INFO 2025-06-26 11:14:16,241 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 11:14:16,241 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Fourth unattended mission done- this one to M2. Outbound at depth , return yo-yo. (A little slower than normal.) - ctdToUse = ctd1 INFO 2025-06-26 11:14:16,241 process.py process_mission():449 [1] Processing AUVCTD mission 2006.108.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:14:16,241 process.py download_process():165 [1] Download and processing steps for 2006.108.03 INFO 2025-06-26 11:14:16,242 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006108/2006.108.03 INFO 2025-06-26 11:14:16,242 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006108/2006.108.03 to /data/auv_data/dorado/missionlogs/2006.108.03 INFO 2025-06-26 11:14:23,213 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.108.03 INFO 2025-06-26 11:14:23,214 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/ctdDriver.log (24881339 bytes) INFO 2025-06-26 11:14:25,065 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/ctdDriver2.log (24881685 bytes) INFO 2025-06-26 11:14:26,822 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.108.03/ctdDriver2.log: [204450] INFO 2025-06-26 11:14:26,894 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/gps.log (119948 bytes) INFO 2025-06-26 11:14:26,916 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/hydroscatlog.log (16961834 bytes) INFO 2025-06-26 11:14:28,921 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/navigation.log (83413146 bytes) INFO 2025-06-26 11:14:34,846 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/isuslog.log (1526421 bytes) INFO 2025-06-26 11:14:34,997 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/parosci.log (36354278 bytes) INFO 2025-06-26 11:14:37,936 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.108.03/parosci.log: [339344 339345 339346 716603] INFO 2025-06-26 11:14:38,023 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/tailCone.log (16970155 bytes) INFO 2025-06-26 11:14:40,096 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.108.03/biolume.log (19238156 bytes) INFO 2025-06-26 11:14:41,903 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:14:42,833 logs2netcdfs.py download_process_logs():807 [1] Time to process: 19.62 seconds WARNING 2025-06-26 11:14:42,833 process.py download_process():196 [1] No lopc.bin file for 2006.108.03 INFO 2025-06-26 11:14:42,833 process.py calibrate():227 [1] Calibration steps for 2006.108.03 INFO 2025-06-26 11:14:43,343 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 11:14:43,345 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:14:44,126 calibrate.py _nudge_pos():1806 [1] 93: 0.160 -0.0003488 -0.0004683 8240 27.46 -1.885 -3.160 2006-04-18T20:27:29.363318912 INFO 2025-06-26 11:14:44,735 calibrate.py _nudge_pos():1806 [1] 153: 0.180 -0.0012072 0.0007099 11075 36.91 -4.855 3.563 2006-04-18T21:05:23.367539200 INFO 2025-06-26 11:14:44,746 calibrate.py _nudge_pos():1806 [1] 154: 0.160 -0.0000467 0.0000351 40 0.13 -53.381 50.003 2006-04-18T21:05:31.366991104 INFO 2025-06-26 11:14:45,323 calibrate.py _nudge_pos():1806 [1] 210: 0.190 -0.0027895 0.0032778 12315 41.05 -10.089 14.797 2006-04-18T21:47:29.364496512 INFO 2025-06-26 11:14:45,967 calibrate.py _nudge_pos():1806 [1] 273: 0.180 -0.0037316 -0.0002788 9680 32.26 -17.173 -1.601 2006-04-18T22:20:47.367623808 INFO 2025-06-26 11:14:46,399 calibrate.py _nudge_pos():1806 [1] 315: 0.180 0.0000404 0.0000058 15 0.05 128.502 23.092 2006-04-18T22:21:31.364609664 INFO 2025-06-26 11:14:46,472 calibrate.py _nudge_pos():1806 [1] 322: 0.170 0.0000135 -0.0000231 15 0.05 43.082 -91.595 2006-04-18T22:21:40.363993344 INFO 2025-06-26 11:14:46,482 calibrate.py _nudge_pos():1806 [1] 323: 0.180 -0.0014455 0.0016378 9995 33.31 -6.443 9.110 2006-04-18T22:54:59.367052288 INFO 2025-06-26 11:14:47,191 calibrate.py _nudge_pos():1806 [1] 391: 0.190 -0.0038617 0.0032910 12410 41.36 -13.864 14.743 2006-04-18T23:37:29.362365440 INFO 2025-06-26 11:14:47,839 calibrate.py _nudge_pos():1806 [1] 451: 0.180 -0.0000353 -0.0000020 15 0.05 -112.340 -7.937 2006-04-18T23:38:32.368049408 INFO 2025-06-26 11:14:47,913 calibrate.py _nudge_pos():1806 [1] 458: 0.190 -0.0000547 0.0001650 9735 32.45 -0.251 0.942 2006-04-19T00:11:05.364259968 INFO 2025-06-26 11:14:48,424 calibrate.py _nudge_pos():1806 [1] 505: 0.190 0.0015417 -0.0020273 11865 39.55 5.791 -9.499 2006-04-19T00:51:26.368409856 INFO 2025-06-26 11:14:48,931 calibrate.py _nudge_pos():1806 [1] 551: 0.190 0.0000054 0.0000149 19 0.06 13.383 45.897 2006-04-19T00:52:15.365053440 INFO 2025-06-26 11:14:49,202 calibrate.py _nudge_pos():1806 [1] 576: 0.010 0.0000236 -0.0000057 11 0.03 105.345 -31.414 2006-04-19T00:52:41.563258624 INFO 2025-06-26 11:14:49,214 calibrate.py _nudge_pos():1806 [1] 577: 0.010 -0.0070914 0.0045968 14789 49.30 -21.367 17.279 2006-04-19T01:41:59.570621312 INFO 2025-06-26 11:14:49,949 calibrate.py _nudge_pos():1806 [1] 646: 0.010 0.0011073 -0.0023036 13336 44.45 3.701 -9.603 2006-04-19T02:27:35.563192832 INFO 2025-06-26 