INFO 2025-06-27 02:54:23,769 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-27 02:54:23,769 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Post CANON CN20F mission - Overnight diamond in Monterey Bay - HS2 turned off - 30120G QC note: Best CTD is ?, a few screwy profiles in each - ctdToUse = ctd1 INFO 2025-06-27 02:54:23,769 process.py process_mission():449 [1] Processing CANON October 2020 Monterey Bay Diamond mission 2020.301.03 by user docker_user on host 355841a7028c INFO 2025-06-27 02:54:23,769 process.py download_process():165 [1] Download and processing steps for 2020.301.03 INFO 2025-06-27 02:54:23,769 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2020/2020301/2020.301.03 INFO 2025-06-27 02:54:23,769 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2020/2020301/2020.301.03 to /data/auv_data/dorado/missionlogs/2020.301.03 INFO 2025-06-27 02:54:32,719 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2020.301.03 INFO 2025-06-27 02:54:32,720 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/ctdDriver.log (28345254 bytes) INFO 2025-06-27 02:54:34,828 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/ctdDriver2.log (28345245 bytes) INFO 2025-06-27 02:54:36,904 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/gps.log (1589900 bytes) INFO 2025-06-27 02:54:37,075 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/navigation.log (109227470 bytes) INFO 2025-06-27 02:54:45,267 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/isuslog.log (1836437 bytes) INFO 2025-06-27 02:54:45,443 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2020.301.03/isuslog.log: [ 1 2 3 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26 28 29 30 31 32 33 34 35 36 38 39 40 41 42 43 44] INFO 2025-06-27 02:54:45,448 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/parosci.log (35272022 bytes) INFO 2025-06-27 02:54:48,433 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/FLBBCD2K.log (27552555 bytes) INFO 2025-06-27 02:54:51,978 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2020.301.03/FLBBCD2K.log: [ 2 3 8 129102 129103 129105 129114] INFO 2025-06-27 02:54:52,089 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/tailCone.log (17711627 bytes) WARNING 2025-06-27 02:54:53,694 logs2netcdfs.py _create_variable():536 [1] rudderCurrent: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,694 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of rudderCurrent.shape[0] (368982) WARNING 2025-06-27 02:54:53,694 logs2netcdfs.py _create_variable():544 [1] rudderCurrent data is short by one, appending the last value: 0 WARNING 2025-06-27 02:54:53,727 logs2netcdfs.py _create_variable():536 [1] propCurrent1: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,727 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of propCurrent1.shape[0] (368982) WARNING 2025-06-27 02:54:53,727 logs2netcdfs.py _create_variable():544 [1] propCurrent1 data is short by one, appending the last value: 0.0 WARNING 2025-06-27 02:54:53,761 logs2netcdfs.py _create_variable():536 [1] propCurrent2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,761 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of propCurrent2.shape[0] (368982) WARNING 2025-06-27 02:54:53,761 logs2netcdfs.py _create_variable():544 [1] propCurrent2 data is short by one, appending the last value: 0 WARNING 2025-06-27 02:54:53,784 logs2netcdfs.py _create_variable():536 [1] propRpm: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,784 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of propRpm.shape[0] (368982) WARNING 2025-06-27 02:54:53,784 logs2netcdfs.py _create_variable():544 [1] propRpm data is short by one, appending the last value: 0 WARNING 2025-06-27 02:54:53,817 logs2netcdfs.py _create_variable():536 [1] elevatorAngle: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,817 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of elevatorAngle.shape[0] (368982) WARNING 2025-06-27 02:54:53,817 logs2netcdfs.py _create_variable():544 [1] elevatorAngle data is short by one, appending the last value: -0.004362570121884346 WARNING 2025-06-27 02:54:53,863 logs2netcdfs.py _create_variable():536 [1] rudderAngle: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,863 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of rudderAngle.shape[0] (368982) WARNING 2025-06-27 02:54:53,863 logs2netcdfs.py _create_variable():544 [1] rudderAngle data is short by one, appending the last value: 0.17545251548290253 WARNING 2025-06-27 02:54:53,898 logs2netcdfs.py _create_variable():536 [1] propPwm: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,898 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of propPwm.shape[0] (368982) WARNING 2025-06-27 02:54:53,898 logs2netcdfs.py _create_variable():544 [1] propPwm data is short by one, appending the last value: 0 WARNING 2025-06-27 02:54:53,921 logs2netcdfs.py _create_variable():536 [1] propTemp: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (368982,) and arg 1 with