INFO 2025-06-26 06:08:43,591 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 06:08:43,591 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/21/05 - ctdToUse = ctd1 INFO 2025-06-26 06:08:43,591 process.py process_mission():449 [1] Processing BIOLUME mission 2004.317.02 by user docker_user on host 671049448ece INFO 2025-06-26 06:08:43,591 process.py download_process():165 [1] Download and processing steps for 2004.317.02 INFO 2025-06-26 06:08:43,591 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004317/2004.317.02 INFO 2025-06-26 06:08:43,592 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004317/2004.317.02 to /data/auv_data/dorado/missionlogs/2004.317.02 INFO 2025-06-26 06:08:45,349 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.317.02 INFO 2025-06-26 06:08:45,350 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/ctdDriver.log (2824491 bytes) INFO 2025-06-26 06:08:45,556 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/ctdDriver2.log (2824485 bytes) INFO 2025-06-26 06:08:45,765 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/gps.log (21884 bytes) INFO 2025-06-26 06:08:45,775 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/hydroscatlog.log (1929134 bytes) INFO 2025-06-26 06:08:46,006 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/navigation.log (6257479 bytes) INFO 2025-06-26 06:08:46,472 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/isuslog.log (165461 bytes) INFO 2025-06-26 06:08:46,493 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/parosci.log (1930262 bytes) INFO 2025-06-26 06:08:46,656 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/tailCone.log (1929979 bytes) INFO 2025-06-26 06:08:46,892 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.317.02/biolume.log (2194364 bytes) INFO 2025-06-26 06:08:47,110 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 06:08:47,216 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.317.02/biolume.log: [4] INFO 2025-06-26 06:08:47,225 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.87 seconds WARNING 2025-06-26 06:08:47,225 process.py download_process():196 [1] No lopc.bin file for 2004.317.02 INFO 2025-06-26 06:08:47,225 process.py calibrate():227 [1] Calibration steps for 2004.317.02 INFO 2025-06-26 06:08:47,330 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 06:08:47,332 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 06:08:47,852 calibrate.py _nudge_pos():1806 [1] 73: 0.120 0.0004429 0.0000399 11850 39.50 1.666 0.187 2004-11-12T10:39:30.342193792 INFO 2025-06-26 06:08:48,276 calibrate.py _nudge_pos():1806 [1] 119: 0.120 0.0001682 0.0002093 10845 36.15 0.692 1.073 2004-11-12T11:16:24.340524672 INFO 2025-06-26 06:08:48,682 calibrate.py _nudge_pos():1806 [1] 162: 0.120 0.0001580 0.0001722 10227 34.10 0.689 0.936 2004-11-12T11:51:12.347486464 INFO 2025-06-26 06:08:49,158 calibrate.py _nudge_pos():1806 [1] 213: 0.150 -0.0000408 0.0000805 2480 8.26 -0.734 1.805 2004-11-12T12:00:18.340083328 INFO 2025-06-26 06:08:49,587 calibrate.py _nudge_pos():1806 [1] 259: 0.130 0.0000327 0.0000919 3375 11.25 0.433 1.514 2004-11-12T12:12:18.340759936 INFO 2025-06-26 06:08:49,920 calibrate.py _nudge_pos():1862 [1] 271: - - - 4 0.01 - - INFO 2025-06-26 06:08:49,920 calibrate.py _nudge_pos():1868 [1] Points in final series = 40104 WARNING 2025-06-26 06:08:49,956 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 06:08:50,263 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:08:50,569 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:08:50,807 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:08:50,808 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.317.02/ctd1.nc INFO 2025-06-26 06:08:50,809 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 06:08:50,810 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 06:08:50,810 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 06:08:51,094 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:08:51,334 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:08:51,336 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.317.02/ctd2.nc INFO 2025-06-26 06:08:51,337 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 06:08:51,337 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 06:08:51,337 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 06:08:51,354 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 06:08:51,697 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828] INFO 2025-06-26 06:08:51,769 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 06:08:51,897 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 06:08:51,898 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.317.02 ERROR 2025-06-26 06:08:51,898 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.317.02 INFO 2025-06-26 06:08:51,932 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_cal.nc INFO 2025-06-26 06:08:52,002 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_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 06:08:52,006 process.py align():251 [1] Alignment steps for 2004.317.02 INFO 2025-06-26 06:08:52,033 align.py process_cal():139 [1] Processing dorado_2004.317.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.317.02 INFO 2025-06-26 06:08:52,054 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:08:52,057 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:08:52,094 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:08:52,097 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:08:52,129 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:08:52,132 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:08:52,151 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 06:08:52,152 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 06:08:52,165 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:08:52,167 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:08:52,199 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:08:52,202 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,232 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:08:52,234 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,264 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:08:52,266 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,296 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,299 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,329 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,331 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,362 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,364 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,395 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,397 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,427 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,430 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,461 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,464 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,494 