INFO 2025-06-26 14:39:22,919 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 14:39:22,919 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - On N-S line by M0 for ESP deployment - ctdToUse = ctd2 INFO 2025-06-26 14:39:22,919 process.py process_mission():449 [1] Processing AUVCTD mission 2009.111.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:39:22,919 process.py download_process():165 [1] Download and processing steps for 2009.111.01 INFO 2025-06-26 14:39:22,919 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009111/2009.111.01 INFO 2025-06-26 14:39:22,919 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009111/2009.111.01 to /data/auv_data/dorado/missionlogs/2009.111.01 INFO 2025-06-26 14:39:30,312 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.111.01 INFO 2025-06-26 14:39:30,313 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/ctdDriver.log (24480500 bytes) INFO 2025-06-26 14:39:32,106 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.111.01/ctdDriver.log: [ 59330 200075] INFO 2025-06-26 14:39:32,184 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/ctdDriver2.log (24480757 bytes) INFO 2025-06-26 14:39:34,009 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.111.01/ctdDriver2.log: [225814] INFO 2025-06-26 14:39:34,123 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/gps.log (133988 bytes) INFO 2025-06-26 14:39:34,145 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/hydroscatlog.log (23375542 bytes) INFO 2025-06-26 14:39:36,600 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.111.01/hydroscatlog.log: [23907] INFO 2025-06-26 14:39:36,698 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/navigation.log (82100278 bytes) INFO 2025-06-26 14:39:42,713 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/isuslog.log (1615317 bytes) INFO 2025-06-26 14:39:42,872 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/parosci.log (28514534 bytes) INFO 2025-06-26 14:39:45,275 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/tailCone.log (3377419 bytes) INFO 2025-06-26 14:39:45,701 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/biolume.log (18938412 bytes) INFO 2025-06-26 14:39:47,528 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:39:48,531 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.22 seconds INFO 2025-06-26 14:39:48,531 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.111.01/lopc.bin (198897718 bytes) INFO 2025-06-26 14:39:48,531 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:39:48 2025 INFO 2025-06-26 14:39:48,532 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.111.01/parosci.nc INFO 2025-06-26 14:39:48,532 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:39:48,532 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.111.01/parosci.nc INFO 2025-06-26 14:39:48,535 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1240350252.2, sensor_off_time = 1240419860.3 INFO 2025-06-26 14:39:48,535 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 69608 seconds. Expecting to read 139216 L frames from the lopc.bin file. INFO 2025-06-26 14:39:48,535 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 139216 records from the lopc.bin file. INFO 2025-06-26 14:39:49,379 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-04-21 21:44:12 Z and endTime = 2009-04-22 17:04:20 Z with 139216 records expected to be read from lopc.bin INFO 2025-06-26 14:39:49,379 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.111.01/lopc.bin INFO 2025-06-26 14:39:49,381 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.111.01/lopc.nc INFO 2025-06-26 14:39:49,381 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.111.01/lopc.nc INFO 2025-06-26 14:39:49,382 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.111.01 INFO 2025-06-26 14:39:49,382 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:39:49,601 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:39:49,601 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:39:49,601 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:39:49,656 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 0: invalid start byte INFO 2025-06-26 14:39:49,656 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 14:39:49,657 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.111.01/parosci.nc INFO 2025-06-26 14:39:49,657 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:39:49,657 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.111.01/parosci.nc INFO 2025-06-26 14:39:49,660 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1240350252.2, sensor_off_time = 1240419860.3 INFO 2025-06-26 14:39:49,661 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 69608 seconds. Expecting to read 139216 L frames from the lopc.bin file. INFO 2025-06-26 14:39:49,661 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 139216 records from the lopc.bin file. INFO 2025-06-26 14:39:49,661 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 536 and len(sampleCountList) = 121 INFO 2025-06-26 14:39:49,661 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 14:39:49,661 