INFO 2025-06-26 10:51:54,421 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 10:51:54,421 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Conducted from the Sproul on John Ryan's LOCO project - ctdToUse = ctd1 INFO 2025-06-26 10:51:54,421 process.py process_mission():449 [1] Processing LOCO mission 2005.240.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:51:54,421 process.py download_process():165 [1] Download and processing steps for 2005.240.02 INFO 2025-06-26 10:51:54,421 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005240/2005.240.02 INFO 2025-06-26 10:51:54,421 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005240/2005.240.02 to /data/auv_data/dorado/missionlogs/2005.240.02 INFO 2025-06-26 10:51:57,179 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.240.02 INFO 2025-06-26 10:51:57,179 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/ctdDriver.log (6345547 bytes) INFO 2025-06-26 10:51:57,628 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.240.02/ctdDriver.log: [6714] INFO 2025-06-26 10:51:57,645 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/ctdDriver2.log (6345453 bytes) INFO 2025-06-26 10:51:58,158 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.240.02/ctdDriver2.log: [6714 6719] INFO 2025-06-26 10:51:58,181 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/gps.log (76316 bytes) INFO 2025-06-26 10:51:58,204 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/hydroscatlog.log (4329134 bytes) INFO 2025-06-26 10:51:58,699 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.240.02/hydroscatlog.log: [6762 6765 6766 6767 6768 6769 6773 6774 6775 6777 6779 6781 6782 6784 6786 6791 6797 6803] INFO 2025-06-26 10:51:58,710 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/navigation.log (21277650 bytes) INFO 2025-06-26 10:52:00,242 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/isuslog.log (389141 bytes) INFO 2025-06-26 10:52:00,283 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/parosci.log (9264950 bytes) INFO 2025-06-26 10:52:01,067 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.240.02/parosci.log: [168570] INFO 2025-06-26 10:52:01,092 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/tailCone.log (4332427 bytes) INFO 2025-06-26 10:52:01,633 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.02/biolume.log (4913548 bytes) INFO 2025-06-26 10:52:02,112 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:52:02,374 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.20 seconds WARNING 2025-06-26 10:52:02,375 process.py download_process():196 [1] No lopc.bin file for 2005.240.02 INFO 2025-06-26 10:52:02,375 process.py calibrate():227 [1] Calibration steps for 2005.240.02 INFO 2025-06-26 10:52:02,543 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 10:52:02,545 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:52:03,255 calibrate.py _nudge_pos():1806 [1] 90: 0.130 -0.0002515 0.0000392 7780 25.93 -1.437 0.280 2005-08-28T14:57:48.154758272 INFO 2025-06-26 10:52:04,146 calibrate.py _nudge_pos():1806 [1] 183: 0.130 -0.0002534 0.0000225 8090 26.96 -1.393 0.155 2005-08-28T15:26:18.147615616 INFO 2025-06-26 10:52:04,981 calibrate.py _nudge_pos():1806 [1] 270: 0.130 -0.0003113 -0.0000032 8480 28.26 -1.633 -0.021 2005-08-28T15:56:00.155539712 INFO 2025-06-26 10:52:05,844 calibrate.py _nudge_pos():1806 [1] 359: 0.130 -0.0002756 -0.0000347 8230 27.43 -1.490 -0.235 2005-08-28T16:24:54.146753024 INFO 2025-06-26 10:52:06,652 calibrate.py _nudge_pos():1806 [1] 442: 0.130 -0.0001862 -0.0001546 7540 25.13 -1.099 -1.140 2005-08-28T16:51:24.147830784 INFO 2025-06-26 10:52:07,459 calibrate.py _nudge_pos():1806 [1] 526: 0.130 0.0000232 -0.0006932 9605 32.01 0.108 -4.013 2005-08-28T17:24:48.150547072 INFO 2025-06-26 10:52:08,285 calibrate.py _nudge_pos():1806 [1] 608: 0.130 -0.0011622 0.0007707 9165 30.55 -5.644 4.675 2005-08-28T17:56:42.149429120 INFO 2025-06-26 10:52:09,086 calibrate.py _nudge_pos():1806 [1] 686: 0.130 -0.0015423 0.0004220 8165 27.21 -8.404 2.873 2005-08-28T18:25:12.152285824 INFO 2025-06-26 10:52:09,984 calibrate.py _nudge_pos():1806 [1] 773: 0.140 -0.0014316 0.0003581 7850 26.16 -8.112 2.536 2005-08-28T18:52:48.148842368 INFO 2025-06-26 10:52:10,887 calibrate.py _nudge_pos():1806 [1] 860: 0.130 -0.0011260 0.0002240 5780 19.26 -8.664 2.154 2005-08-28T19:13:30.153759232 INFO 2025-06-26 10:52:11,873 calibrate.py _nudge_pos():1806 [1] 954: 0.140 -0.0011170 -0.0010974 4395 14.65 -11.303 -13.884 2005-08-28T19:29:42.147173120 INFO 2025-06-26 10:52:12,885 calibrate.py _nudge_pos():1862 [1] 1026: - - - 1 0.00 - - INFO 2025-06-26 10:52:12,886 calibrate.py _nudge_pos():1868 [1] Points in final series = 90150 WARNING 2025-06-26 10:52:16,150 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:52:25,945 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:52:31,244 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:52:31,813 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:52:31,815 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.240.02/ctd1.nc INFO 2025-06-26 10:52:31,816 calibrate.py _range_qc_combined_nc():898 [1] Setting 5 ctd1_salinity values to NaN INFO 2025-06-26 10:52:31,816 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 10:52:31,817 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:52:35,934 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:52:36,505 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:52:36,507 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.240.02/ctd2.nc INFO 2025-06-26 10:52:36,509 calibrate.py _range_qc_combined_nc():898 [1] Setting 4 ctd2_salinity values to NaN INFO 2025-06-26 10:52:36,509 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 10:52:36,509 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:52:36,538 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:52:37,390 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 101940 101941 101942 101943 101944 101945 101946 101947 101948 101949 101950 101951 101952 101953 101954 101955 101956 101957 101958 101959 101960 101961 101962 101963 101964 101965 101966 101967 101968 101969 101970 101971 101972 101973 101974 101975 101976 101977 101978 101979 101980 101981 101982 101983 101984 101985 101986 101987 