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,497 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,527 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,530 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,564 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,595 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,597 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,627 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,630 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,661 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,664 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,695 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,698 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,728 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,732 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,763 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,766 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,796 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,799 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,830 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.317.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:08:52,832 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:08:52,867 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:08:52,892 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:08:52,917 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:08:52,942 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 06:08:52,970 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:08:52,995 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_align.nc INFO 2025-06-26 06:08:53,054 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_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 06:08:53,056 process.py resample():273 [1] Resampling steps for 2004.317.02 INFO 2025-06-26 06:08:53,057 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 06:08:53,080 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_align.nc mission netCDF file INFO 2025-06-26 06:08:53,086 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_align.nc mission netCDF file INFO 2025-06-26 06:08:53,087 resample.py get_mission_start_end():1145 [1] navigation: 2004-11-12T09:59:09.968000896 to 2004-11-12T12:12:51.138513152 (0 days 00:00:00.099993216 before mission_end) INFO 2025-06-26 06:08:53,088 resample.py get_mission_start_end():1145 [1] hs2 : 2004-11-12T09:58:53.379137280 to 2004-11-12T12:12:51.238506368 (0 days 00:00:00 before mission_end) INFO 2025-06-26 06:08:53,090 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-11-12T09:59:09.058063232 to 2004-11-12T12:12:51.118514560 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 06:08:53,091 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-11-12T09:59:09.398040064 to 2004-11-12T12:12:51.208508288 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 06:08:53,093 resample.py get_mission_start_end():1145 [1] isus : 2004-11-12T10:00:04.614257280 to 2004-11-12T12:12:49.788605696 (0 days 00:00:01.449900672 before mission_end) INFO 2025-06-26 06:08:53,094 resample.py get_mission_start_end():1145 [1] biolume : 2004-11-12T09:58:47.099533312 to 2004-11-12T12:12:49.988557568 (0 days 00:00:01.249948800 before mission_end) INFO 2025-06-26 06:08:53,095 resample.py get_mission_start_end():1145 [1] tailcone : 2004-11-12T09:58:49.929373696 to 2004-11-12T12:12:51.138513152 (0 days 00:00:00.099993216 before mission_end) INFO 2025-06-26 06:08:53,096 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_align.nc mission netCDF file INFO 2025-06-26 06:08:53,096 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,204 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,224 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,244 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,263 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,282 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,300 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,318 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,336 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,352 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,368 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,384 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,400 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,416 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,433 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,449 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,466 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,484 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,502 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,518 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,536 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,553 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,569 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,580 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,591 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,601 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,612 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,631 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 06:08:53,768 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_1S.nc INFO 2025-06-26 06:08:54,607 create_products.py gulper_odv():401 [1] No gulper times found for 2004.317.02 INFO 2025-06-26 06:08:54,608 process.py archive():337 [1] Archiving steps for 2004.317.02 INFO 2025-06-26 06:08:54,608 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02, BASE_PATH = /data/auv_data INFO 2025-06-26 06:08:54,608 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 06:08:54,609 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.317.02_1S.nc INFO 2025-06-26 06:08:54,623 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:08:54,623 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.317.02_cal.nc INFO 2025-06-26 06:08:54,663 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:08:54,664 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.317.02_align.nc INFO 2025-06-26 06:08:54,702 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:08:54,718 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,732 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,749 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,773 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,780 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,792 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,806 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,833 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004317/2004.317.02 done. INFO 2025-06-26 06:08:54,834 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 06:08:54,834 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.317.02/dorado_2004.317.02_processing.log /Volumes/AUVCTD/surveys/2004/netcdf