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 536 537 538 539 540 541 542 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768] INFO 2025-06-26 14:39:49,662 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 14:39:49,662 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 14:39:49,662 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 1 3113 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1] INFO 2025-06-26 14:39:49,663 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [7] INFO 2025-06-26 14:39:49,663 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 3655 at index = 7 INFO 2025-06-26 14:39:49,663 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 14:39:49,663 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 536 537 538 539 540 541 542 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768] INFO 2025-06-26 14:39:49,663 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 536 537 538 539 540 541 542 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768] with len(correctedSampleCountList) = 121 INFO 2025-06-26 14:39:49,664 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 536 from all values of correctedSampleCountList INFO 2025-06-26 14:39:49,664 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 14:39:49,664 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 1.5000e+00 2.0000e+00 2.5000e+00 3.0000e+00 1.5595e+03 1.5600e+03 1.5605e+03 1.5610e+03 1.5615e+03 1.5620e+03 1.5625e+03 1.5630e+03 1.5635e+03 1.5640e+03 1.5645e+03 1.5650e+03 1.5655e+03 1.5660e+03 1.5665e+03 1.5670e+03 1.5675e+03 1.5680e+03 1.5685e+03 1.5690e+03 1.5695e+03 1.5700e+03 1.5705e+03 1.5710e+03 1.5715e+03 1.5720e+03 1.5725e+03 1.5730e+03 1.5735e+03 1.5740e+03 1.5745e+03 1.5750e+03 1.5755e+03 1.5760e+03 1.5765e+03 1.5770e+03 1.5775e+03 1.5780e+03 1.5785e+03 1.5790e+03 1.5795e+03 1.5800e+03 1.5805e+03 1.5810e+03 1.5815e+03 1.5820e+03 1.5825e+03 1.5830e+03 1.5835e+03 1.5840e+03 1.5845e+03 1.5850e+03 1.5855e+03 1.5860e+03 1.5865e+03 1.5870e+03 1.5875e+03 1.5880e+03 1.5885e+03 1.5890e+03 1.5895e+03 1.5900e+03 1.5905e+03 1.5910e+03 1.5915e+03 1.5920e+03 1.5925e+03 1.5930e+03 1.5935e+03 1.5940e+03 1.5945e+03 1.5950e+03 1.5955e+03 1.5960e+03 1.5965e+03 1.5970e+03 1.5975e+03 1.5980e+03 1.5985e+03 1.5990e+03 1.5995e+03 1.6000e+03 1.6005e+03 1.6010e+03 1.6015e+03 1.6020e+03 1.6025e+03 1.6030e+03 1.6035e+03 1.6040e+03 1.6045e+03 1.6050e+03 1.6055e+03 1.6060e+03 1.6065e+03 1.6070e+03 1.6075e+03 1.6080e+03 1.6085e+03 1.6090e+03 1.6095e+03 1.6100e+03 1.6105e+03 1.6110e+03 1.6115e+03 1.6120e+03 1.6125e+03 1.6130e+03 1.6135e+03 1.6140e+03 1.6145e+03 1.6150e+03 1.6155e+03 1.6160e+03] INFO 2025-06-26 14:39:49,665 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.24035025e+09 1.24035025e+09 1.24035025e+09 1.24035025e+09 1.24035025e+09 1.24035025e+09 1.24035026e+09 1.24035181e+09 1.24035181e+09 1.24035181e+09 1.24035181e+09 1.24035181e+09 1.24035181e+09 1.24035181e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035182e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035183e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035184e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035185e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035186e+09 1.24035187e+09 1.24035187e+09 1.24035187e+09 1.24035187e+09 1.24035187e+09 1.24035187e+09 1.24035187e+09] INFO 2025-06-26 14:39:49,666 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1240350252.2 1240350252.7, ..., timestampArray[-2:] = 1240351867.7 1240351868.2] INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1240350252.1611435), np.float64(1240350252.6611435)], ..., timestampList[-2:] = [np.float64(1240351867.6611435), np.float64(1240351868.1611435)]] INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 121) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [83, 104] INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 5 INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 121 INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1240350252.1611435), np.float64(1240350252.6611435)], ..., timestampList[-2:] = [np.float64(1240351867.6611435), np.float64(1240351868.1611435)]] INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 121) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(82), np.int32(103)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 5 INFO 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 14:39:49,667 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 5 INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1240351817.6611435)], ..., tsList[-2:] = [np.float64(1240351849.1611435), np.float64(1240351859.6611435)] INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-04-21 22:10:17 Z INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-04-21 22:10:59 Z INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 121 INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:39:49,669 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:39:49,673 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.111.01/lopc.nc INFO 2025-06-26 14:39:49,673 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 14:39:49 