11:14:50,048 calibrate.py _nudge_pos():1806 [1] 655: 0.020 0.0000097 -0.0000741 15 0.05 31.029 -294.269 2006-04-19T02:27:46.562439424 INFO 2025-06-26 11:14:50,357 calibrate.py _nudge_pos():1806 [1] 684: 0.200 -0.0000174 -0.0001194 44 0.14 -18.067 -154.325 2006-04-19T02:28:23.369917824 INFO 2025-06-26 11:14:50,421 calibrate.py _nudge_pos():1806 [1] 690: 0.020 -0.0058730 0.0012681 13550 45.16 -19.319 5.203 2006-04-19T03:13:38.563914496 INFO 2025-06-26 11:14:50,646 calibrate.py _nudge_pos():1806 [1] 711: 0.020 0.0000570 -0.0000154 15 0.05 181.353 -61.151 2006-04-19T03:14:01.562338816 INFO 2025-06-26 11:14:51,124 calibrate.py _nudge_pos():1806 [1] 752: 0.010 -0.0000047 -0.0000205 30 0.10 -7.181 -39.204 2006-04-19T03:14:48.569118720 INFO 2025-06-26 11:14:51,168 calibrate.py _nudge_pos():1806 [1] 756: 0.010 -0.0000040 -0.0000117 15 0.05 -12.847 -46.436 2006-04-19T03:14:54.568707712 INFO 2025-06-26 11:14:51,242 calibrate.py _nudge_pos():1806 [1] 763: 0.010 -0.0091559 -0.0012263 15165 50.55 -26.913 -4.496 2006-04-19T04:05:34.570453376 INFO 2025-06-26 11:14:51,726 calibrate.py _nudge_pos():1806 [1] 808: 0.030 -0.0002652 -0.0001370 1490 4.96 -7.939 -5.113 2006-04-19T04:11:16.567024896 INFO 2025-06-26 11:14:52,224 calibrate.py _nudge_pos():1806 [1] 854: 0.030 0.0005481 -0.0046482 16579 55.26 1.474 -15.586 2006-04-19T05:07:17.566780800 INFO 2025-06-26 11:14:52,295 calibrate.py _nudge_pos():1806 [1] 860: 0.050 0.0005460 -0.0047151 80 0.26 308.069 -3318.103 2006-04-19T05:07:38.565342208 INFO 2025-06-26 11:14:52,588 calibrate.py _nudge_pos():1806 [1] 887: 0.040 0.0000819 0.0001678 15 0.05 260.863 666.372 2006-04-19T05:08:07.563355648 INFO 2025-06-26 11:14:53,307 calibrate.py _nudge_pos():1806 [1] 953: 0.040 0.0013230 -0.0053394 16369 54.56 3.602 -18.133 2006-04-19T06:03:47.564549888 INFO 2025-06-26 11:14:53,826 calibrate.py _nudge_pos():1806 [1] 1001: 0.030 0.0020079 -0.0035785 16565 55.21 5.403 -12.010 2006-04-19T06:59:47.564374272 INFO 2025-06-26 11:14:53,881 calibrate.py _nudge_pos():1806 [1] 1006: 0.030 0.0000054 -0.0000030 15 0.05 17.223 -12.044 2006-04-19T06:59:54.563894784 INFO 2025-06-26 11:14:54,254 calibrate.py _nudge_pos():1806 [1] 1040: 0.030 -0.0000861 -0.0000138 65 0.21 -59.926 -12.020 2006-04-19T07:00:40.570743040 INFO 2025-06-26 11:14:54,352 calibrate.py _nudge_pos():1806 [1] 1048: 0.050 0.0038879 -0.0020242 16500 55.00 10.502 -6.820 2006-04-19T07:55:47.564198528 INFO 2025-06-26 11:14:55,125 calibrate.py _nudge_pos():1806 [1] 1119: 0.060 0.0022668 -0.0007517 16535 55.11 6.109 -2.527 2006-04-19T08:52:04.562858112 INFO 2025-06-26 11:14:55,698 calibrate.py _nudge_pos():1806 [1] 1171: 0.040 -0.0000468 -0.0000057 30 0.10 -71.952 -10.939 2006-04-19T08:53:02.568884608 INFO 2025-06-26 11:14:55,800 calibrate.py _nudge_pos():1806 [1] 1180: 0.050 0.0000084 0.0000184 15 0.05 26.878 73.026 2006-04-19T08:53:13.568130944 INFO 2025-06-26 11:14:55,901 calibrate.py _nudge_pos():1806 [1] 1189: 0.060 0.0022952 0.0003398 16299 54.33 6.274 1.159 2006-04-19T09:47:41.564257920 INFO 2025-06-26 11:14:56,618 calibrate.py _nudge_pos():1806 [1] 1253: 0.060 0.0018206 0.0018222 16215 54.05 5.002 6.247 2006-04-19T10:42:47.567781248 INFO 2025-06-26 11:14:57,409 calibrate.py _nudge_pos():1806 [1] 1323: 0.070 0.0009841 0.0030390 16365 54.55 2.679 10.324 2006-04-19T11:38:29.568838400 INFO 2025-06-26 11:14:57,990 calibrate.py _nudge_pos():1806 [1] 1373: 0.070 0.0031404 0.0016864 14695 48.98 9.519 6.380 2006-04-19T12:28:17.564146816 INFO 2025-06-26 11:14:58,683 calibrate.py _nudge_pos():1806 [1] 1434: 0.070 0.0034948 0.0014836 12870 42.90 12.095 6.409 2006-04-19T13:12:11.563705472 INFO 2025-06-26 11:14:59,241 calibrate.py _nudge_pos():1806 [1] 1484: 0.070 0.0026482 0.0016450 11935 39.78 9.882 7.663 2006-04-19T13:52:47.566827776 INFO 2025-06-26 11:14:59,843 calibrate.py _nudge_pos():1806 [1] 1538: 0.080 0.0023806 0.0013874 13145 43.81 8.065 5.868 2006-04-19T14:37:29.563098368 INFO 2025-06-26 11:15:00,519 calibrate.py _nudge_pos():1806 [1] 1597: 0.080 0.0004766 0.0006758 4480 14.93 4.738 8.388 2006-04-19T14:53:23.567744768 INFO 2025-06-26 11:15:01,131 calibrate.py _nudge_pos():1806 [1] 1650: 0.070 0.0014631 0.0011766 12805 42.68 5.088 5.108 2006-04-19T15:36:56.568741760 INFO 2025-06-26 11:15:01,175 calibrate.py _nudge_pos():1862 [1] 1632: - - - 1 0.00 - - INFO 2025-06-26 11:15:01,176 calibrate.py _nudge_pos():1868 [1] Points in final series = 353356 WARNING 2025-06-26 11:15:13,648 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:15:16,236 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:15:18,998 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:15:21,132 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:15:21,138 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.108.03/ctd1.nc INFO 2025-06-26 11:15:21,140 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 11:15:21,140 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 11:15:21,140 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:15:36,739 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:15:38,862 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:15:38,868 