INFO 2025-06-26 11:25:32,395 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 11:25:32,395 process.py process_mission():434 [1] dorado_info[mission]["comment"] = LOCO mission - as part of MB06 - John Ryan - ctdToUse = ctd1 INFO 2025-06-26 11:25:32,395 process.py process_mission():449 [1] Processing LOCO mission 2006.200.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:25:32,395 process.py download_process():165 [1] Download and processing steps for 2006.200.01 INFO 2025-06-26 11:25:32,395 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006200/2006.200.01 INFO 2025-06-26 11:25:32,395 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006200/2006.200.01 to /data/auv_data/dorado/missionlogs/2006.200.01 INFO 2025-06-26 11:25:40,057 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.200.01 INFO 2025-06-26 11:25:40,057 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/ctdDriver.log (29115987 bytes) INFO 2025-06-26 11:25:42,276 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/ctdDriver2.log (29115805 bytes) INFO 2025-06-26 11:25:44,353 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.200.01/ctdDriver2.log: [141920] INFO 2025-06-26 11:25:44,447 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/gps.log (99140 bytes) INFO 2025-06-26 11:25:44,466 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/hydroscatlog.log (19847894 bytes) INFO 2025-06-26 11:25:46,767 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.200.01/hydroscatlog.log: [212159 212160 212161 212162] INFO 2025-06-26 11:25:46,822 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/navigation.log (97605242 bytes) INFO 2025-06-26 11:25:53,867 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/isuslog.log (1820181 bytes) INFO 2025-06-26 11:25:54,046 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/parosci.log (42449030 bytes) INFO 2025-06-26 11:25:57,550 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.200.01/parosci.log: [438245 438247 569317 787771 787773 787774 875152 884328] INFO 2025-06-26 11:25:57,659 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/tailCone.log (19856299 bytes) INFO 2025-06-26 11:26:00,073 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.200.01/biolume.log (22511132 bytes) INFO 2025-06-26 11:26:02,285 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:26:03,489 logs2netcdfs.py download_process_logs():807 [1] Time to process: 23.43 seconds WARNING 2025-06-26 11:26:03,489 process.py download_process():196 [1] No lopc.bin file for 2006.200.01 INFO 2025-06-26 11:26:03,489 process.py calibrate():227 [1] Calibration steps for 2006.200.01 INFO 2025-06-26 11:26:04,118 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 11:26:04,120 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:26:04,752 calibrate.py _nudge_pos():1806 [1] 79: 0.180 -0.0002405 0.0001293 1505 5.01 -7.116 4.777 2006-07-19T17:20:53.914633984 INFO 2025-06-26 11:26:05,217 calibrate.py _nudge_pos():1806 [1] 125: 0.190 -0.0011710 -0.0007914 6160 20.55 -8.452 -7.137 2006-07-19T17:42:11.917084672 INFO 2025-06-26 11:26:05,673 calibrate.py _nudge_pos():1806 [1] 170: 0.190 -0.0023332 -0.0018877 14179 47.26 -7.319 -7.401 2006-07-19T18:30:11.909791744 INFO 2025-06-26 11:26:06,121 calibrate.py _nudge_pos():1806 [1] 214: 0.010 -0.0041168 -0.0024346 16043 53.48 -11.409 -8.436 2006-07-19T19:24:24.117000448 INFO 2025-06-26 11:26:06,586 calibrate.py _nudge_pos():1806 [1] 260: 0.010 -0.0025320 -0.0019942 12615 42.05 -8.922 -8.789 2006-07-19T20:07:12.111080704 INFO 2025-06-26 11:26:07,059 calibrate.py _nudge_pos():1806 [1] 306: 0.020 -0.0014048 -0.0016873 13965 46.55 -4.471 -6.717 2006-07-19T20:54:30.116663808 INFO 2025-06-26 11:26:07,494 calibrate.py _nudge_pos():1806 [1] 348: 0.040 0.0007700 0.0014579 17614 58.71 1.943 4.601 2006-07-19T21:53:54.112513536 INFO 2025-06-26 11:26:08,030 calibrate.py _nudge_pos():1806 [1] 400: 0.040 0.0004482 0.0005148 15559 51.86 1.281 1.839 2006-07-19T22:46:37.115833088 INFO 2025-06-26 11:26:08,450 calibrate.py _nudge_pos():1806 [1] 440: 0.050 -0.0001374 0.0000962 18430 61.43 -0.332 0.290 2006-07-19T23:48:42.110653440 INFO 2025-06-26 11:26:08,968 calibrate.py _nudge_pos():1806 [1] 489: 0.070 0.0002678 0.0003788 16110 53.70 0.740 1.307 2006-07-20T00:43:12.116642560 INFO 2025-06-26 11:26:09,465 calibrate.py _nudge_pos():1806 [1] 536: 0.070 -0.0000359 0.0001110 6580 21.93 -0.243 0.938 2006-07-20T01:05:54.113339392 INFO 2025-06-26 11:26:09,899 calibrate.py _nudge_pos():1806 [1] 577: 0.070 -0.0013224 -0.0009037 5590 18.63 -10.527 -8.988 2006-07-20T01:25:12.114010880 INFO 2025-06-26 11:26:10,386 calibrate.py _nudge_pos():1806 [1] 622: 0.080 -0.0024878 -0.0019664 13309 44.36 -8.314 -8.214 2006-07-20T02:10:18.118636800 INFO 2025-06-26 11:26:10,846 calibrate.py _nudge_pos():1806 [1] 665: 0.090 -0.0043087 -0.0025588 16500 55.00 -11.611 -8.621 2006-07-20T03:06:00.109694720 