2025 Elapsed processing time from start of processing = 1 seconds INFO 2025-06-26 14:39:49,675 process.py calibrate():227 [1] Calibration steps for 2009.111.01 INFO 2025-06-26 14:39:50,319 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 14:39:50,321 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:39:51,029 calibrate.py _nudge_pos():1806 [1] 94: 0.160 -0.0002583 0.0004301 2290 7.63 -5.023 10.446 2009-04-21T21:53:22.173465344 INFO 2025-06-26 14:39:51,461 calibrate.py _nudge_pos():1806 [1] 136: 0.160 -0.0002761 0.0007701 7745 25.81 -1.587 5.528 2009-04-21T22:19:52.174542592 INFO 2025-06-26 14:39:51,948 calibrate.py _nudge_pos():1806 [1] 184: 0.170 0.0002384 0.0001757 7655 25.51 1.386 1.276 2009-04-21T22:46:10.176442112 INFO 2025-06-26 14:39:52,326 calibrate.py _nudge_pos():1806 [1] 221: 0.180 0.0002140 -0.0009463 11844 39.48 0.804 -4.442 2009-04-21T23:26:16.171620096 INFO 2025-06-26 14:39:52,700 calibrate.py _nudge_pos():1806 [1] 257: 0.170 0.0004870 -0.0006669 7355 24.51 2.946 -5.041 2009-04-21T23:51:22.178451456 INFO 2025-06-26 14:39:53,107 calibrate.py _nudge_pos():1806 [1] 297: 0.190 0.0001823 -0.0008797 13605 45.35 0.596 -3.595 2009-04-22T00:37:22.169379328 INFO 2025-06-26 14:39:53,539 calibrate.py _nudge_pos():1806 [1] 339: 0.190 0.0002495 -0.0004278 6425 21.41 1.728 -3.702 2009-04-22T00:59:28.178541312 INFO 2025-06-26 14:39:53,951 calibrate.py _nudge_pos():1806 [1] 379: 0.190 0.0001990 -0.0000091 5805 19.35 1.525 -0.087 2009-04-22T01:19:28.176336128 INFO 2025-06-26 14:39:54,375 calibrate.py _nudge_pos():1806 [1] 420: 0.190 0.0001904 -0.0000083 4839 16.13 1.750 -0.096 2009-04-22T01:36:16.177283328 INFO 2025-06-26 14:39:54,805 calibrate.py _nudge_pos():1806 [1] 461: 0.200 0.0002145 -0.0000478 5020 16.73 1.901 -0.530 2009-04-22T01:53:40.175764224 INFO 2025-06-26 14:39:55,163 calibrate.py _nudge_pos():1806 [1] 495: 0.200 0.0002383 0.0000160 5234 17.44 2.025 0.170 2009-04-22T02:11:40.171779584 INFO 2025-06-26 14:39:55,846 calibrate.py _nudge_pos():1806 [1] 560: 0.200 0.0002265 0.0000048 5409 18.03 1.862 0.049 2009-04-22T02:30:46.173273088 INFO 2025-06-26 14:39:56,347 calibrate.py _nudge_pos():1806 [1] 607: 0.010 0.0025841 0.0001320 6549 21.83 17.544 1.121 2009-04-22T02:53:22.370367232 INFO 2025-06-26 14:39:56,647 calibrate.py _nudge_pos():1806 [1] 635: 0.200 0.0025576 -0.0001608 5864 19.54 19.399 -1.525 2009-04-22T03:13:22.178174720 INFO 2025-06-26 14:39:57,091 calibrate.py _nudge_pos():1806 [1] 676: 0.010 0.0023200 -0.0001944 5710 19.03 18.074 -1.893 2009-04-22T03:33:04.377188608 INFO 2025-06-26 14:39:57,562 calibrate.py _nudge_pos():1806 [1] 720: 0.010 0.0022275 -0.0001768 5155 17.18 19.225 -1.907 2009-04-22T03:50:58.373614848 INFO 2025-06-26 14:39:58,006 calibrate.py _nudge_pos():1806 [1] 762: 0.020 0.0020979 -0.0000943 5015 16.71 18.614 -1.046 2009-04-22T04:08:22.372096000 INFO 2025-06-26 14:39:58,363 calibrate.py _nudge_pos():1806 [1] 795: 0.020 0.0010089 -0.0011092 12830 42.76 3.499 -4.806 2009-04-22T04:51:40.374120704 INFO 2025-06-26 14:39:58,871 calibrate.py _nudge_pos():1806 [1] 843: 0.030 0.0006631 -0.0004377 5975 19.91 4.939 -4.073 2009-04-22T05:12:22.369038080 INFO 2025-06-26 14:39:59,309 calibrate.py _nudge_pos():1806 [1] 884: 0.030 0.0010615 -0.0011677 13269 44.23 3.560 -4.892 2009-04-22T05:57:16.374486272 INFO 2025-06-26 14:39:59,709 calibrate.py _nudge_pos():1806 [1] 921: 0.030 0.0006398 -0.0004259 5880 19.60 4.843 -4.027 2009-04-22T06:17:28.371458816 INFO 2025-06-26 14:40:00,150 calibrate.py _nudge_pos():1806 [1] 961: 0.030 0.0037849 -0.0001584 8475 28.25 19.880 -1.039 2009-04-22T06:46:22.372671488 INFO 2025-06-26 14:40:00,598 calibrate.py _nudge_pos():1806 [1] 1002: 0.040 0.0030383 -0.0009917 8020 26.73 16.867 -6.874 2009-04-22T07:13:46.370050048 INFO 2025-06-26 14:40:00,976 calibrate.py _nudge_pos():1806 [1] 1037: 0.040 -0.0003922 -0.0002766 9460 31.53 -1.845 -1.625 2009-04-22T07:45:52.378109440 INFO 2025-06-26 14:40:01,360 calibrate.py _nudge_pos():1806 [1] 1072: 0.050 0.0002196 -0.0000848 8440 28.13 1.158 -0.558 2009-04-22T08:14:34.370144768 INFO 2025-06-26 14:40:01,769 calibrate.py _nudge_pos():1806 [1] 1108: 0.050 0.0001310 -0.0010680 12215 40.71 0.477 -4.861 2009-04-22T08:55:52.370390272 INFO 2025-06-26 14:40:02,099 calibrate.py _nudge_pos():1806 [1] 1138: 0.040 -0.0000053 0.0000005 25 0.08 -9.836 1.235 2009-04-22T08:56:26.378060544 INFO 2025-06-26 14:40:02,111 calibrate.py _nudge_pos():1806 [1] 1139: 0.050 0.0003035 -0.0004858 7300 24.33 1.850 -3.700 2009-04-22T09:20:46.378043648 INFO 2025-06-26 14:40:02,476 calibrate.py _nudge_pos():1806 [1] 1172: 0.050 0.0001460 -0.0010313 13725 45.75 0.473 -4.177 2009-04-22T10:07:03.377806080 INFO 2025-06-26 14:40:02,859 calibrate.py _nudge_pos():1806 [1] 1207: 0.060 0.0001837 -0.0003729 6765 22.55 1.209 -3.065 2009-04-22T10:30:10.372790528 INFO 2025-06-26 14:40:03,243 calibrate.py _nudge_pos():1806 [1] 1241: 0.060 0.0001678 0.0000989 5805 19.35 1.286 0.947 2009-04-22T10:50:04.370995968 INFO 2025-06-26 14:40:03,642 calibrate.py _nudge_pos():1806 [1] 1277: 0.070 0.0001674 -0.0000090 5585 18.61 1.333 -0.090 2009-04-22T11:09:16.372078336 