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.108.03/ctd2.nc INFO 2025-06-26 11:15:38,869 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 11:15:38,869 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 11:15:38,870 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:15:38,978 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:15:42,251 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 600 601 602 603 604 605 166800 169560 282480 284700 285120 285540 286440 395880 397980 398160 510600 510960 512160 512700 513060 513480 514800 515580 741420 858960 971640 3414360 3591540] INFO 2025-06-26 11:15:42,952 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:15:42,960 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 11:15:42,960 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.108.03 ERROR 2025-06-26 11:15:42,961 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.108.03 INFO 2025-06-26 11:15:43,234 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_cal.nc INFO 2025-06-26 11:15:52,198 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 11:15:52,203 process.py align():251 [1] Alignment steps for 2006.108.03 INFO 2025-06-26 11:15:52,314 align.py process_cal():139 [1] Processing dorado_2006.108.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.108.03 INFO 2025-06-26 11:15:52,417 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:15:52,427 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:15:52,685 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:15:52,702 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:15:52,952 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:15:52,965 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:15:53,116 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:15:53,116 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:15:53,216 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:15:53,230 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:15:53,471 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:15:53,482 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:53,687 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:15:53,697 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:53,905 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:15:53,917 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:54,129 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:54,139 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:54,347 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:54,358 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:54,629 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:54,643 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:54,876 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:54,886 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:55,102 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:55,113 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:55,339 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:55,353 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:55,566 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:55,576 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:55,780 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:55,790 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:56,001 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:56,012 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:56,224 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:56,234 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:56,455 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:56,467 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:56,674 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:56,686 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:56,898 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:56,908 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:57,114 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:57,125 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:57,339 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:57,349 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:57,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:57,569 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:57,787 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.108.