INFO 2025-06-26 05:48:56,375 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 05:48:56,375 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ??? Reference to non-existent field 'depth'. Error in ==> /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/process/build_auv_survey.m On line 118 ==> hs2depth=[hs2depth;HS2.depth]; No variables in the hydroscatlog.nc file, hydroscat.log file is 0 size Will need to get those data Portaled 8/11/05 - no hs2 data - ctdToUse = ctd1 INFO 2025-06-26 05:48:56,375 process.py process_mission():449 [1] Processing AUVCTD mission 2004.167.04 by user docker_user on host 671049448ece INFO 2025-06-26 05:48:56,375 process.py download_process():165 [1] Download and processing steps for 2004.167.04 INFO 2025-06-26 05:48:56,375 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004167/2004.167.04 INFO 2025-06-26 05:48:56,375 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004167/2004.167.04 to /data/auv_data/dorado/missionlogs/2004.167.04 INFO 2025-06-26 05:49:01,228 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.167.04 INFO 2025-06-26 05:49:01,229 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/ctdDriver.log (7093635 bytes) INFO 2025-06-26 05:49:01,817 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/ctdDriver2.log (7093365 bytes) INFO 2025-06-26 05:49:02,349 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/gps.log (243572 bytes) INFO 2025-06-26 05:49:02,382 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/hydroscatlog.log (0 bytes) WARNING 2025-06-26 05:49:02,383 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2004.167.04/hydroscatlog.log is empty INFO 2025-06-26 05:49:02,383 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/navigation.log (15717007 bytes) INFO 2025-06-26 05:49:03,551 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/isuslog.log (390485 bytes) INFO 2025-06-26 05:49:03,593 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/parosci.log (4825910 bytes) INFO 2025-06-26 05:49:04,001 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/tailCone.log (4832107 bytes) INFO 2025-06-26 05:49:04,642 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.167.04/biolume.log (5490188 bytes) INFO 2025-06-26 05:49:05,157 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:49:05,445 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.22 seconds WARNING 2025-06-26 05:49:05,445 process.py download_process():196 [1] No lopc.bin file for 2004.167.04 INFO 2025-06-26 05:49:05,445 process.py calibrate():227 [1] Calibration steps for 2004.167.04 INFO 2025-06-26 05:49:05,614 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 05:49:05,616 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:49:07,004 calibrate.py _nudge_pos():1806 [1] 166: 0.040 0.0000044 -0.0000402 15 0.05 13.825 -158.922 2004-06-15T16:56:47.456948736 INFO 2025-06-26 05:49:07,163 calibrate.py _nudge_pos():1806 [1] 183: 0.050 0.0039318 0.0011673 11360 37.86 15.422 5.713 2004-06-15T17:34:55.450210560 INFO 2025-06-26 05:49:07,817 calibrate.py _nudge_pos():1806 [1] 253: 0.040 0.0037731 0.0006675 11475 38.25 14.650 3.234 2004-06-15T18:14:19.448265600 INFO 2025-06-26 05:49:08,245 calibrate.py _nudge_pos():1806 [1] 299: 0.050 0.0030652 0.0010043 11445 38.15 11.931 4.879 2004-06-15T18:53:13.448375680 INFO 2025-06-26 05:49:08,641 calibrate.py _nudge_pos():1806 [1] 341: 0.040 0.0000062 -0.0000132 15 0.05 19.688 -52.508 2004-06-15T18:53:57.455360896 INFO 2025-06-26 05:49:08,736 calibrate.py _nudge_pos():1806 [1] 351: 0.040 0.0000097 -0.0000586 45 0.15 9.805 -73.985 2004-06-15T18:54:16.454059392 INFO 2025-06-26 05:49:08,811 calibrate.py _nudge_pos():1806 [1] 359: 0.050 0.0029601 0.0010415 11500 38.33 11.465 5.035 2004-06-15T19:32:43.456018944 INFO 2025-06-26 05:49:08,850 calibrate.py _nudge_pos():1806 [1] 363: 0.050 0.0029721 0.0009850 20 0.06 6967.698 2882.015 2004-06-15T19:32:50.455539456 INFO 2025-06-26 05:49:09,349 calibrate.py _nudge_pos():1806 [1] 416: 0.050 0.0020501 0.0013711 11315 37.71 8.070 6.736 2004-06-15T20:11:25.456951168 INFO 2025-06-26 05:49:09,849 calibrate.py _nudge_pos():1806 [1] 469: 0.060 0.0020360 0.0023686 11410 38.03 7.947 11.541 2004-06-15T20:50:19.447061760 INFO 2025-06-26 05:49:10,281 calibrate.py _nudge_pos():1806 [1] 513: 0.050 0.0026273 0.0036300 11125 37.08 10.516 18.140 2004-06-15T21:28:07.451692800 INFO 2025-06-26 05:49:10,857 calibrate.py _nudge_pos():1806 [1] 571: 0.060 -0.0000058 -0.0000071 15 0.05 -18.585 -28.221 2004-06-15T21:29:07.447582720 INFO 2025-06-26 05:49:10,917 calibrate.py _nudge_pos():1806 [1] 577: 0.060 -0.0007708 0.0006005 4235 14.11 -8.106 7.884 2004-06-15T21:43:19.449216640 INFO 2025-06-26 05:49:17,006 calibrate.py _nudge_pos():1806 [1] 1206: 0.050 -0.0000030 -0.0000179 20 0.06 -6.919 -52.426 2004-06-15T21:53:51.455921152 INFO 2025-06-26 05:49:19,289 calibrate.py _nudge_pos():1806 [1] 1438: 0.050 0.0000150 -0.0000100 15 0.05 47.781 -39.621 2004-06-15T21:57:45.449891584 INFO 2025-06-26 05:49:34,677 calibrate.py _nudge_pos():1806 [1] 2999: 0.170 0.0001630 -0.0000080 17 0.05 453.590 -27.797 2004-06-15T22:23:49.052777472 INFO 2025-06-26 05:49:34,766 calibrate.py _nudge_pos():1806 [1] 3010: 0.070 0.0001475 0.0000052 16 0.05 436.366 19.085 2004-06-15T22:24:00.861968512 INFO 2025-06-26 05:49:34,809 calibrate.py _nudge_pos():1806 [1] 3015: 0.050 0.0001328 0.0000402 11 0.03 591.428 223.302 2004-06-15T22:24:05.851626624 INFO 2025-06-26 05:49:34,869 calibrate.py _nudge_pos():1806 [1] 3021: 0.010 0.0001293 0.0000113 18 0.06 338.732 37.063 2004-06-15T22:24:14.051064960 INFO 2025-06-26 05:49:34,882 calibrate.py _nudge_pos():1806 [1] 3023: 0.040 0.0001448 0.0000110 13 0.04 537.380 50.961 2004-06-15T22:24:16.650886784 INFO 2025-06-26 05:49:34,895 calibrate.py _nudge_pos():1806 [1] 3025: 0.060 0.0001540 0.0000245 13 0.04 571.391 113.504 2004-06-15T22:24:19.250708864 INFO 2025-06-26 05:49:34,905 calibrate.py _nudge_pos():1806 [1] 3026: 0.190 0.0001617 0.0000117 11 0.03 723.422 65.185 2004-06-15T22:24:21.450557952 INFO 2025-06-26 05:49:34,926 calibrate.py _nudge_pos():1806 [1] 3028: 0.060 0.0002137 0.0000403 34 0.11 288.281 67.948 2004-06-15T22:24:28.450078464 INFO 2025-06-26 05:49:34,946 calibrate.py _nudge_pos():1806 [1] 3033: 0.060 0.0001448 0.0000222 13 0.04 537.379 102.694 2004-06-15T22:24:31.049900544 INFO 2025-06-26 05:49:36,175 calibrate.py _nudge_pos():1806 [1] 3152: 0.050 0.0001195 0.0000418 15 0.05 380.036 166.120 2004-06-15T22:26:31.651638784 INFO 2025-06-26 05:49:37,240 calibrate.py _nudge_pos():1806 [1] 3260: 0.100 0.0001533 0.0000203 14 0.04 525.135 86.954 2004-06-15T22:28:20.654171520 INFO 2025-06-26 05:49:38,323 calibrate.py _nudge_pos():1862 [1] 3338: - - - 1 0.00 - - INFO 2025-06-26 05:49:38,324 calibrate.py _nudge_pos():1868 [1] Points in final series = 100730 WARNING 2025-06-26 05:49:38,404 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:49:39,140 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:49:39,724 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:49:39,726 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.167.04/ctd1.nc WARNING 2025-06-26 05:49:39,727 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (7770) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 05:49:39,727 calibrate.py _range_qc_combined_nc():898 [1] Setting 7770 ctd1_salinity values to NaN INFO 2025-06-26 05:49:39,728 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 05:49:39,728 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:49:40,419 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:49:41,004 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:49:41,007 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.167.04/ctd2.nc WARNING 2025-06-26 05:49:41,008 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (8305) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 05:49:41,009 calibrate.py _range_qc_combined_nc():898 [1] Setting 8305 ctd2_salinity values to NaN INFO 2025-06-26 05:49:41,009 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 05:49:41,009 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:49:41,043 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:49:41,972 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 1149660 1149661 1149662 1149663 1149664 1149665 1152900 1152901 1152902 1152903 1152904 1152905 1153800 1153801 1153802 1153803 1153804 1153920 1153921 1153922 1155240 1155241 1155242 1155243 1155480 1155481 1155482 1155483 1155484 1155485 1156080 1156081 1156082 1156083 1156084 1156140 1156920 1156921 1156922 1156923 1156924 1156925 1157160 1157161 1157162 1157163 1158840 1158841 1158842 1159200 1159201 1159202 1159620 1159621 1159622 1160400 1160401 1160402 1160403 1161180 1161181 1161182 1161183 1161184 1161660 1161661 1161662 1161840 1162020 1163340 1163341 1163342 1163343 1163344 1163700 1165440 1165441 1167060 1167061 1167062 1169580 1169581 1169582 1169583 1169584 1170000 1170420 1170421 1170422 1170423 1170424 1170425 1170840 1170841 1170842 1170843 1170844 1173000 1174800 1175460 1175461 1175462 1176240 1176241 1176242 1176243 1177020 1177021 1178700 1179660 1183080 1184460 1185900 1186140 1186141 1186142 1186380 1186381 1186382 1186620 1187040 1187280 1187400 1187580 1187581 1187582 1188240 1188241 1188360 1188420 1188780 1189200 1189201 1189260 1189500 1189620 1189621 1189622 1189860 1189980 1189981 1189982 1190280 1190281 1190282 1190520 1190940 1191060 1191300 1191540 1191541 1191900 1191901 1192260 1192261 1192920 1193580 1193760 