shape (368981,). INFO 2025-06-27 02:54:53,922 logs2netcdfs.py _create_variable():537 [1] len(data) (368981) does not match shape of propTemp.shape[0] (368982) WARNING 2025-06-27 02:54:53,922 logs2netcdfs.py _create_variable():544 [1] propTemp data is short by one, appending the last value: 0 INFO 2025-06-27 02:54:54,397 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/biolume.log (20618538 bytes) INFO 2025-06-27 02:54:56,511 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-27 02:54:57,524 logs2netcdfs.py download_process_logs():807 [1] Time to process: 24.80 seconds INFO 2025-06-27 02:54:57,524 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2020.301.03/lopc.bin (62803644 bytes) INFO 2025-06-27 02:54:57,524 lopcToNetCDF.py main():2297 [1] Processing begun: Fri Jun 27 02:54:57 2025 INFO 2025-06-27 02:54:57,524 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2020.301.03/parosci.nc INFO 2025-06-27 02:54:57,524 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-27 02:54:57,524 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2020.301.03/parosci.nc INFO 2025-06-27 02:54:57,528 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1603826538.3, sensor_off_time = 1603900375.2 INFO 2025-06-27 02:54:57,528 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 73836 seconds. Expecting to read 147672 L frames from the lopc.bin file. INFO 2025-06-27 02:54:57,528 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 147672 records from the lopc.bin file. INFO 2025-06-27 02:54:58,396 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2020-10-27 19:22:18 Z and endTime = 2020-10-28 15:52:55 Z with 147672 records expected to be read from lopc.bin INFO 2025-06-27 02:54:58,396 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2020.301.03/lopc.bin INFO 2025-06-27 02:54:58,396 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2020.301.03/lopc.nc WARNING 2025-06-27 02:54:58,396 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A075978 WARNING 2025-06-27 02:54:58,396 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-27 02:54:58,397 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2020.301.03/lopc.nc INFO 2025-06-27 02:54:58,397 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2020.301.03 INFO 2025-06-27 02:54:58,397 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-27 02:54:58,431 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-27 02:54:58,431 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-27 02:54:58,431 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-27 02:55:03,844 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10834 12898 0 0 0 0 0 5.4 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:07,835 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 20834 21432 0 0 0 0 0 4.0 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:12,165 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 30834 31678 0 0 0 0 0 4.3 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:16,095 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 40834 40481 0 0 0 0 0 3.9 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:20,041 lopcToNetCDF.py unpackLOPCbin():1013 [1] 50000 50834 48976 0 0 0 0 0 3.9 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:23,898 lopcToNetCDF.py unpackLOPCbin():1013 [1] 60000 60834 55928 0 0 0 0 0 3.9 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:27,839 lopcToNetCDF.py unpackLOPCbin():1013 [1] 70000 5298 63138 0 0 0 0 0 3.9 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:32,993 lopcToNetCDF.py unpackLOPCbin():1013 [1] 80000 15298 74429 0 0 0 0 0 5.2 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:39,121 lopcToNetCDF.py unpackLOPCbin():1013 [1] 90000 25298 88791 0 0 0 0 0 6.1 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:44,807 lopcToNetCDF.py unpackLOPCbin():1013 [1] 100000 35298 101952 0 0 0 0 0 5.7 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:49,051 lopcToNetCDF.py unpackLOPCbin():1013 [1] 110000 45298 110776 0 0 0 0 0 4.2 seconds, last L Frame: 147672 INFO 2025-06-27 02:55:53,661 lopcToNetCDF.py unpackLOPCbin():1013 [1] 120000 55298 121234 0 0 0 0 0 4.6 seconds, last L Frame: 147672 INFO 2025-06-27 02:56:01,193 lopcToNetCDF.py unpackLOPCbin():1013 [1] 130000 65298 140270 0 0 0 0 0 7.5 seconds, last L Frame: 147672 INFO 2025-06-27 02:56:07,968 lopcToNetCDF.py unpackLOPCbin():1013 [1] 140000 9762 157291 0 0 0 0 0 6.8 seconds, last L Frame: 147672 INFO 2025-06-27 02:56:17,160 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-27 02:56:17,160 lopcToNetCDF.py main():2346 [1] lFrameCount = 147672, mFrameCount = 183524 INFO 2025-06-27 02:56:17,160 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2020.301.03/parosci.nc INFO 2025-06-27 02:56:17,160 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-27 02:56:17,160 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2020.301.03/parosci.nc INFO 2025-06-27 02:56:17,164 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1603826538.3, sensor_off_time = 1603900375.2 INFO 2025-06-27 02:56:17,164 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 73836 seconds. Expecting to read 147672 L frames from the lopc.bin file. INFO 2025-06-27 02:56:17,164 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 147672 records from the lopc.bin file. INFO 2025-06-27 02:56:17,164 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 835 and len(sampleCountList) = 147672 INFO 2025-06-27 02:56:17,177 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [ 64701 130237] INFO 2025-06-27 02:56:17,177 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 64701, i = 1 INFO 2025-06-27 02:56:17,181 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 130237, i = 2 INFO 2025-06-27 02:56:17,182 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 835 836 837 ... 148506 148507 148508] INFO 2025-06-27 02:56:17,182 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-27 02:56:17,182 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-27 02:56:17,182 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-27 02:56:17,183 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-27 02:56:17,183 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 835 836 837 ... 148506 148507 148508] INFO 2025-06-27 02:56:17,183 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 835 836 837 ... 148506 148507 148508] with len(correctedSampleCountList) = 147672 INFO 2025-06-27 02:56:17,184 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 835 from all values of correctedSampleCountList INFO 2025-06-27 02:56:17,184 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-27 02:56:17,184 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 7.38355e+04 7.38360e+04 7.38365e+04] INFO 2025-06-27 02:56:17,185 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.60382654e+09 1.60382654e+09 1.60382654e+09 ... 1.60390037e+09 1.60390037e+09 1.60390037e+09] INFO 2025-06-27 02:56:17,185 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1603826538.3 1603826538.8, ..., timestampArray[-2:] = 1603900374.3 1603900374.8] INFO 2025-06-27 02:56:17,339 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1603826538.3451374), np.float64(1603826538.8451374)], ..., timestampList[-2:] = [np.float64(1603900374.3451374), np.float64(1603900374.8451374)]] INFO 2025-06-27 02:56:17,339 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 147672) according to what got written to the netCDF file by the binning interval INFO 2025-06-27 02:56:17,340 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [147650, 147671] INFO 2025-06-27 02:56:17,340 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 7032 INFO 2025-06-27 02:56:17,340 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 147672 INFO 2025-06-27 02:56:17,340 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1603826538.3451374), np.float64(1603826538.8451374)], ..., timestampList[-2:] = [np.float64(1603900374.3451374), np.float64(1603900374.8451374)]] INFO 2025-06-27 02:56:17,340 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 147672) according to what got written to the netCDF file by the binning interval INFO 2025-06-27 02:56:17,342 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(147649), np.int32(147670)]] from timestampList to create subSampledTimestampList INFO 2025-06-27 02:56:17,349 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 7032 INFO 2025-06-27 02:56:17,351 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 7032 INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1603826547.8451374)], ..., tsList[-2:] = [np.float64(1603900363.8451374), np.float64(1603900374.3451374)] INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2020-10-27 19:22:27 Z INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2020-10-28 15:52:54 Z INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 7032 INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.60382696e+09], ..., cFrameEsecsList[-2:] = [1.60383524e+09 1.60383525e+09] INFO 2025-06-27 02:56:17,389 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2020-10-27 19:29:20 Z INFO 2025-06-27 02:56:17,390 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2020-10-27 21:47:30 Z INFO 2025-06-27 02:56:17,394 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2020.301.03/lopc.nc INFO 2025-06-27 02:56:17,394 lopcToNetCDF.py main():2384 [1] Processing finished: Fri Jun 27 02:56:17 2025 Elapsed processing time from start of processing = 79 seconds INFO 2025-06-27 02:56:17,400 process.py calibrate():227 [1] Calibration steps for 2020.301.03 INFO 2025-06-27 02:56:17,991 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 2025-06-27 02:56:17,993 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-27 02:56:19,156 calibrate.py _nudge_pos():1806 [1] 141: 0.160 0.0003469 -0.0011087 8705 29.01 1.774 -7.081 2020-10-27T19:53:35.836520448 INFO 2025-06-27 02:56:23,454 calibrate.py _nudge_pos():1806 [1] 563: 0.130 0.0005875 0.0002289 7695 25.65 3.400 1.654 2020-10-27T20:26:16.042236928 INFO 