 process.py archive():337 [1] Archiving steps for 2006.221.00 INFO 2025-06-26 11:41:29,044 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00, BASE_PATH = /data/auv_data INFO 2025-06-26 11:41:29,045 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:41:29,047 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.221.00_1S.nc INFO 2025-06-26 11:41:29,092 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:41:29,093 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.221.00_cal.nc INFO 2025-06-26 11:41:29,358 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:41:29,359 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.221.00_align.nc INFO 2025-06-26 11:41:29,612 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:41:29,683 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:29,750 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:29,756 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:29,800 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,035 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,046 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,152 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,207 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,406 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006221/2006.221.00 done. INFO 2025-06-26 11:41:30,406 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:41:30,406 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.221.00/dorado_2006.221.00_processing.log /Volumes/AUVCTD/surveys/2006/netcdf