INFO 2025-06-26 14:40:04,071 calibrate.py _nudge_pos():1806 [1] 1314: 0.060 0.0001616 -0.0000250 4770 15.90 1.507 -0.292 2009-04-22T11:25:46.374258688 INFO 2025-06-26 14:40:04,471 calibrate.py _nudge_pos():1806 [1] 1351: 0.060 0.0001562 0.0000163 4650 15.50 1.494 0.195 2009-04-22T11:41:52.378083072 INFO 2025-06-26 14:40:04,847 calibrate.py _nudge_pos():1806 [1] 1385: 0.070 0.0002323 0.0000420 5145 17.15 2.007 0.454 2009-04-22T11:59:34.375331072 INFO 2025-06-26 14:40:05,287 calibrate.py _nudge_pos():1806 [1] 1424: 0.070 0.0024391 0.0000455 6230 20.76 17.411 0.406 2009-04-22T12:20:58.377370880 INFO 2025-06-26 14:40:05,644 calibrate.py _nudge_pos():1806 [1] 1455: 0.070 0.0026789 -0.0001266 6360 21.20 18.734 -1.107 2009-04-22T12:42:40.378177792 INFO 2025-06-26 14:40:06,037 calibrate.py _nudge_pos():1806 [1] 1490: 0.080 0.0020894 -0.0002565 4840 16.13 19.204 -2.946 2009-04-22T12:59:22.369536512 INFO 2025-06-26 14:40:06,437 calibrate.py _nudge_pos():1806 [1] 1526: 0.090 0.0024379 -0.0001177 5585 18.61 19.421 -1.172 2009-04-22T13:18:34.370619392 INFO 2025-06-26 14:40:06,902 calibrate.py _nudge_pos():1806 [1] 1568: 0.080 0.0020947 -0.0001683 5345 17.81 17.438 -1.750 2009-04-22T13:37:04.374578688 INFO 2025-06-26 14:40:07,355 calibrate.py _nudge_pos():1806 [1] 1608: 0.090 0.0008540 -0.0009807 12255 40.85 3.101 -4.449 2009-04-22T14:18:34.374001920 INFO 2025-06-26 14:40:07,730 calibrate.py _nudge_pos():1806 [1] 1642: 0.090 0.0006880 -0.0003443 5415 18.05 5.654 -3.535 2009-04-22T14:37:10.377550592 INFO 2025-06-26 14:40:08,098 calibrate.py _nudge_pos():1806 [1] 1675: 0.090 0.0008585 -0.0010328 13220 44.06 2.890 -4.343 2009-04-22T15:21:46.374232320 INFO 2025-06-26 14:40:08,535 calibrate.py _nudge_pos():1806 [1] 1713: 0.100 0.0006469 -0.0003414 5245 17.48 5.490 -3.619 2009-04-22T15:39:52.369836544 INFO 2025-06-26 14:40:08,966 calibrate.py _nudge_pos():1806 [1] 1750: 0.100 0.0036818 0.0002617 8310 27.70 19.722 1.751 2009-04-22T16:08:10.373515008 INFO 2025-06-26 14:40:09,403 calibrate.py _nudge_pos():1806 [1] 1788: 0.100 0.0049193 -0.0001430 8155 27.18 26.858 -0.975 2009-04-22T16:35:58.369249792 INFO 2025-06-26 14:40:09,852 calibrate.py _nudge_pos():1806 [1] 1827: 0.100 0.0039382 -0.0012405 8210 27.36 21.362 -8.400 2009-04-22T17:03:58.374161408 INFO 2025-06-26 14:40:10,102 calibrate.py _nudge_pos():1862 [1] 1816: - - - 4 0.01 - - INFO 2025-06-26 14:40:10,102 calibrate.py _nudge_pos():1868 [1] Points in final series = 347728 WARNING 2025-06-26 14:40:10,555 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:40:45,326 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 278267 INFO 2025-06-26 14:40:47,489 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:41:07,172 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:41:09,234 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:41:09,238 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.111.01/ctd1.nc INFO 2025-06-26 14:41:09,239 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:41:09,240 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 14:41:09,240 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:41:24,632 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:41:26,683 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:41:26,687 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.111.01/ctd2.nc INFO 2025-06-26 14:41:26,689 calibrate.py _range_qc_combined_nc():898 [1] Setting 126 ctd2_salinity values to NaN INFO 2025-06-26 14:41:26,689 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 14:41:26,689 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:41:26,786 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:41:29,971 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 87000 87360 374460 609300 1348140 1802640 2030100 3561840 3797400] INFO 2025-06-26 14:41:30,591 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:41:30,598 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 14:41:30,609 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.111.01 INFO 2025-06-26 14:41:30,665 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_cal.nc INFO 2025-06-26 14:41:52,358 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_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 2025-06-26 14:41:52,370 process.py align():251 [1] Alignment steps for 2009.111.01 INFO 2025-06-26 14:41:52,411 align.py process_cal():139 [1] Processing dorado_2009.111.