INFO 2025-06-26 11:26:11,395 calibrate.py _nudge_pos():1806 [1] 716: 0.090 -0.0025747 -0.0019586 12410 41.36 -9.223 -8.774 2006-07-20T03:48:12.116240384 INFO 2025-06-26 11:26:11,832 calibrate.py _nudge_pos():1806 [1] 757: 0.100 -0.0013894 -0.0016785 13893 46.33 -4.442 -6.713 2006-07-20T04:35:12.113057280 INFO 2025-06-26 11:26:12,222 calibrate.py _nudge_pos():1806 [1] 791: 0.110 0.0007521 0.0014569 17650 58.83 1.894 4.589 2006-07-20T05:34:35.118974976 INFO 2025-06-26 11:26:12,658 calibrate.py _nudge_pos():1806 [1] 831: 0.120 0.0005571 0.0005105 15380 51.26 1.611 1.845 2006-07-20T06:26:30.115582976 INFO 2025-06-26 11:26:13,081 calibrate.py _nudge_pos():1806 [1] 870: 0.130 0.0005082 -0.0001095 18319 61.06 1.234 -0.332 2006-07-20T07:28:12.111978752 INFO 2025-06-26 11:26:13,257 calibrate.py _nudge_pos():1806 [1] 886: 0.150 -0.0006265 0.0003405 130 0.43 -216.012 146.758 2006-07-20T07:28:53.109170432 INFO 2025-06-26 11:26:13,312 calibrate.py _nudge_pos():1806 [1] 891: 0.140 0.0003212 0.0004039 16395 54.65 0.872 1.370 2006-07-20T08:23:36.114268928 INFO 2025-06-26 11:26:13,749 calibrate.py _nudge_pos():1806 [1] 931: 0.160 -0.0000197 0.0000940 6015 20.05 -0.146 0.869 2006-07-20T08:44:18.109186560 INFO 2025-06-26 11:26:14,164 calibrate.py _nudge_pos():1806 [1] 969: 0.150 -0.0011202 -0.0008518 5935 19.78 -8.399 -7.979 2006-07-20T09:04:42.115336448 INFO 2025-06-26 11:26:14,656 calibrate.py _nudge_pos():1806 [1] 1014: 0.150 -0.0023591 -0.0018904 14150 47.16 -7.416 -7.427 2006-07-20T09:52:36.118453760 INFO 2025-06-26 11:26:15,147 calibrate.py _nudge_pos():1806 [1] 1058: 0.170 -0.0039360 -0.0023505 16825 56.08 -10.402 -7.766 2006-07-20T10:49:24.114990080 INFO 2025-06-26 11:26:15,643 calibrate.py _nudge_pos():1806 [1] 1103: 0.190 -0.0023377 -0.0018409 12764 42.56 -8.138 -8.014 2006-07-20T11:32:42.117014528 INFO 2025-06-26 11:26:16,101 calibrate.py _nudge_pos():1806 [1] 1144: 0.180 -0.0012230 -0.0014945 14440 48.13 -3.764 -5.754 2006-07-20T12:21:30.116432896 INFO 2025-06-26 11:26:16,519 calibrate.py _nudge_pos():1806 [1] 1181: 0.200 0.0007350 0.0013530 16650 55.50 1.962 4.518 2006-07-20T13:17:36.115846144 INFO 2025-06-26 11:26:16,978 calibrate.py _nudge_pos():1806 [1] 1222: 0.200 0.0004440 0.0004663 14319 47.73 1.379 1.810 2006-07-20T14:06:00.116908544 INFO 2025-06-26 11:26:17,433 calibrate.py _nudge_pos():1806 [1] 1263: 0.030 0.0000594 0.0002333 17499 58.33 0.151 0.741 2006-07-20T15:05:00.314388224 INFO 2025-06-26 11:26:17,942 calibrate.py _nudge_pos():1806 [1] 1308: 0.020 0.0004180 0.0005171 14510 48.36 1.282 1.981 2006-07-20T15:54:06.312573696 INFO 2025-06-26 11:26:18,429 calibrate.py _nudge_pos():1806 [1] 1350: 0.040 0.0000095 -0.0000196 5585 18.61 0.076 -0.196 2006-07-20T16:13:24.313245184 INFO 2025-06-26 11:26:18,601 calibrate.py _nudge_pos():1862 [1] 1343: - - - 3 0.01 - - INFO 2025-06-26 11:26:18,601 calibrate.py _nudge_pos():1868 [1] Points in final series = 413486 WARNING 2025-06-26 11:26:33,130 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:27:17,661 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:27:20,922 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:27:23,440 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:27:23,445 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.200.01/ctd1.nc INFO 2025-06-26 11:27:23,446 calibrate.py _range_qc_combined_nc():898 [1] Setting 194 ctd1_salinity values to NaN INFO 2025-06-26 11:27:23,447 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 11:27:23,447 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:27:41,995 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:27:44,451 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:27:44,456 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.200.01/ctd2.nc INFO 2025-06-26 11:27:44,457 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 11:27:44,458 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 11:27:44,458 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:27:44,569 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:27:48,427 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 97380 97920 98100 98220 98640 99480 99600 100680 101100 101700 101880 102000 102780 103200 103560 104400 104760 104880 105120 214680 218700 328200 439800 446160 446940 447060 447900 448260 449400 561360 561720 561840 562560 562860 563040 563280 563820 565740 568980 681540 790740 795540 903060 1139220 1139520 1140360 1141560 1142100 1143120 1143660 1253040 1253880 1254000 1255560 1255920 1256280 1256400 1256760 1257120 1257240 1257660 1258680 1259940 1260300 1261140 1375200 1481640 1523820 1605960 1605961 1605962 1605963 1605964 1605965 1605966 1605967 1605968 1605969 1831020 1831200 1831560 1831980 1832760 1834320 1834860 1835280 1835820 1836240 1945500 1947600 1947840 1950300 1966560 2060640 2062920 2063100 2064660 2084400 2409720 2639160 2642160 2759040 3215340 