101988 101989 101990 101991 101992 101993 101994 101995 101996 101997 102060 102061 102062 102063 102064 102065 102066 102067 102068 102069 102070 102071 102072 102073 102074 102075 102076 102077 102078 102079 102080 102081 102082 102083 102084 102085 102086 102087 102088 102089 102090 102091 102092 102093 102094 102095 102096 102097 102098 102099 102100 102101 102102 102103 102104 102105 102106 102107 102108 102109 102110 102111 102112 102113 102114 102115 102116 102120 102121 102122 102123 102124 102125 102126 102127 102128 102129 102130 102131 102132 102133 102134 102135 102136 102137 102138 102139 102140 102141 102142 102143 102144 102145 102146 102147 102148 102149 102150 102151 102152 102153 102154 102155 102156 102157 102158 102159 102160 102161 102162 102163 102164 102165 102166 102167 102168 102169 102170 102171 102172 102173 102174 102175 102176 102240 102241 102242 102243 102244 102245 102246 102247 102248 102249 102250 102251 102252 102253 102254 102255 102256 102257 102258 102259 102260 102261 102262 102263 102264 102265 102266 102267 102268 102269 102270 102271 102272 102273 102274 102275 102276 102277 102278 102279 102280 102281 102282 102283 102284 102285 102286 102287 102288 102289 102290 102291 102292 102293 102294 102295 102296 102297 102360 102361 102362 102363 102364 102365 102366 102367 102368 102369 102370 102371 102372 102373 102374 102375 102376 102377 102378 102379 102380 102381 102382 102383 102384 102385 102386 102387 102388 102389 102390 102391 102392 102393 102394 102395 102396 102397 102398 102399 102400 102401 102402 102403 102404 102405 102406 102407 102408 102409 102410 102411 102412 102413 102414 102415 102420 102421 102422 102423 102424 102425 102426 102427 102428 102429 102430 102431 102432 102433 102434 102435 102436 102437 102438 102439 102440 102441 102442 102443 102444 102445 102446 102447 102448 102449 102450 102451 102452 102453 102454 102455 102456 102457 102458 102459 102460 102461 102462 102463 102464 102465 102466 102467 102468 102469 102470 102471 102472 102473 102474 102480 102481 102482 102483 102484 102485 102486 102487 102488 102489 102490 102491 102492 102493 102494 102495 102496 102497 102498 102499 102500 102501 102502 102503 102504 102505 102506 102507 102508 102509 102510 102511 102512 102513 102514 102515 102516 102517 102518 102519 102520 102521 102522 102523 102524 102525 102526 102527 102528 102529 102530 102531 102540 102541 102542 102543 102544 102545 102546 102547 102548 102549 102550 102551 102552 102553 102554 102555 102556 102557 102558 102559 102560 102561 102562 102563 102564 102565 102566 102567 102568 102569 102570 102571 102572 102573 102574 102575 102576 102577 102578 102579 102580 102581 102582 102583 102584 102585 102586 102587 102588 102589 102590 102591 102592 102593 102594 102595 102596 102600 102601 102602 102603 102604 102605 102606 102607 102608 102609 102610 102611 102612 102613 102614 102615 102616 102617 102618 102619 102620 102621 102622 102623 102624 102625 102626 102627 102628 102629 102630 102631 102632 102633 102634 102635 102636 102637 102638 102639 102640 102641 102642 102643 102644 102645 102660 103260 103261 202260 446100 609840 778380 906480 1081260 1081440] INFO 2025-06-26 10:52:37,565 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:52:37,571 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 10:52:37,572 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.240.02 ERROR 2025-06-26 10:52:37,572 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.240.02 INFO 2025-06-26 10:52:37,646 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_cal.nc INFO 2025-06-26 10:52:43,538 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 10:52:43,543 process.py align():251 [1] Alignment steps for 2005.240.02 INFO 2025-06-26 10:52:43,573 align.py process_cal():139 [1] Processing dorado_2005.240.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.240.02 INFO 2025-06-26 10:52:43,602 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:52:43,606 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:52:43,671 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:52:43,675 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:52:43,738 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:52:43,742 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:52:43,781 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:52:43,781 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:52:43,807 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:52:43,812 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:52:43,876 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:52:43,880 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:43,937 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:52:43,941 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:43,999 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:52:44,003 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,061 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,064 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,121 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,125 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,182 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,186 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,244 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,248 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,304 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,308 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,366 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,370 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,426 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,430 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,486 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,490 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,547 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,551 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,610 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,613 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,670 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,674 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,731 