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.111.01 INFO 2025-06-26 14:41:52,508 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:41:52,516 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:41:52,748 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:41:52,762 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:41:52,971 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:41:52,987 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:41:53,114 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:41:53,114 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:41:53,211 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:41:53,223 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:41:53,430 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:53,440 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:53,623 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:53,633 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:53,816 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:53,826 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,007 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,017 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,202 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,212 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,391 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,401 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,585 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,595 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,785 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,794 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:54,978 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:54,988 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:55,172 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:55,184 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:55,368 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:55,378 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:55,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:55,571 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:55,755 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:55,764 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:55,947 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:55,957 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:56,157 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:56,167 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:56,347 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:56,357 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:56,539 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:56,549 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:56,732 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:56,744 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:56,930 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:56,940 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:57,124 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.111.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:41:57,133 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:41:57,352 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:41:57,484 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:41:57,625 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:41:57,768 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:41:57,911 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:41:58,029 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:41:58,145 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:41:58,261 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:41:58,378 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:41:58,497 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:41:58,541 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_align.nc INFO 2025-06-26 14:41:58,693 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_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, 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 2025-06-26 14:41:58,695 process.py resample():273 [1] Resampling steps for 2009.111.01 INFO 2025-06-26 14:41:58,696 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:41:58,730 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_align.nc mission netCDF file INFO 2025-06-26 14:41:58,739 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_align.nc mission netCDF file INFO 2025-06-26 14:41:58,741 resample.py get_mission_start_end():1145 [1] navigation: 2009-04-21T21:44:44.998894080 to 2009-04-22T17:04:20.172668160 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 14:41:58,744 resample.py get_mission_start_end():1145 [1] hs2 : 2009-04-21T21:44:17.500777728 to 2009-04-22T17:04:20.122671616 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 14:41:58,747 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-04-21T21:44:39.499270912 to 2009-04-22T17:04:20.072675072 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 14:41:58,749 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-04-21T21:44:39.239288576 to 2009-04-22T17:04:20.202665984 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:41:58,751 resample.py get_mission_start_end():1145 [1] isus : 2009-04-21T21:45:29.695832064 to 2009-04-22T17:04:19.742697728 (0 days 00:00:00.459968256 before mission_end) INFO 2025-06-26 14:41:58,753 resample.py get_mission_start_end():1145 [1] biolume : 2009-04-21T21:44:11.391162112 to 2009-04-22T17:04:19.012713472 (0 days 00:00:01.189952512 before mission_end) INFO 2025-06-26 14:41:58,754 resample.py get_mission_start_end():1145 [1] lopc : 2009-04-21T22:10:17.661143552 to 2009-04-21T22:10:59.661143552 (0 days 18:53:20.541522432 before mission_end) WARNING 2025-06-26 14:41:58,755 