3331260 3334680 3335100 3336240 3336600 3447480 3447840 3449580 3449940 4023960 4025700 4027800 4027980 4601220 4718880 4720980 4833720 4965000 4965001 4965002] INFO 2025-06-26 11:27:49,275 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:27:49,283 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 11:27:49,284 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.200.01 ERROR 2025-06-26 11:27:49,284 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.200.01 INFO 2025-06-26 11:27:49,596 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_cal.nc INFO 2025-06-26 11:28:00,148 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 11:28:00,154 process.py align():251 [1] Alignment steps for 2006.200.01 INFO 2025-06-26 11:28:00,204 align.py process_cal():139 [1] Processing dorado_2006.200.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.200.01 INFO 2025-06-26 11:28:00,316 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:28:00,328 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:28:00,620 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:28:00,640 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:28:00,890 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:28:00,905 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:28:01,068 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:28:01,068 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:28:01,183 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:28:01,201 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:28:01,446 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:28:01,459 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:01,681 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:28:01,693 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:01,911 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:28:01,922 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:02,148 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:02,159 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:02,377 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:02,388 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:02,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:02,617 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:02,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:02,857 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:03,070 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:03,082 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:03,299 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:03,310 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:03,521 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:03,533 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:03,751 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:03,762 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:03,979 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:03,990 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:04,206 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:04,217 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:04,433 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:04,444 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:04,661 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:04,673 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:04,888 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:04,902 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:05,126 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:05,138 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:05,351 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:05,363 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:05,580 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:05,592 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:05,805 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.200.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:28:05,816 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:28:06,099 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.69 INFO 2025-06-26 11:28:06,278 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.69 INFO 2025-06-26 11:28:06,454 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.69 INFO 2025-06-26 11:28:06,636 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:28:06,834 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:28:06,996 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_align.nc INFO 2025-06-26 11:28:07,188 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 11:28:07,192 process.py resample():273 [1] Resampling steps for 2006.200.01 INFO 2025-06-26 11:28:07,193 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:28:07,232 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_align.nc mission netCDF file INFO 2025-06-26 11:28:07,242 