INFO 2025-10-20 23:07:42,007 process.py process_mission():429 [1] commandline = /src/data/process_i2map.py -v --noinput --start_year 2019 --end_year 2019 --start_yd 1 --end_yd 365 --num_cores 1 --clobber INFO 2025-10-20 23:07:42,007 process.py process_mission():449 [1] Processing i2map mission 2019.190.00 by user docker_user on host bc943cff5f21 INFO 2025-10-20 23:07:42,008 process.py download_process():165 [1] Download and processing steps for 2019.190.00 INFO 2025-10-20 23:07:42,008 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/M3/master/i2MAP/2019/07/20190709/2019.190.00 INFO 2025-10-20 23:07:42,008 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/M3/master/i2MAP/2019/07/20190709/2019.190.00 to /data/auv_data/i2map/missionlogs/2019.190.00 INFO 2025-10-20 23:07:42,613 logs2netcdfs.py download_process_logs():779 [1] Processing mission: i2map 2019.190.00 INFO 2025-10-20 23:07:42,614 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.190.00/gps.log (788 bytes) INFO 2025-10-20 23:07:42,619 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.190.00/navigation.log (0 bytes) WARNING 2025-10-20 23:07:42,619 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/i2map/missionlogs/2019.190.00/navigation.log is empty INFO 2025-10-20 23:07:42,619 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.190.00/parosci.log (31686982 bytes) WARNING 2025-10-20 23:07:44,397 logs2netcdfs.py _create_variable():536 [1] temp_period: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (660139,) and arg 1 with shape (660138,). INFO 2025-10-20 23:07:44,398 logs2netcdfs.py _create_variable():537 [1] len(data) (660138) does not match shape of temp_period.shape[0] (660139) WARNING 2025-10-20 23:07:44,398 logs2netcdfs.py _create_variable():544 [1] temp_period data is short by one, appending the last value: 0.0 WARNING 2025-10-20 23:07:44,457 logs2netcdfs.py _create_variable():536 [1] pres_period: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (660139,) and arg 1 with shape (660138,). INFO 2025-10-20 23:07:44,457 logs2netcdfs.py _create_variable():537 [1] len(data) (660138) does not match shape of pres_period.shape[0] (660139) WARNING 2025-10-20 23:07:44,457 logs2netcdfs.py _create_variable():544 [1] pres_period data is short by one, appending the last value: 0.0 INFO 2025-10-20 23:07:45,237 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.190.00/parosci.log: [ 45230 45231 45232 45233 45234 45235 45236 45237 45238 45239 45240 72171 72172 72173 72174 72175 72176 72177 72178 72179 72180 72181 72182 72183 72184 72185 72186 72187 72188 72189 72190 72191 99250 99251 99252 99253 99254 99255 99256 99257 99258 99259 99260 99261 99262 99263 99264 99265 99266 99267 99268 99269 99270 127965 127966 127967 127968 127969 127970 127971 127972 127973 127974 127975 127976 127977 127978 127979 127980 127981 127982 127983 127984 127985 153952 153953 153954 153955 153956 153957 153958 153959 153960 153961 153962 153963 153964 153965 153966 153967 153968 153969 153970 153971 153972 182287 182288 182289 182290 182291 182292 182293 182294 182295 182296 182297 182298 182299 182300 182301 182302 182303 182304 182305 182306 182307 208243 208244 208245 208246 208247 208248 208249 208250 208251 208252 208253 208254 208255 208256 208257 208258 208259 208260 208261 208262 208263 235025 235026 235027 235028 235029 235030 235031 235032 235033 235034 235035 235036 235037 235038 235039 235040 235041 235042 235043 235044 235045 262654 262655 262656 262657 262658 262659 262660 262661 262662 262663 262664 262665 262666 262667 262668 262669 262670 262671 262672 262673 262674 275804 275805 275806 275807 275808 275809 275810 275811 275812 275813 275814 275815 275816 327539 327540 327541 327647 327648 327649 327650 327651 327652 327653 327654 391395 391396 391397 391398 391399 391400 391401 391402 391403 391404 391405 418178 418179 418180 418181 418182 418183 418184 418185 418186 418187 418188 418189 418190 418191 418192 418193 418194 418195 418196 418197 418198 445281 445282 445283 445284 445285 445286 445287 445288 445289 445290 445291 445292 445293 445294 445295 445296 445297 445298 445299 445300 445301 482336 482337 482338 482339 482340 482341 482342 482343 482344 482345 482346 482347 482348 482349 482350 482351 482352 482353 482354 