1193761 1193940 1193941 1194120 1194240 1194241 1194242 1194480 1194481 1194660 1194661 1194840 1194841 1195080 1195081 1195082 1195260 1195261 1195440 1195441 1195442 1195800 1195801 1196040 1196220 1196700 1196760 1196761 1196762 1197060 1197240 1197360 1197480 1197660 1197661 1197780 1198200 1198380 1198381 1198680 1198980 1198981 1198982 1199160 1199280 1199460 1199640 1199700 1199701 1199880 1200180 1200181 1200540 1200960 1200961 1201260 1201380 1201381 1201382 1201620 1201920 1202220 1202640 1202820 1202821 1202822 1202940 1203060 1203061 1203062 1203180 1203181 1203300 1203420 1203540 1203541 1203660 1204020 1204021 1204200 1204201 1204202 1204620 1204621 1204800 1204801 1204980 1204981 1204982 1206240] INFO 2025-06-26 05:49:42,145 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 05:49:42,150 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 05:49:42,150 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.167.04 ERROR 2025-06-26 05:49:42,151 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.167.04 INFO 2025-06-26 05:49:42,230 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_cal.nc INFO 2025-06-26 05:49:42,313 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, 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 05:49:42,317 process.py align():251 [1] Alignment steps for 2004.167.04 INFO 2025-06-26 05:49:42,343 align.py process_cal():139 [1] Processing dorado_2004.167.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.167.04 INFO 2025-06-26 05:49:42,373 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:49:42,376 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:49:42,450 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:49:42,455 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:49:42,526 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:49:42,530 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:49:42,572 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:49:42,572 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:49:42,602 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:49:42,606 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:49:42,676 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:42,680 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:42,743 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:42,747 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:42,809 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:42,813 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:42,875 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:42,879 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:42,941 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:42,945 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,006 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,074 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,137 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,141 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,202 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,206 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,268 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,272 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,334 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,338 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,399 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,404 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,467 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,471 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,534 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,538 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,600 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,604 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,666 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,671 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,734 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,739 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,802 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.167.