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:15:57,796 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:15:58,060 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:15:58,230 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:15:58,400 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:15:58,583 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:15:58,774 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:15:58,932 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_align.nc INFO 2025-06-26 11:15:59,096 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 11:15:59,099 process.py resample():273 [1] Resampling steps for 2006.108.03 INFO 2025-06-26 11:15:59,100 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:15:59,136 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_align.nc mission netCDF file INFO 2025-06-26 11:15:59,145 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_align.nc mission netCDF file INFO 2025-06-26 11:15:59,148 resample.py get_mission_start_end():1145 [1] navigation: 2006-04-18T19:58:51.780981504 to 2006-04-19T15:36:59.768522752 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 11:15:59,151 resample.py get_mission_start_end():1145 [1] hs2 : 2006-04-18T19:58:34.072194560 to 2006-04-19T15:36:59.908513024 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:15:59,153 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-04-18T19:58:56.840634880 to 2006-04-19T15:36:59.738524672 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 11:15:59,156 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-04-18T19:58:56.930628736 to 2006-04-19T15:36:59.848517120 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 11:15:59,158 resample.py get_mission_start_end():1145 [1] isus : 2006-04-18T19:59:56.846524288 to 2006-04-19T15:36:59.578535552 (0 days 00:00:00.329977472 before mission_end) INFO 2025-06-26 11:15:59,160 resample.py get_mission_start_end():1145 [1] biolume : 2006-04-18T19:58:29.252490496 to 2006-04-19T15:36:58.798554880 (0 days 00:00:01.109958144 before mission_end) INFO 2025-06-26 11:15:59,162 resample.py get_mission_start_end():1145 [1] tailcone : 2006-04-18T19:58:29.622499456 to 2006-04-19T15:36:59.798520576 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 11:15:59,163 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_align.nc mission netCDF file INFO 2025-06-26 11:15:59,164 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:15:59,866 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:15:59,985 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,099 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,209 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,303 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,399 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,494 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,586 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,675 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,773 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,861 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:00,948 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,036 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,124 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,213 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,300 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,392 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,483 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,572 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,662 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,751 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,840 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,872 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,902 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,928 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:01,962 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:02,074 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:16:02,571 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_1S.nc INFO 2025-06-26 11:16:05,393 create_products.py gulper_odv():401 [1] No gulper times found for 2006.108.03 INFO 2025-06-26 11:16:05,393 process.py archive():337 [1] Archiving steps for 2006.108.03 INFO 2025-06-26 11:16:05,393 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03, BASE_PATH = /data/auv_data INFO 2025-06-26 11:16:05,394 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:16:05,395 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.108.03_1S.nc INFO 2025-06-26 11:16:05,448 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:16:05,449 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.108.03_cal.nc INFO 2025-06-26 11:16:05,727 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:16:05,728 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.108.03_align.nc INFO 2025-06-26 11:16:05,992 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:16:06,062 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,133 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,138 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,186 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,400 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,410 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,515 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,582 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,773 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006108/2006.108.03 done. INFO 2025-06-26 11:16:06,774 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:16:06,775 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.108.03/dorado_2006.108.03_processing.log /Volumes/AUVCTD/surveys/2006/netcdf