INFO 2025-06-26 10:32:38,643 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 10:32:38,643 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Depth abort problems - lots of missions for this biolume survey - ctdToUse = ctd1 
INFO 2025-06-26 10:32:38,643 process.py process_mission():449 [1] Processing BIOLUME mission 2005.027.08 by user docker_user on host eae60d30a712
INFO 2025-06-26 10:32:38,643 process.py download_process():165 [1] Download and processing steps for 2005.027.08
INFO 2025-06-26 10:32:38,643 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005027/2005.027.08
INFO 2025-06-26 10:32:38,644 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005027/2005.027.08 to /data/auv_data/dorado/missionlogs/2005.027.08
INFO 2025-06-26 10:32:38,712 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.027.08
INFO 2025-06-26 10:32:38,712 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/ctdDriver.log (0 bytes)
WARNING 2025-06-26 10:32:38,713 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2005.027.08/ctdDriver.log is empty
INFO 2025-06-26 10:32:38,713 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/ctdDriver2.log (0 bytes)
WARNING 2025-06-26 10:32:38,713 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2005.027.08/ctdDriver2.log is empty
INFO 2025-06-26 10:32:38,713 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/gps.log (1724 bytes)
INFO 2025-06-26 10:32:38,721 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/hydroscatlog.log (2354 bytes)
INFO 2025-06-26 10:32:38,728 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/navigation.log (0 bytes)
WARNING 2025-06-26 10:32:38,728 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2005.027.08/navigation.log is empty
INFO 2025-06-26 10:32:38,728 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/isuslog.log (44241 bytes)
INFO 2025-06-26 10:32:38,736 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/parosci.log (82406 bytes)
INFO 2025-06-26 10:32:38,747 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/tailCone.log (3019 bytes)
INFO 2025-06-26 10:32:38,753 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.027.08/biolume.log (5852 bytes)
INFO 2025-06-26 10:32:38,757 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data
INFO 2025-06-26 10:32:38,759 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.05 seconds
WARNING 2025-06-26 10:32:38,759 process.py download_process():196 [1] No lopc.bin file for 2005.027.08
INFO 2025-06-26 10:32:38,760 process.py calibrate():227 [1] Calibration steps for 2005.027.08
ERROR 2025-06-26 10:32:38,786 calibrate.py process_logs():3542 [1] Error processing navigation: navigation has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.027.08
ERROR 2025-06-26 10:32:38,789 calibrate.py process_logs():3542 [1] Error processing gps: No navigation_longitude data in combined_nc
WARNING 2025-06-26 10:32:38,792 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 4.76 Hz
ERROR 2025-06-26 10:32:38,806 calibrate.py process_logs():3542 [1] Error processing hs2: No navigation_time or navigation_pitch in combined_nc.
ERROR 2025-06-26 10:32:38,806 calibrate.py process_logs():3542 [1] Error processing ctd1: ctd1 has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.027.08
ERROR 2025-06-26 10:32:38,806 calibrate.py process_logs():3542 [1] Error processing ctd2: ctd2 has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.027.08
INFO 2025-06-26 10:32:38,812 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz
ERROR 2025-06-26 10:32:38,813 calibrate.py process_logs():3542 [1] Error processing biolume: No navigation_time or navigation_pitch in combined_nc.
ERROR 2025-06-26 10:32:38,814 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.027.08
ERROR 2025-06-26 10:32:38,814 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.027.08
INFO 2025-06-26 10:32:38,817 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.027.08/dorado_2005.027.08_cal.nc
INFO 2025-06-26 10:32:38,830 calibrate.py write_netcdf():3512 [1] Data variables written: depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, tailcone_propRpm, tailcone_time
INFO 2025-06-26 10:32:38,832 process.py align():251 [1] Alignment steps for 2005.027.08
INFO 2025-06-26 10:32:38,842 align.py process_cal():139 [1] Processing dorado_2005.027.08_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.027.08
ERROR 2025-06-26 10:32:38,842 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 dorado_2005.027.08_cal.nc
ERROR 2025-06-26 10:32:38,844 process.py process_mission_exception_wrapper():538 [1] Failed to process to completion: 2005.027.08
INFO 2025-06-26 10:32:38,844 process.py archive():337 [1] Archiving steps for 2005.027.08
INFO 2025-06-26 10:32:38,844 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.027.08/dorado_2005.027.08, BASE_PATH = /data/auv_data
INFO 2025-06-26 10:32:38,845 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.027.08/dorado_2005.027.08 files to /Volumes/AUVCTD/surveys/2005/netcdf
INFO 2025-06-26 10:32:38,846 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.027.08_cal.nc
INFO 2025-06-26 10:32:38,851 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/dorado_2005.027.08_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done.
INFO 2025-06-26 10:32:38,856 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,860 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,864 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,869 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,872 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,876 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005027/2005.027.08 done.
INFO 2025-06-26 10:32:38,877 archive.py copy_to_AUVTCD():116 [1] Archiving product files
INFO 2025-06-26 10:32:38,877 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.027.08/dorado_2005.027.08_processing.log /Volumes/AUVCTD/surveys/2005/netcdf