2025-06-27 02:56:23,765 calibrate.py _nudge_pos():1806 [1] 592: 0.030 0.0006878 -0.0000635 8826 29.42 3.471 -0.400 2020-10-27T20:56:09.239394560 INFO 2025-06-27 02:56:27,073 calibrate.py _nudge_pos():1806 [1] 894: 0.200 0.0005744 -0.0000267 7650 25.50 3.345 -0.194 2020-10-27T21:26:40.233962752 INFO 2025-06-27 02:56:27,976 calibrate.py _nudge_pos():1806 [1] 981: 0.090 0.0005983 -0.0001041 7916 26.38 3.368 -0.731 2020-10-27T21:54:29.439614464 INFO 2025-06-27 02:56:28,084 calibrate.py _nudge_pos():1806 [1] 991: 0.080 0.0000216 -0.0000297 15 0.05 68.825 -117.794 2020-10-27T21:54:41.438792448 INFO 2025-06-27 02:56:33,010 calibrate.py _nudge_pos():1806 [1] 1462: 0.040 0.0005013 -0.0000917 6251 20.83 3.575 -0.815 2020-10-27T22:23:21.640950528 INFO 2025-06-27 02:56:33,208 calibrate.py _nudge_pos():1806 [1] 1480: 0.120 0.0006090 -0.0001290 6885 22.95 3.944 -1.041 2020-10-27T22:46:35.635455488 INFO 2025-06-27 02:56:38,524 calibrate.py _nudge_pos():1806 [1] 1979: 0.060 0.0004397 -0.0000544 6581 21.93 2.979 -0.460 2020-10-27T23:16:49.841173760 INFO 2025-06-27 02:56:39,192 calibrate.py _nudge_pos():1806 [1] 2042: 0.180 0.0005155 -0.0000002 7275 24.25 3.160 -0.002 2020-10-27T23:42:06.837252352 INFO 2025-06-27 02:56:42,060 calibrate.py _nudge_pos():1806 [1] 2306: 0.140 0.0008965 0.0003833 9791 32.63 4.083 2.176 2020-10-28T00:19:08.035089920 INFO 2025-06-27 02:56:42,640 calibrate.py _nudge_pos():1806 [1] 2358: 0.070 0.0005882 0.0003886 9081 30.27 2.888 2.379 2020-10-28T00:50:15.237177856 INFO 2025-06-27 02:56:45,282 calibrate.py _nudge_pos():1806 [1] 2589: 0.020 0.0008219 0.0003678 7771 25.90 4.715 2.632 2020-10-28T01:19:59.434951936 INFO 2025-06-27 02:56:45,728 calibrate.py _nudge_pos():1806 [1] 2632: 0.120 0.0008989 0.0004013 7486 24.95 5.352 2.981 2020-10-28T01:45:38.439523072 INFO 2025-06-27 02:56:48,382 calibrate.py _nudge_pos():1806 [1] 2877: 0.050 0.0006759 0.0004829 7801 26.00 3.861 3.441 2020-10-28T02:15:42.635927040 INFO 2025-06-27 02:56:48,750 calibrate.py _nudge_pos():1806 [1] 2912: 0.160 -0.0016523 -0.0000278 7820 26.06 -9.415 -0.198 2020-10-28T02:42:20.636456448 INFO 2025-06-27 02:56:48,930 calibrate.py _nudge_pos():1806 [1] 2929: 0.190 0.0000515 0.0000503 185 0.61 12.476 15.192 2020-10-28T02:43:13.632825856 INFO 2025-06-27 02:56:50,885 calibrate.py _nudge_pos():1806 [1] 3110: 0.100 -0.0008722 0.0002005 7701 25.67 -5.046 1.447 2020-10-28T03:11:53.834984192 INFO 2025-06-27 02:56:51,677 calibrate.py _nudge_pos():1806 [1] 3183: 0.040 -0.0007758 0.0000152 7791 25.97 -4.436 0.108 2020-10-28T03:39:04.033307904 INFO 2025-06-27 02:56:54,270 calibrate.py _nudge_pos():1806 [1] 3428: 0.130 0.0005222 -0.0004961 6080 20.26 3.826 -4.537 2020-10-28T04:03:24.033290752 INFO 2025-06-27 02:56:57,113 calibrate.py _nudge_pos():1806 [1] 3693: 0.090 0.0023519 -0.0013469 9641 32.13 10.864 -7.767 2020-10-28T04:39:56.233114880 INFO 2025-06-27 02:56:57,716 calibrate.py _nudge_pos():1806 [1] 3749: 0.020 0.0027428 -0.0011694 7771 25.90 15.715 -8.366 2020-10-28T05:06:45.432877312 INFO 2025-06-27 02:57:00,427 calibrate.py _nudge_pos():1806 [1] 3986: 0.170 0.0038625 -0.0015507 9630 32.10 17.853 -8.952 2020-10-28T05:42:47.434769920 INFO 2025-06-27 02:57:01,060 calibrate.py _nudge_pos():1806 [1] 4042: 0.090 0.0030749 -0.0012481 7901 26.33 17.320 -8.783 2020-10-28T06:10:02.632751104 INFO 2025-06-27 02:57:03,809 calibrate.py _nudge_pos():1806 [1] 4289: 0.190 0.0028190 -0.0007020 8981 29.93 13.965 -4.345 2020-10-28T06:44:04.832850944 INFO 2025-06-27 02:57:04,700 calibrate.py _nudge_pos():1806 [1] 4368: 0.180 0.0024176 -0.0006261 9580 31.93 11.224 -3.633 2020-10-28T07:17:18.836252416 INFO 2025-06-27 02:57:04,995 calibrate.py _nudge_pos():1806 [1] 4394: 0.180 -0.0000211 0.0000441 70 0.23 -13.571 35.495 2020-10-28T07:17:58.833512192 INFO 2025-06-27 02:57:08,268 calibrate.py _nudge_pos():1806 [1] 4688: 0.180 0.0021738 -0.0005543 8669 28.90 11.149 -3.555 2020-10-28T07:51:46.034639616 INFO 2025-06-27 02:57:09,860 calibrate.py _nudge_pos():1806 [1] 4831: 0.060 0.0017980 -0.0004260 7301 24.33 10.949 -3.244 2020-10-28T08:18:28.234881280 INFO 2025-06-27 02:57:17,192 calibrate.py _nudge_pos():1806 [1] 5483: 0.160 0.0002210 0.0002763 3780 12.60 2.600 4.065 2020-10-28T08:41:55.238494976 INFO 2025-06-27 02:57:18,985 calibrate.py _nudge_pos():1806 [1] 5643: 0.090 0.0001337 0.0002245 9181 30.60 0.648 1.360 2020-10-28T09:15:10.441814272 INFO 2025-06-27 02:57:24,612 calibrate.py _nudge_pos():1806 [1] 6140: 0.020 0.0003380 0.0002681 5546 18.48 2.711 2.688 2020-10-28T09:41:55.641850368 INFO 2025-06-27 02:57:35,206 calibrate.py _nudge_pos():1806 [1] 7085: 0.180 0.0000180 0.0001238 3755 12.51 0.213 1.834 2020-10-28T10:10:10.635735552 INFO 2025-06-27 02:57:39,114 calibrate.py _nudge_pos():1806 [1] 7433: 0.060 0.0002685 0.0004383 7561 25.20 1.580 3.223 2020-10-28T10:41:09.838371328 INFO 2025-06-27 02:57:49,098 calibrate.py _nudge_pos():1806 [1] 8322: 0.050 0.0002052 0.0001702 5106 17.02 1.789 1.853 2020-10-28T11:13:00.037513728 INFO 2025-06-27 02:57:51,783 calibrate.py _nudge_pos():1806 [1] 8563: 0.190 0.0003121 0.0004348 10080 33.60 1.378 2.398 2020-10-28T11:50:36.032967424 INFO 2025-06-27 02:59:35,204 calibrate.py _nudge_pos():1806 [1] 17866: 0.160 -0.0005342 0.0005383 5160 17.20 -4.609 5.800 2020-10-28T14:42:50.834984960 INFO 2025-06-27 03:00:23,165 calibrate.py _nudge_pos():1862 [1] 22031: - - - 5 0.01 - - INFO 2025-06-27 03:00:23,165 calibrate.py _nudge_pos():1868 [1] Points in final series = 367989 INFO 2025-06-27 03:00:26,454 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:00:28,610 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:00:28,614 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2020.301.03/ctd1.nc WARNING 2025-06-27 03:00:28,616 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1510) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-27 03:00:28,616 calibrate.py _range_qc_combined_nc():898 [1] Setting 1510 ctd1_salinity values to NaN INFO 2025-06-27 03:00:28,616 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 2025-06-27 03:00:28,616 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-27 03:00:31,233 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:00:33,380 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:00:33,385 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2020.301.03/ctd2.nc WARNING 2025-06-27 03:00:33,386 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (5644) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-27 03:00:33,387 calibrate.py _range_qc_combined_nc():898 [1] Setting 5644 ctd2_salinity values to NaN INFO 2025-06-27 03:00:33,387 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 2025-06-27 03:00:33,387 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-27 03:00:36,147 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-27 03:00:39,453 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [120] INFO 2025-06-27 03:00:40,119 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:02:26,284 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_cal.nc INFO 2025-06-27 03:02:26,740 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_time, gps_latitude, gps_longitude, gps_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, 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 2025-06-27 03:02:26,749 process.py align():251 [1] Alignment steps for 2020.301.03 INFO 2025-06-27 03:02:26,851 align.py process_cal():139 [1] Processing dorado_2020.301.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2020.301.03 INFO 2025-06-27 03:02:26,944 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:02:26,954 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:02:27,184 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:02:27,198 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:02:27,420 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:02:27,436 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:02:27,572 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-27 03:02:27,572 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-27 03:02:27,661 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:02:27,674 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:02:27,895 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:27,906 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:28,118 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:28,129 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:28,330 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:28,342 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:28,558 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:28,569 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:28,769 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:28,784 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:28,989 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:29,000 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:29,204 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:29,215 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:29,414 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:29,426 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:29,627 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:29,638 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:29,833 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:29,844 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:30,041 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:30,054 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:30,249 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:30,259 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:30,456 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:30,467 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:30,668 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:30,679 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:30,880 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:30,892 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:31,091 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:31,103 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:31,304 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:31,315 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:31,512 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:31,524 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:31,725 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:31,735 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:31,932 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.301.