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 18:53:20.541522432 INFO 2025-06-26 14:41:58,756 resample.py get_mission_start_end():1145 [1] tailcone : 2009-04-21T21:44:16.890819584 to 2009-04-22T17:04:20.082674176 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 14:41:58,757 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_align.nc mission netCDF file INFO 2025-06-26 14:41:58,758 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,454 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,565 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,672 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,780 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,871 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 14:41:59,962 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,056 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,145 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,230 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,314 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,398 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,482 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,568 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,654 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,737 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,820 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,909 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:00,998 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,095 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,183 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,269 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,356 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,388 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,416 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,442 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,474 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,489 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,489 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 18:53:20.541522432 of NaNs to the end of mission INFO 2025-06-26 14:42:01,501 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,501 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 18:53:20.541522432 of NaNs to the end of mission INFO 2025-06-26 14:42:01,511 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,511 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 18:53:20.541522432 of NaNs to the end of mission INFO 2025-06-26 14:42:01,522 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,522 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 18:53:20.541522432 of NaNs to the end of mission INFO 2025-06-26 14:42:01,533 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:01,534 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 18:53:20.541522432 of NaNs to the end of mission INFO 2025-06-26 14:42:01,562 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:42:02,061 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_1S.nc INFO 2025-06-26 14:42:05,379 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:42:16,300 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.111.01/dorado_2009.111.01_1S_Gulper.txt INFO 2025-06-26 14:42:16,300 process.py archive():337 [1] Archiving steps for 2009.111.01 INFO 2025-06-26 14:42:16,301 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01, BASE_PATH = /data/auv_data INFO 2025-06-26 14:42:16,302 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 14:42:16,303 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.111.01_1S.nc INFO 2025-06-26 14:42:16,359 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:42:16,360 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.111.01_cal.nc INFO 2025-06-26 14:42:16,599 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:42:16,600 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.111.01_align.nc INFO 2025-06-26 14:42:16,823 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:42:16,890 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:16,953 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:16,959 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,021 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,230 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,241 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,323 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,340 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,543 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,549 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009111/2009.111.01 done. INFO 2025-06-26 14:42:17,550 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:42:17,551 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.111.01_1S_Gulper.txt INFO 2025-06-26 14:42:17,556 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.111.01/dorado_2009.111.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 14:42:17,556 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.111.01/dorado_2009.111.01_processing.log /Volumes/AUVCTD/surveys/2009/netcdf