# plugin error from phylogeny raxml (default): returned non-zero exit status 255 **URL:** https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765 **Category:** Technical Support **Tags:** phylogeny, raxml **Created:** [November 15, 2022, 3:07pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765 "2022-11-15T15:07:33Z") **Posts on this page:** 1 **Showing post:** 3
### Author: ![Shuqi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/shuqi/32/13104_2.png) [@Shuqi](https://forum.qiime2.org/u/Shuqi) #### Post date: [December 7, 2022, 3:18pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765/3 "2022-12-07T15:18:09Z")
Hi Mike, Thank you for your suggestion, but it seems re-installing lastest qiime2 2022.8 did not solve my problem. I am using macOS Monterey version 12.6 but with an intel core i5. I reinstalled qiime2 following [Brett's suggestion](https://forum.qiime2.org/t/qiime-2-2022-8-is-now-available/23994/14). The detailed commands are listed below: > (base) sl@SHUQI-only-one-U CL-04-NOMMS % wget [https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml](https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml) > --2022-12-07 09:33:45-- [https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml](https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml) > Resolving [data.qiime2.org](http://data.qiime2.org)... 54.200.1.12 > Connecting to data.qiime2.org|54.200.1.12|:443... connected. > HTTP request sent, awaiting response... 302 FOUND > Location: [https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml](https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml) [following] > --2022-12-07 09:33:45-- [https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml](https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml) > Resolving [raw.githubusercontent.com](http://raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ... > Connecting to raw.githubusercontent.com|185.199.109.133|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: 8573 (8.4K) [text/plain] > Saving to: 'qiime2-2022.8-py38-osx-conda.yml' > > qiime2-2022.8-py38-o 100%[=====================\>] 8.37K --.-KB/s in 0.001s > > 2022-12-07 09:33:45 (10.6 MB/s) - 'qiime2-2022.8-py38-osx-conda.yml' saved [8573/8573] > > (base) sl@SHUQI-only-one-U CL-04-NOMMS % conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-osx-conda.yml > > CondaValueError: prefix already exists: /opt/anaconda3/envs/qiime2-2022.8 > > (base) sl@SHUQI-only-one-U CL-04-NOMMS % conda env remove -n qiime2-2022.8 > > Remove all packages in environment /opt/anaconda3/envs/qiime2-2022.8: > > (base) sl@SHUQI-only-one-U CL-04-NOMMS % CONDA\_SUBDIR=osx-64 conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-osx-conda.yml > Collecting package metadata (repodata.json): done > Solving environment: done > > ==\> WARNING: A newer version of conda exists. \<== > current version: 22.9.0 > latest version: 22.11.1 > > Please update conda by running > > ``` > $ conda update -n base -c defaults conda > > ``` > > Downloading and Extracting Packages > scipy-1.8.1 | 21.8 MB | ######################1 | 55% scipy-1.8.1 | 21.8 MB | ######################################## | 100% > backports-1.0 | 6 KB | ######################################## | 100% > libgfortran-5.0.0 | 149 KB | ######################################## | 100% > python\_abi-3.8 | 6 KB | ######################################## | 100% > libgfortran5-11.3.0 | 1.9 MB | ######################################## | 100% > fastcluster-1.2.6 | 47 KB | ######################################## | 100% > libgfortran-devel\_os | 455 KB | ######################################## | 100% > Preparing transaction: done > Verifying transaction: done > Executing transaction: done > > # > > # To activate this environment, use > > # > > # $ conda activate qiime2-2022.8 > > # > > # To deactivate an active environment, use > > # > > # $ conda deactivate > > Retrieving notices: ...working... done > (base) sl@SHUQI-only-one-U CL-04-NOMMS % conda activate qiime2-2022.8 > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % conda info --envs > > # conda environments: > > # > > ``` > /Users/sl/opt/miniconda3 > > ``` > > base /opt/anaconda3 > qiime2-2022.8 \* /opt/anaconda3/envs/qiime2-2022.8 > > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % conda config --env --set subdir osx-64 > > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % qiime phylogeny align-to-tree-mafft-raxml --i-sequences 03-features/filtered-rep-seqs.qza --output-dir 04-alignment-raxml > Plugin error from phylogeny: > > Command '['raxmlHPC', '-m', 