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:02:31,943 align.py process_cal():249 [1] ctd2_par: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:02:32,190 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:02:32,346 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:02:32,504 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:02:32,668 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 03:02:32,837 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 03:02:33,173 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.98 INFO 2025-06-27 03:02:35,183 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:02:35,319 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:02:35,455 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:02:35,590 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:02:35,726 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:02:35,880 align.py process_cal():249 [1] ecopuck_bbp700: instrument_sample_rate_hz = 10.36 INFO 2025-06-27 03:02:36,358 align.py process_cal():249 [1] ecopuck_cdom: instrument_sample_rate_hz = 10.36 INFO 2025-06-27 03:02:36,783 align.py process_cal():249 [1] ecopuck_chl: instrument_sample_rate_hz = 10.36 INFO 2025-06-27 03:02:37,226 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:02:37,375 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_align.nc INFO 2025-06-27 03:02:37,859 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_depth, ecopuck_latitude, ecopuck_longitude, ecopuck_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, 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 2025-06-27 03:02:37,863 process.py resample():273 [1] Resampling steps for 2020.301.03 INFO 2025-06-27 03:02:37,864 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-27 03:02:37,958 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_align.nc mission netCDF file INFO 2025-06-27 03:02:37,969 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_align.nc mission netCDF file INFO 2025-06-27 03:02:37,972 resample.py get_mission_start_end():1145 [1] navigation: 2020-10-27T19:22:54.672648704 to 2020-10-28T15:52:55.236963840 (0 days 00:00:00 before mission_end) INFO 2025-06-27 03:02:37,975 resample.py get_mission_start_end():1145 [1] ctd1 : 2020-10-27T19:22:37.673812992 to 2020-10-28T15:52:55.066975232 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-27 03:02:37,978 resample.py get_mission_start_end():1145 [1] ctd2 : 2020-10-27T19:22:37.673812992 to 2020-10-28T15:52:55.156969216 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-27 03:02:37,980 resample.py get_mission_start_end():1145 [1] isus : 2020-10-27T19:23:15.211241728 to 2020-10-28T15:52:55.166968576 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-27 03:02:37,981 resample.py get_mission_start_end():1145 [1] biolume : 2020-10-27T19:22:13.895407872 to 2020-10-28T15:52:54.456982784 (0 days 00:00:00.779981056 before mission_end) INFO 2025-06-27 03:02:37,983 resample.py get_mission_start_end():1145 [1] lopc : 2020-10-27T19:22:27.845137408 to 2020-10-28T15:52:54.345137408 (0 days 00:00:00.891826432 before mission_end) INFO 2025-06-27 03:02:37,987 resample.py get_mission_start_end():1145 [1] ecopuck : 2020-10-27T19:22:13.645459200 to 2020-10-28T15:52:55.196966400 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-27 03:02:37,991 resample.py get_mission_start_end():1145 [1] tailcone : 2020-10-27T19:22:23.924755200 to 2020-10-28T15:52:20.089371392 (0 days 00:00:35.147592448 before mission_end) INFO 2025-06-27 03:02:37,992 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_align.nc mission netCDF file INFO 2025-06-27 03:02:37,992 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:38,753 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:38,873 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:38,989 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,108 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,206 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,300 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,404 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,498 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,593 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,686 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,779 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,874 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:39,969 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,064 