482355 482356 509582 509583 509584 509585 509586 509587 509588 509589 509590 509591 509592 509593 509594 509595 509596 509597 509598 509599 509600 509601 509602 509603 509604 509605 509606 509607 572799 572800 572801 572802 572803 572804 572805 572806 572807 572808 572809 572810 572811 572812 572813 572814 572815 572816 572817 572818 572819 614311 614312 614313 614314 614315 614316 614317 614318 614319 614320 614321 614322 614323 614324 614325 614326 614327 614328 614329 614330 614331 640286 640287 640288 640289 640290 640291 640292 640293 640294 640295 640296 640297 640298 640299 640300 640301 640302 640303 640304 640305 640306] INFO 2025-10-20 23:07:45,318 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.190.00/seabird25p.log (21857106 bytes) WARNING 2025-10-20 23:07:46,510 logs2netcdfs.py _create_variable():536 [1] spare1: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,510 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of spare1.shape[0] (182136) WARNING 2025-10-20 23:07:46,510 logs2netcdfs.py _create_variable():544 [1] spare1 data is short by one, appending the last value: 0.0026702880859375 WARNING 2025-10-20 23:07:46,535 logs2netcdfs.py _create_variable():536 [1] dissolvedO2_port: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,535 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of dissolvedO2_port.shape[0] (182136) WARNING 2025-10-20 23:07:46,535 logs2netcdfs.py _create_variable():544 [1] dissolvedO2_port data is short by one, appending the last value: 0.8420562744140625 WARNING 2025-10-20 23:07:46,561 logs2netcdfs.py _create_variable():536 [1] spare2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,561 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of spare2.shape[0] (182136) WARNING 2025-10-20 23:07:46,561 logs2netcdfs.py _create_variable():544 [1] spare2 data is short by one, appending the last value: 0.0006103515625 WARNING 2025-10-20 23:07:46,587 logs2netcdfs.py _create_variable():536 [1] dissolvedO2_stbd: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,588 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of dissolvedO2_stbd.shape[0] (182136) WARNING 2025-10-20 23:07:46,588 logs2netcdfs.py _create_variable():544 [1] dissolvedO2_stbd data is short by one, appending the last value: 0.785675048828125 WARNING 2025-10-20 23:07:46,614 logs2netcdfs.py _create_variable():536 [1] spare3: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,614 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of spare3.shape[0] (182136) WARNING 2025-10-20 23:07:46,614 logs2netcdfs.py _create_variable():544 [1] spare3 data is short by one, appending the last value: 0.0006103515625 WARNING 2025-10-20 23:07:46,641 logs2netcdfs.py _create_variable():536 [1] spare4: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,642 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of spare4.shape[0] (182136) WARNING 2025-10-20 23:07:46,642 logs2netcdfs.py _create_variable():544 [1] spare4 data is short by one, appending the last value: 0.0 WARNING 2025-10-20 23:07:46,669 logs2netcdfs.py _create_variable():536 [1] spare5: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,669 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of spare5.shape[0] (182136) WARNING 2025-10-20 23:07:46,669 logs2netcdfs.py _create_variable():544 [1] spare5 data is short by one, appending the last value: 0.0 WARNING 2025-10-20 23:07:46,700 logs2netcdfs.py _create_variable():536 [1] salinity: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (182136,) and arg 1 with shape (182135,). INFO 2025-10-20 23:07:46,700 logs2netcdfs.py _create_variable():537 [1] len(data) (182135) does not match shape of salinity.shape[0] (182136) WARNING 2025-10-20 23:07:46,700 logs2netcdfs.py _create_variable():544 [1] salinity data is short by one, appending the last value: 34.16441629488118 INFO 2025-10-20 23:07:46,963 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.190.00/seabird25p.log: [ 1 36333 36334 36335 36336 36337 36338 36339 36340 36341 57975 57976 57977 57978 57979 57980 57981 57982 57983 57984 57985 57986 57987 57988 57989 57990 57991 79730 79731 79732 79733 79734 79735 79736 79737 79738 79739 79740 79741 79742 79743 79744 79745 79746 102795 102796 102797 102798 102799 102800 102801 102802 102803 