INFO 2025-06-26 17:35:56,541 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 17:35:56,542 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Yanwu trigger on front servey mission in north bay. Hans said it aborted earlly. Maybe it hit something. - ctdToUse = ctd1 INFO 2025-06-26 17:35:56,542 process.py process_mission():449 [1] Processing AUVCTD mission 2011.115.10 by user docker_user on host eae60d30a712 INFO 2025-06-26 17:35:56,542 process.py download_process():165 [1] Download and processing steps for 2011.115.10 INFO 2025-06-26 17:35:56,542 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011115/2011.115.10 INFO 2025-06-26 17:35:56,542 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011115/2011.115.10 to /data/auv_data/dorado/missionlogs/2011.115.10 INFO 2025-06-26 17:36:03,175 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.115.10 INFO 2025-06-26 17:36:03,175 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/ctdDriver.log (19816907 bytes) INFO 2025-06-26 17:36:04,821 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/ctdDriver2.log (19823135 bytes) INFO 2025-06-26 17:36:06,351 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2011.115.10/ctdDriver2.log: [1] INFO 2025-06-26 17:36:06,448 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/gps.log (343652 bytes) INFO 2025-06-26 17:36:06,495 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/hydroscatlog.log (17343670 bytes) INFO 2025-06-26 17:36:08,341 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2011.115.10/hydroscatlog.log: [123202] INFO 2025-06-26 17:36:08,425 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/navigation.log (70192182 bytes) INFO 2025-06-26 17:36:13,912 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/isuslog.log (1283733 bytes) INFO 2025-06-26 17:36:14,045 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/parosci.log (21005414 bytes) INFO 2025-06-26 17:36:15,938 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/tailCone.log (12395467 bytes) INFO 2025-06-26 17:36:17,572 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/biolume.log (14424782 bytes) INFO 2025-06-26 17:36:18,992 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 17:36:19,723 logs2netcdfs.py download_process_logs():807 [1] Time to process: 16.55 seconds INFO 2025-06-26 17:36:19,723 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.115.10/lopc.bin (225151000 bytes) INFO 2025-06-26 17:36:19,723 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 17:36:19 2025 INFO 2025-06-26 17:36:19,723 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.115.10/parosci.nc INFO 2025-06-26 17:36:19,723 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 17:36:19,723 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.115.10/parosci.nc INFO 2025-06-26 17:36:19,727 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1303767610.4, sensor_off_time = 1303819257.3 INFO 2025-06-26 17:36:19,727 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 51646 seconds. Expecting to read 103292 L frames from the lopc.bin file. INFO 2025-06-26 17:36:19,727 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 103292 records from the lopc.bin file. INFO 2025-06-26 17:36:20,341 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-04-25 21:40:10 Z and endTime = 2011-04-26 12:00:57 Z with 103292 records expected to be read from lopc.bin INFO 2025-06-26 17:36:20,341 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.115.10/lopc.bin INFO 2025-06-26 17:36:20,341 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.115.10/lopc.nc INFO 2025-06-26 17:36:20,342 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.115.10/lopc.nc INFO 2025-06-26 17:36:20,342 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.115.10 INFO 2025-06-26 17:36:20,342 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 17:36:20,506 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 17:36:20,506 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 17:36:20,506 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 17:36:20,643 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 17:36:20,644 process.py calibrate():227 [1] Calibration steps for 2011.115.10 INFO 2025-06-26 17:36:21,003 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 17:36:21,005 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 17:36:21,835 calibrate.py _nudge_pos():1806 [1] 111: 0.010 0.0377003 -0.0009585 1135 3.78 1479.189 -46.985 2011-04-25T21:45:46.479900672 INFO 2025-06-26 17:36:22,718 calibrate.py _nudge_pos():1806 [1] 198: 0.010 0.0007677 -0.0063700 13850 46.16 2.467 -25.569 2011-04-25T22:33:22.474251520 INFO 2025-06-26 17:36:23,753 calibrate.py _nudge_pos():1806 [1] 298: 0.010 -0.0006771 -0.0061886 14655 48.85 -2.056 -23.476 2011-04-25T23:23:52.476682240 INFO 2025-06-26 17:36:25,094 calibrate.py _nudge_pos():1806 [1] 432: 0.020 -0.0012564 -0.0054819 12565 41.88 -4.450 -24.255 2011-04-26T00:07:58.475418880 INFO 2025-06-26 17:36:25,144 calibrate.py _nudge_pos():1806 [1] 437: 0.020 -0.0000140 -0.0000221 25 0.08 -25.893 -51.229 2011-04-26T00:08:07.474802432 INFO 2025-06-26 17:36:25,832 calibrate.py _nudge_pos():1806 [1] 507: 0.010 -0.0000120 -0.0000081 20 0.06 -28.012 -23.682 2011-04-26T00:09:20.479801088 INFO 2025-06-26 17:36:25,882 calibrate.py _nudge_pos():1806 [1] 512: 0.020 -0.0008011 -0.0074021 16790 55.96 -2.123 -24.509 2011-04-26T01:05:22.479488256 INFO 2025-06-26 17:36:25,942 calibrate.py _nudge_pos():1806 [1] 518: 0.020 -0.0000241 -0.0000553 50 0.16 -21.903 -62.772 2011-04-26T01:05:37.478460928 INFO 2025-06-26 17:36:26,454 calibrate.py _nudge_pos():1806 [1] 569: 0.030 -0.0000157 -0.0000047 15 0.05 -50.030 -18.678 2011-04-26T01:06:30.474830336 INFO 2025-06-26 17:36:26,524 calibrate.py _nudge_pos():1806 [1] 576: 0.020 0.0000409 -0.0000302 35 0.11 53.514 -49.351 2011-04-26T01:06:43.473939968 INFO 2025-06-26 17:36:26,650 calibrate.py _nudge_pos():1806 [1] 588: 0.030 -0.0003615 -0.0081726 17295 57.65 -0.930 -26.270 2011-04-26T02:04:34.476160000 INFO 2025-06-26 17:36:26,760 calibrate.py _nudge_pos():1806 [1] 599: 0.030 0.0000039 -0.0000568 85 0.28 2.056 -37.582 2011-04-26T02:05:02.474242048 INFO 2025-06-26 17:36:27,350 calibrate.py _nudge_pos():1806 [1] 658: 0.020 0.0000674 -0.0000921 20 0.06 157.916 -269.339 2011-04-26T02:06:04.479994368 INFO 2025-06-26 17:36:27,381 calibrate.py _nudge_pos():1806 [1] 661: 0.030 -0.0012017 -0.0061916 13310 44.36 -4.018 -25.861 2011-04-26T02:50:28.477498112 INFO 2025-06-26 17:36:27,412 calibrate.py _nudge_pos():1806 [1] 664: 0.030 -0.0000025 0.0000202 20 0.06 -5.950 58.994 2011-04-26T02:50:34.477086976 INFO 2025-06-26 17:36:27,453 calibrate.py _nudge_pos():1806 [1] 668: 0.030 -0.0000577 -0.0000539 35 0.11 -75.528 -88.110 2011-04-26T02:50:44.476401920 INFO 2025-06-26 17:36:27,494 calibrate.py _nudge_pos():1806 [1] 672: 0.030 0.0000097 -0.0000230 30 0.10 14.935 -44.088 2011-04-26T02:50:53.475785472 INFO 2025-06-26 17:36:28,332 calibrate.py _nudge_pos():1806 [1] 755: 0.040 -0.0012821 -0.0053844 13320 44.40 -4.284 -22.473 2011-04-26T03:36:40.477603072 INFO 2025-06-26 17:36:29,126 calibrate.py _nudge_pos():1806 [1] 833: 0.040 -0.0000074 -0.0000220 15 0.05 -23.551 -87.451 2011-04-26T03:38:00.472122880 INFO 2025-06-26 17:36:29,307 calibrate.py _nudge_pos():1806 [1] 851: 0.040 -0.0035216 -0.0023083 14185 47.28 -11.045 -9.047 2011-04-26T04:25:34.476610304 INFO 2025-06-26 17:36:29,834 calibrate.py _nudge_pos():1806 [1] 895: 0.040 0.0000317 0.0000207 20 0.06 74.163 60.592 2011-04-26T04:26:21.473390848 INFO 2025-06-26 17:36:30,165 calibrate.py _nudge_pos():1806 [1] 927: 0.050 -0.0027776 -0.0006775 14370 47.90 -8.596 -2.621 2011-04-26T05:14:46.474384640 INFO 2025-06-26 17:36:30,741 calibrate.py _nudge_pos():1806 [1] 980: 0.040 0.0000420 0.0000066 135 0.45 13.937 2.746 2011-04-26T05:16:05.478972416 INFO 2025-06-26 17:36:30,762 calibrate.py _nudge_pos():1806 [1] 982: 0.040 0.0001190 -0.0000850 4370 14.56 1.211 -1.082 2011-04-26T05:30:40.479030784 INFO 2025-06-26 17:36:31,345 calibrate.py _nudge_pos():1806 [1] 1038: 0.050 -0.0000189 0.0000099 20 0.06 -44.220 29.037 2011-04-26T05:31:39.474989312 INFO 2025-06-26 17:36:31,606 calibrate.py _nudge_pos():1806 [1] 1063: 0.040 -0.0010749 -0.0071418 14105 47.01 -3.389 -28.149 2011-04-26T06:19:04.480092928 INFO 2025-06-26 17:36:32,377 calibrate.py _nudge_pos():1806 [1] 1137: 0.050 0.0006853 -0.0071223 14305 47.68 2.131 -27.679 2011-04-26T07:07:58.479100416 INFO 2025-06-26 17:36:33,231 calibrate.py _nudge_pos():1806 [1] 1219: 0.050 0.0007931 -0.0071598 15765 52.55 2.237 -25.248 2011-04-26T08:01:52.477556224 INFO 2025-06-26 17:36:34,142 calibrate.py _nudge_pos():1806 [1] 1306: 0.070 0.0007866 -0.0068587 14900 49.66 2.348 -25.591 2011-04-26T08:52:58.477520896 INFO 2025-06-26 17:36:35,050 calibrate.py _nudge_pos():1806 [1] 1392: 0.070 0.0005403 -0.0069136 17095 56.98 1.406 -22.483 2011-04-26T09:51:22.477480448 INFO 2025-06-26 17:36:35,989 calibrate.py _nudge_pos():1806 [1] 1480: 0.070 0.0018302 -0.0040627 9735 32.45 8.361 -23.201 2011-04-26T10:25:16.478141952 INFO 2025-06-26 17:36:36,956 calibrate.py _nudge_pos():1806 [1] 1571: 0.070 -0.0019918 -0.0012109 7620 25.40 -11.623 -8.835 2011-04-26T10:52:10.477575424 INFO 2025-06-26 17:36:37,135 calibrate.py _nudge_pos():1806 [1] 1588: 0.080 -0.0008190 -0.0011091 4690 15.63 -7.765 -13.148 2011-04-26T11:08:04.472222208 INFO 2025-06-26 17:37:11,154 calibrate.py _nudge_pos():1862 [1] 4724: - - - 4 0.01 - - INFO 2025-06-26 17:37:11,154 calibrate.py _nudge_pos():1868 [1] Points in final series = 257984 WARNING 2025-06-26 17:37:11,486 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 17:37:37,257 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 24 of 206459 INFO 2025-06-26 17:37:38,809 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:37:40,782 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:37:42,296 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:37:42,300 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.115.10/ctd1.nc INFO 2025-06-26 17:37:42,301 calibrate.py _range_qc_combined_nc():898 [1] Setting 12 ctd1_salinity values to NaN INFO 2025-06-26 17:37:42,302 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 17:37:42,302 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 17:37:53,785 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:37:55,335 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:37:55,338 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.115.10/ctd2.nc WARNING 2025-06-26 17:37:55,340 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (7916) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 17:37:55,340 calibrate.py _range_qc_combined_nc():898 [1] Setting 7916 ctd2_salinity values to NaN INFO 2025-06-26 17:37:55,341 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 17:37:55,341 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 17:37:55,415 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 17:37:57,709 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76] INFO 