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,164 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,261 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,374 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,471 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,568 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,665 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,760 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,856 resample.py resample_variable():1031 [1] Resampling ctd2_par with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,893 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,926 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,957 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:40,989 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:41,022 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:41,032 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-27 03:02:41,032 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-27 03:02:43,824 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-27 03:02:44,693 resample.py add_biolume_proxies():633 [1] Zero flow values found: 2886 of 73842 - replaced with 350 ml/s INFO 2025-06-27 03:02:44,694 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-27 03:02:45,030 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-27 03:02:45,199 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-27 03:02:45,287 resample.py select_nighttime_bl_raw():408 [1] Extracting biolume_raw data between sunset 2020-10-28 02:12:54.634052864 and sunrise 2020-10-28 13:22:54.836916480 INFO 2025-06-27 03:02:45,590 resample.py add_biolume_proxies():700 [1] No hs2_fl700 data. Not computing adinos, diatoms, and hdinos INFO 2025-06-27 03:02:45,621 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:45,637 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:45,650 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:45,663 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:45,677 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:45,881 resample.py resample_variable():1031 [1] Resampling ecopuck_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:46,114 resample.py resample_variable():1031 [1] Resampling ecopuck_cdom with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:46,345 resample.py resample_variable():1031 [1] Resampling ecopuck_chl with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:46,479 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-27 03:02:47,029 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_1S.nc INFO 2025-06-27 03:02:52,109 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-27 03:03:15,127 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2020.301.03/dorado_2020.301.03_1S_Gulper.txt INFO 2025-06-27 03:03:15,127 process.py archive():337 [1] Archiving steps for 2020.301.03 INFO 2025-06-27 03:03:15,128 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03, BASE_PATH = /data/auv_data INFO 2025-06-27 03:03:15,130 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03 files to /Volumes/AUVCTD/surveys/2020/netcdf INFO 2025-06-27 03:03:15,132 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.301.03_1S.nc INFO 2025-06-27 03:03:15,222 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_1S.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:03:15,223 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.301.03_cal.nc INFO 2025-06-27 03:03:15,889 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_cal.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:03:15,890 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.301.03_align.nc INFO 2025-06-27 03:03:16,898 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_align.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:03:17,050 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,157 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,183 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,562 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,576 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,701 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,794 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/FLBBCD2K.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:17,879 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:18,131 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:18,407 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020301/2020.301.03 done. INFO 2025-06-27 03:03:18,407 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-27 03:03:18,414 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2020/odv/dorado_2020.301.03_1S_Gulper.txt INFO 2025-06-27 03:03:18,426 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2020.301.03/dorado_2020.301.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2020/odv done. INFO 2025-06-27 03:03:18,426 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.301.03/dorado_2020.301.03_processing.log /Volumes/AUVCTD/surveys/2020/netcdf