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,735 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,793 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,797 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,855 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,859 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,917 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,921 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:44,979 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:44,983 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:45,043 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:52:45,046 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:52:45,119 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:52:45,169 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:52:45,220 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:52:45,279 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:52:45,335 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:52:45,381 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_align.nc INFO 2025-06-26 10:52:45,455 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 10:52:45,458 process.py resample():273 [1] Resampling steps for 2005.240.02 INFO 2025-06-26 10:52:45,458 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:52:45,483 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_align.nc mission netCDF file INFO 2025-06-26 10:52:45,489 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_align.nc mission netCDF file INFO 2025-06-26 10:52:45,490 resample.py get_mission_start_end():1145 [1] navigation: 2005-08-28T14:30:45.365926784 to 2005-08-28T19:31:15.350788096 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:52:45,491 resample.py get_mission_start_end():1145 [1] hs2 : 2005-08-28T14:30:29.267029504 to 2005-08-28T19:31:15.310791040 (0 days 00:00:00.039997056 before mission_end) INFO 2025-06-26 10:52:45,493 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-08-28T14:30:43.016087808 to 2005-08-28T19:31:15.350788096 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:52:45,495 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-08-28T14:30:42.996089216 to 2005-08-28T19:31:15.330789504 (0 days 00:00:00.019998592 before mission_end) INFO 2025-06-26 10:52:45,496 resample.py get_mission_start_end():1145 [1] isus : 2005-08-28T14:31:52.131353088 to 2005-08-28T19:31:15.000812288 (0 days 00:00:00.349975808 before mission_end) INFO 2025-06-26 10:52:45,497 resample.py get_mission_start_end():1145 [1] biolume : 2005-08-28T14:30:23.457393408 to 2005-08-28T19:31:14.540809344 (0 days 00:00:00.809978752 before mission_end) INFO 2025-06-26 10:52:45,499 resample.py get_mission_start_end():1145 [1] tailcone : 2005-08-28T14:30:23.937394816 to 2005-08-28T19:31:15.320790272 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 10:52:45,499 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_align.nc mission netCDF file INFO 2025-06-26 10:52:45,500 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,711 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,748 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,783 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,821 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,854 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,886 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,917 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,948 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:45,977 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,009 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,040 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,069 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,097 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,127 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,157 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,184 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,214 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,243 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,274 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,303 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,332 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,362 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,377 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,391 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,404 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,419 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,455 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:52:46,658 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_1S.nc INFO 2025-06-26 10:52:47,853 create_products.py gulper_odv():401 [1] No gulper times found for 2005.240.02 INFO 2025-06-26 10:52:47,853 process.py archive():337 [1] Archiving steps for 2005.240.02 INFO 2025-06-26 10:52:47,853 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02, BASE_PATH = /data/auv_data INFO 2025-06-26 10:52:47,853 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:52:47,855 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.02_1S.nc INFO 2025-06-26 10:52:47,874 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:52:47,875 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.02_cal.nc INFO 2025-06-26 10:52:47,956 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:52:47,957 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.02_align.nc INFO 2025-06-26 10:52:48,034 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:52:48,056 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,078 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,083 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,098 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,158 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,164 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,194 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,213 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.02 done. INFO 2025-06-26 10:52:48,267 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:52:48,267 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.02/dorado_2005.240.02_processing.log /Volumes/AUVCTD/surveys/2005/netcdf