2025-06-26 17:37:58,155 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 17:38:45,258 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.115.10 ERROR 2025-06-26 17:38:45,258 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.115.10 INFO 2025-06-26 17:38:45,455 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_cal.nc INFO 2025-06-26 17:38:55,269 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 17:38:55,276 process.py align():251 [1] Alignment steps for 2011.115.10 INFO 2025-06-26 17:38:55,345 align.py process_cal():139 [1] Processing dorado_2011.115.10_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.115.10 INFO 2025-06-26 17:38:55,413 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:38:55,420 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:38:55,591 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:38:55,600 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:38:55,761 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:38:55,772 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:38:55,869 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 17:38:55,869 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 17:38:55,933 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:38:55,943 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:38:56,103 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,111 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,250 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,258 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,399 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,407 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,548 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,557 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,708 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,847 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:56,855 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:56,996 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,005 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,144 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,152 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,294 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,302 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,440 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,450 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,592 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,601 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,740 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,748 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:57,891 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:57,899 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,040 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,048 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,188 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,196 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,339 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,347 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,491 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,499 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,642 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,651 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,793 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,801 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:58,941 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:58,951 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:59,095 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:59,104 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:59,245 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.115.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:38:59,253 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:38:59,424 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:38:59,532 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:38:59,642 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:38:59,754 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:38:59,873 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:39:00,113 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 17:39:01,452 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:39:01,562 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_align.nc INFO 2025-06-26 17:39:01,856 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 17:39:01,860 process.py resample():273 [1] Resampling steps for 2011.115.10 INFO 2025-06-26 17:39:01,861 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 17:39:01,916 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_align.nc mission netCDF file INFO 2025-06-26 17:39:01,924 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_align.nc mission netCDF file INFO 2025-06-26 17:39:01,927 resample.py get_mission_start_end():1145 [1] navigation: 2011-04-25T21:40:47.300395776 to 2011-04-26T12:00:57.274870272 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 17:39:01,929 resample.py get_mission_start_end():1145 [1] hs2 : 2011-04-25T21:40:16.592499456 to 2011-04-26T12:00:57.204875264 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 17:39:01,932 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-04-25T21:40:53.939940864 to 2011-04-26T12:00:57.294868992 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 17:39:01,934 