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_align.nc mission netCDF file INFO 2025-06-26 11:28:07,244 resample.py get_mission_start_end():1145 [1] navigation: 2006-07-19T17:14:57.719034880 to 2006-07-20T16:13:38.912244992 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:28:07,247 resample.py get_mission_start_end():1145 [1] hs2 : 2006-07-19T17:14:41.570141440 to 2006-07-20T16:13:38.902245632 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 11:28:07,251 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-07-19T17:15:04.788550656 to 2006-07-20T16:13:38.762255360 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 11:28:07,253 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-07-19T17:15:04.808549376 to 2006-07-20T16:13:38.792253184 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 11:28:07,255 resample.py get_mission_start_end():1145 [1] isus : 2006-07-19T17:16:08.254203136 to 2006-07-20T16:13:38.022306048 (0 days 00:00:00.889938944 before mission_end) INFO 2025-06-26 11:28:07,257 resample.py get_mission_start_end():1145 [1] biolume : 2006-07-19T17:14:36.310467328 to 2006-07-20T16:13:37.612300032 (0 days 00:00:01.299944960 before mission_end) INFO 2025-06-26 11:28:07,260 resample.py get_mission_start_end():1145 [1] tailcone : 2006-07-19T17:14:35.480558336 to 2006-07-20T16:13:38.902245632 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 11:28:07,261 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_align.nc mission netCDF file INFO 2025-06-26 11:28:07,261 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,087 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,218 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,346 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,475 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,583 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,694 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,802 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:08,908 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,010 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,119 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,222 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,322 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,422 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,523 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,624 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,725 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,831 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:09,936 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,043 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,154 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,259 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,363 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,399 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,433 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,464 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,504 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:10,627 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:28:11,215 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_1S.nc INFO 2025-06-26 11:28:14,811 create_products.py gulper_odv():401 [1] No gulper times found for 2006.200.01 INFO 2025-06-26 11:28:14,811 process.py archive():337 [1] Archiving steps for 2006.200.01 INFO 2025-06-26 11:28:14,811 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01, BASE_PATH = /data/auv_data INFO 2025-06-26 11:28:14,813 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:28:14,814 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.200.01_1S.nc INFO 2025-06-26 11:28:14,875 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:28:14,876 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.200.01_cal.nc INFO 2025-06-26 11:28:15,222 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:28:15,223 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.200.01_align.nc INFO 2025-06-26 11:28:15,535 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:28:15,623 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:15,707 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:15,712 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:15,771 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,005 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,016 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,129 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,201 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,431 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006200/2006.200.01 done. INFO 2025-06-26 11:28:16,431 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:28:16,431 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.200.01/dorado_2006.200.01_processing.log /Volumes/AUVCTD/surveys/2006/netcdf