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:49:43,806 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:49:43,873 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:49:43,918 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:49:43,970 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.61 INFO 2025-06-26 05:49:44,017 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:49:44,064 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 05:49:44,111 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_align.nc INFO 2025-06-26 05:49:44,180 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, 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 05:49:44,182 process.py resample():273 [1] Resampling steps for 2004.167.04 INFO 2025-06-26 05:49:44,183 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:49:44,207 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_align.nc mission netCDF file INFO 2025-06-26 05:49:44,212 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_align.nc mission netCDF file INFO 2025-06-26 05:49:44,213 resample.py get_mission_start_end():1145 [1] navigation: 2004-06-15T16:54:21.256964224 to 2004-06-15T22:30:10.656635776 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:49:44,215 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-06-15T16:54:18.517151872 to 2004-06-15T22:30:10.566642048 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 05:49:44,216 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-06-15T16:54:18.297167104 to 2004-06-15T22:30:10.566642048 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 05:49:44,218 resample.py get_mission_start_end():1145 [1] isus : 2004-06-15T16:55:15.333259776 to 2004-06-15T22:30:09.376723584 (0 days 00:00:01.279912192 before mission_end) INFO 2025-06-26 05:49:44,219 resample.py get_mission_start_end():1145 [1] biolume : 2004-06-15T16:53:58.708474624 to 2004-06-15T22:30:09.956649600 (0 days 00:00:00.699986176 before mission_end) INFO 2025-06-26 05:49:44,221 resample.py get_mission_start_end():1145 [1] tailcone : 2004-06-15T16:54:00.588380160 to 2004-06-15T22:30:10.606639104 (0 days 00:00:00.049996672 before mission_end) INFO 2025-06-26 05:49:44,221 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_align.nc mission netCDF file INFO 2025-06-26 05:49:44,222 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,441 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,480 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,518 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,556 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,588 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,617 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,663 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,692 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,722 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,752 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,781 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,811 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,839 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,871 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,904 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,954 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:44,986 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,019 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,051 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,066 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,080 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,092 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,108 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,144 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 05:49:45,344 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_1S.nc INFO 2025-06-26 05:49:46,503 create_products.py gulper_odv():401 [1] No gulper times found for 2004.167.04 INFO 2025-06-26 05:49:46,503 process.py archive():337 [1] Archiving steps for 2004.167.04 INFO 2025-06-26 05:49:46,503 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04, BASE_PATH = /data/auv_data INFO 2025-06-26 05:49:46,505 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 05:49:46,506 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.167.04_1S.nc INFO 2025-06-26 05:49:46,525 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:49:46,526 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.167.04_cal.nc INFO 2025-06-26 05:49:46,606 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:49:46,607 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.167.04_align.nc INFO 2025-06-26 05:49:46,678 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:49:46,705 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,734 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,785 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,791 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,811 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,834 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,897 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004167/2004.167.04 done. INFO 2025-06-26 05:49:46,897 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:49:46,897 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.167.04/dorado_2004.167.04_processing.log /Volumes/AUVCTD/surveys/2004/netcdf