102804 102805 102806 102807 102808 102809 102810 102811 123670 123671 123672 123673 123674 123675 123676 123677 123678 123679 123680 123681 123682 123683 123684 123685 123686 146432 146433 146434 146435 146436 146437 146438 146439 146440 146441 146442 146443 146444 146445 146446 146447 146448 167283 167284 167285 167286 167287 167288 167289 167290 167291 167292 167293 167294 167295 167296 167297 167298 167299] INFO 2025-10-20 23:07:47,047 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.190.00/tailCone.log (523 bytes) INFO 2025-10-20 23:07:47,051 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.44 seconds INFO 2025-10-20 23:07:47,051 process.py calibrate():227 [1] Calibration steps for 2019.190.00 WARNING 2025-10-20 23:07:47,057 calibrate.py _read_data():999 [1] /data/auv_data/i2map/missionnetcdfs/2019.190.00/gps.nc: No summary field WARNING 2025-10-20 23:07:47,085 calibrate.py _read_data():999 [1] /data/auv_data/i2map/missionnetcdfs/2019.190.00/tailCone.nc: No summary field ERROR 2025-10-20 23:07:47,085 calibrate.py process_logs():3542 [1] Error processing navigation: navigation has no orig_data - likely a missing or zero-sized .log file in missionlogs/2019.190.00 ERROR 2025-10-20 23:07:47,086 calibrate.py process_logs():3546 [1] Error processing gps Traceback (most recent call last): File "/src/data/calibrate.py", line 3535, in process_logs self._process(sensor, logs_dir, netcdfs_dir) File "/src/data/calibrate.py", line 3480, in _process self._gps_process(sensor) File "/src/data/calibrate.py", line 2011, in _gps_process raise ValueError(error_message) ValueError: No latitude data found in gps.log INFO 2025-10-20 23:08:09,392 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 2935 on port side INFO 2025-10-20 23:08:09,392 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "2935" INFO 2025-10-20 23:08:09,545 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2014_Nov 2021_Mar 2022_Apr WARNING 2025-10-20 23:08:09,549 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2014_Nov INFO 2025-10-20 23:08:09,549 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:08:09,555 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2021_Mar INFO 2025-10-20 23:08:09,555 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:08:09,559 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr INFO 2025-10-20 23:08:09,559 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} INFO 2025-10-20 23:08:09,569 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml has CalibrationDate 2022-03-22 00:00:00+00:00 INFO 2025-10-20 23:08:09,570 calibrate.py _read_oxy_coeffs():1253 [1] Breaking from loop as /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is after 2019.190.00 with mission_start=2019-07-09T16:05:39.624456704 INFO 2025-10-20 23:08:09,570 calibrate.py _read_oxy_coeffs():1270 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is the first calibration file, but is after 2019.190.00 with mission_start=2019-07-09T16:05:39.624456704 INFO 2025-10-20 23:08:12,858 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_port: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml file: {'Soc': 0.42595, 'offset': -0.5339, 'A': -0.0041113, 'B': 0.00020802, 'C': -3.0027e-06, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.09, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0} INFO 2025-10-20 23:08:12,862 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 3488 on stbd side INFO 2025-10-20 23:08:12,862 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "3488" INFO 2025-10-20 23:08:13,004 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2016_dec 2021_mar 2022_Jan WARNING 2025-10-20 23:08:13,009 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec INFO 2025-10-20 23:08:13,009 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:08:13,013 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2021_mar INFO 2025-10-20 23:08:13,013 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:08:13,017 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2022_Jan INFO 2025-10-20 23:08:13,017 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} INFO 2025-10-20 23:08:13,023 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml has CalibrationDate 2016-12-16 00:00:00+00:00 INFO 2025-10-20 