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-04-25T21:40:38.001032704 to 2011-04-26T12:00:57.284869632 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 17:39:01,936 resample.py get_mission_start_end():1145 [1] isus : 2011-04-25T21:41:26.217729792 to 2011-04-26T12:00:56.304936960 (0 days 00:00:01.029929216 before mission_end) INFO 2025-06-26 17:39:01,938 resample.py get_mission_start_end():1145 [1] biolume : 2011-04-25T21:40:10.472884480 to 2011-04-26T12:00:56.504888832 (0 days 00:00:00.829977344 before mission_end) INFO 2025-06-26 17:39:01,940 resample.py get_mission_start_end():1145 [1] tailcone : 2011-04-25T21:40:11.292862464 to 2011-04-26T12:00:57.334866176 (0 days 00:00:00 before mission_end) INFO 2025-06-26 17:39:01,941 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_align.nc mission netCDF file INFO 2025-06-26 17:39:01,941 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,474 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,559 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,642 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,725 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,796 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,868 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:02,940 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,011 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,077 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,147 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,222 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,288 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,354 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,422 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,488 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,554 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,621 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,690 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,762 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,851 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,921 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:03,990 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,061 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,131 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,160 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,184 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,206 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,229 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,252 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:04,260 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 17:39:04,260 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 17:39:06,176 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 17:39:06,809 resample.py add_biolume_proxies():633 [1] Zero flow values found: 55 of 51647 - replaced with 350 ml/s INFO 2025-06-26 17:39:06,809 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 17:39:07,050 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 17:39:07,132 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 17:39:07,192 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 17:39:07,192 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 17:39:07,283 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 17:39:07,699 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_1S.nc INFO 2025-06-26 17:39:10,542 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 17:39:21,946 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2011.115.10/dorado_2011.115.10_1S_Gulper.txt INFO 2025-06-26 17:39:21,946 process.py archive():337 [1] Archiving steps for 2011.115.10 INFO 2025-06-26 17:39:21,946 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10, BASE_PATH = /data/auv_data INFO 2025-06-26 17:39:21,948 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 17:39:21,949 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.115.10_1S.nc INFO 2025-06-26 17:39:21,994 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:39:21,995 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.115.10_cal.nc INFO 2025-06-26 17:39:22,300 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:39:22,302 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.115.10_align.nc INFO 2025-06-26 17:39:22,732 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:39:22,789 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:22,843 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:22,849 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:22,900 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,080 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,090 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,152 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,196 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,328 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,334 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011115/2011.115.10 done. INFO 2025-06-26 17:39:23,335 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 17:39:23,336 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2011/odv/dorado_2011.115.10_1S_Gulper.txt INFO 2025-06-26 17:39:23,341 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2011.115.10/dorado_2011.115.10_1S_Gulper.txt /Volumes/AUVCTD/surveys/2011/odv done. INFO 2025-06-26 17:39:23,341 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.115.10/dorado_2011.115.10_processing.log /Volumes/AUVCTD/surveys/2011/netcdf