23:08:13,023 calibrate.py _read_oxy_coeffs():1263 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml is just before 2019.190.00 with mission_start=2019-07-09T16:05:39.624456704 INFO 2025-10-20 23:08:16,307 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_stbd: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml file: {'Soc': 0.44664, 'offset': -0.507, 'A': -0.0030812, 'B': 7.8442e-05, 'C': -9.0601e-07, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.44, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0} ERROR 2025-10-20 23:08:19,520 calibrate.py process_logs():3542 [1] Error processing seabird25p: No navigation_time or navigation_pitch in combined_nc. ERROR 2025-10-20 23:08:19,521 calibrate.py process_logs():3546 [1] Error processing tailcone Traceback (most recent call last): File "/src/data/calibrate.py", line 3535, in process_logs self._process(sensor, logs_dir, netcdfs_dir) File "/src/data/calibrate.py", line 3488, in _process self._tailcone_process(sensor) File "/src/data/calibrate.py", line 2964, in _tailcone_process raise ValueError(error_message) from None ValueError: No data in tailcone.nc - likely empty tailcone.log file INFO 2025-10-20 23:08:19,522 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/i2map/missionnetcdfs/2019.190.00/i2map_2019.190.00_cal.nc INFO 2025-10-20 23:08:32,731 calibrate.py write_netcdf():3512 [1] Data variables written: depth_filtdepth, depth_filtpres, depth_time, seabird25p_beam_transmittance, seabird25p_conductivity, seabird25p_conductivity_onboard, seabird25p_dissolvedO2_port, seabird25p_dissolvedO2_stbd, seabird25p_oxygen_mll_port, seabird25p_oxygen_mll_stbd, seabird25p_oxygen_umolkg_port, seabird25p_oxygen_umolkg_stbd, seabird25p_salinity, seabird25p_salinity_onboard, seabird25p_temperature, seabird25p_temperature_onboard, seabird25p_time INFO 2025-10-20 23:08:32,732 process.py align():251 [1] Alignment steps for 2019.190.00 INFO 2025-10-20 23:08:32,752 align.py process_cal():139 [1] Processing i2map_2019.190.00_cal.nc from /data/auv_data/i2map/missionnetcdfs/2019.190.00 ERROR 2025-10-20 23:08:32,752 process.py process_mission_exception_wrapper():537 [1] An exception occurred Traceback (most recent call last): File "/src/data/process.py", line 529, in process_mission_exception_wrapper self.process_mission(mission, src_dir=src_dir) File "/src/data/process.py", line 485, in process_mission self.align(mission) File "/src/data/process.py", line 263, in align netcdf_dir = align_netcdf.process_cal() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/src/data/align.py", line 182, in process_cal raise InvalidCalFile(error_message) from None align.InvalidCalFile: No nudged_latitude data in i2map_2019.190.00_cal.nc ERROR 2025-10-20 23:08:32,753 process.py process_mission_exception_wrapper():538 [1] Failed to process to completion: 2019.190.00 INFO 2025-10-20 23:08:32,754 process.py archive():337 [1] Archiving steps for 2019.190.00 INFO 2025-10-20 23:08:32,754 process.py archive():347 [1] nc_file_base = /data/auv_data/i2map/missionnetcdfs/2019.190.00/i2map_2019.190.00, BASE_PATH = /data/auv_data INFO 2025-10-20 23:08:32,755 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/i2map/missionnetcdfs/2019.190.00/i2map_2019.190.00 files to /Volumes/AUVCTD/surveys/2019/netcdf INFO 2025-10-20 23:08:32,756 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2019/netcdf/i2map_2019.190.00_cal.nc INFO 2025-10-20 23:08:32,854 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/i2map_2019.190.00_cal.nc /Volumes/AUVCTD/surveys/2019/netcdf done. INFO 2025-10-20 23:08:32,863 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019190/2019.190.00 done. INFO 2025-10-20 23:08:32,953 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019190/2019.190.00 done. INFO 2025-10-20 23:08:33,017 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/seabird25p.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019190/2019.190.00 done. INFO 2025-10-20 23:08:33,021 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019190/2019.190.00 done. INFO 2025-10-20 23:08:33,022 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-10-20 23:08:33,022 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.190.00/i2map_2019.190.00_processing.log /Volumes/AUVCTD/surveys/2019/netcdf