'GTRGAMMA', '-p', '6913', '-N', '1', '-s', '/var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta', '-w', '/var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/tmpfqmrssqb', '-n', 'q2']' returned non-zero exit status 255. > > Debug info has been saved to /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2-q2cli-err-ynqzt6bz.log And the debug info is as follows: > Blockquote > Running external command line application. This may print messages to stdout and/or stderr. > The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. > > Command: mafft --preservecase --inputorder --thread 1 /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/94f5292a-1f75-48a3-8924-62f0b6c35c44/data/dna-sequences.fasta > > inputfile = orig > 900 x 382 - 362 d > nthread = 1 > nthreadpair = 1 > nthreadtb = 1 > ppenalty\_ex = 0 > stacksize: 8192 kb > generating a scoring matrix for nucleotide (dist=200) ... done > Gap Penalty = -1.53, +0.00, +0.00 > > Making a distance matrix .. > > ``` > 1 / 900 (thread 0) > > ``` > > 101 / 900 (thread 0) > 201 / 900 (thread 0) > 301 / 900 (thread 0) > 401 / 900 (thread 0) > 501 / 900 (thread 0) > 601 / 900 (thread 0) > 701 / 900 (thread 0) > 801 / 900 (thread 0) > done. > > Constructing a UPGMA tree (efffree=0) ... > > ``` > 0 / 900 > > ``` > > 10 / 900 > 20 / 900 > 30 / 900 > 40 / 900 > 50 / 900 > 60 / 900 > 70 / 900 > 80 / 900 > 90 / 900 > 100 / 900 > 110 / 900 > 120 / 900 > 130 / 900 > 140 / 900 > 150 / 900 > 160 / 900 > 170 / 900 > 180 / 900 > 190 / 900 > 200 / 900 > 210 / 900 > 220 / 900 > 230 / 900 > 240 / 900 > 250 / 900 > 260 / 900 > 270 / 900 > 280 / 900 > 290 / 900 > 300 / 900 > 310 / 900 > 320 / 900 > 330 / 900 > 340 / 900 > 350 / 900 > 360 / 900 > 370 / 900 > 380 / 900 > 390 / 900 > 400 / 900 > 410 / 900 > 420 / 900 > 430 / 900 > 440 / 900 > 450 / 900 > 460 / 900 > 470 / 900 > 480 / 900 > 490 / 900 > 500 / 900 > 510 / 900 > 520 / 900 > 530 / 900 > 540 / 900 > 550 / 900 > 560 / 900 > 570 / 900 > 580 / 900 > 590 / 900 > 600 / 900 > 610 / 900 > 620 / 900 > 630 / 900 > 640 / 900 > 650 / 900 > 660 / 900 > 670 / 900 > 680 / 900 > 690 / 900 > 700 / 900 > 710 / 900 > 720 / 900 > 730 / 900 > 740 / 900 > 750 / 900 > 760 / 900 > 770 / 900 > 780 / 900 > 790 / 900 > 800 / 900 > 810 / 900 > 820 / 900 > 830 / 900 > 840 / 900 > 850 / 900 > 860 / 900 > 870 / 900 > 880 / 900 > 890 / 900 > done. > > Progressive alignment 1/2... > > STEP 1 / 899 (thread 0) f > STEP 2 / 899 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372 / 899 (thread 0) f > STEP 373 / 899 (thread 0) f > STEP 374 / 899 (thread 0) f > STEP 375 / 899 (thread 0) f > STEP 376 / 899 (thread 0) f > STEP 377 / 899 (thread 0) f > STEP 378 / 899 (thread 0) f > STEP 379 / 899 (thread 0) f > STEP 380 / 899 (thread 0) f > STEP 381 / 899 (thread 0) f > STEP 382 / 899 (thread 0) f > STEP 383 / 899 (thread 0) f > STEP 384 / 899 (thread 0) f > STEP 385 / 899 (thread 0) f > STEP 386 / 899 (thread 0) f > STEP 387 / 899 (thread 0) f > STEP 388 / 899 (thread 0) f > STEP 389 / 899 (thread 0) f > STEP 390 / 899 (thread 0) f > STEP 391 / 899 (thread 0) f > STEP 392 / 899 (thread 0) f > STEP 393 / 899 (thread 0) f > STEP 394 / 899 (thread 0) f > STEP 395 / 899 (thread 0) f > STEP 396 / 899 (thread 0) f > STEP 397 / 899 (thread 0) f > STEP 398 / 899 (thread 0) f > STEP 399 / 899 (thread 0) f > STEP 400 / 899 (thread 0) f > STEP 401 / 899 (thread 0) f > STEP 402 / 899 (thread 0) f > STEP 403 / 899 (thread 0) f > STEP 404 / 899 (thread 0) f > STEP 405 / 899 (thread 0) f > STEP 406 / 899 (thread 0) f > STEP 407 / 899 (thread 0) f > STEP 408 / 899 (thread 0) f > STEP 409 / 899 (thread 0) f > STEP 410 / 899 (thread 0) f > STEP 411 / 899 (thread 0) f > STEP 412 / 899 (thread 0) f > STEP 413 / 899 (thread 0) f > STEP 414 / 899 (thread 0) f > STEP 415 / 899 (thread 0) f > STEP 416 / 899 (thread 0) f > STEP 417 / 899 (thread 0) f > STEP 418 / 899 (thread 0) f > STEP 419 / 899 (thread 0) f > STEP 420 / 899 (thread 0) f > STEP 421 / 899 (thread 0) f > STEP 422 / 899 (thread 0) f > STEP 423 / 899 (thread 0) f > STEP 424 / 899 (thread 0) f > STEP 425 / 899 (thread 0) f > STEP 426 / 899 (thread 0) f > STEP 427 / 899 (thread 0) f > STEP 428 / 899 (thread 0) f > STEP 429 / 899 (thread 0) f > STEP 430 / 899 (thread 0) f > STEP 431 / 899 (thread 0) f > STEP 432 / 899 (thread 0) f > STEP 433 / 899 (thread 0) f > STEP 434 / 899 (thread 0) f > STEP 435 / 899 (thread 0) f > STEP 436 / 899 (thread 0) f > STEP 437 / 899 (thread 0) f > STEP 438 / 899 (thread 0) f > STEP 439 / 899 (thread 0) f > STEP 440 / 899 (thread 0) f > STEP 441 / 899 (thread 0) f > STEP 442 / 899 (thread 0) f > STEP 443 / 899 (thread 0) f > STEP 444 / 899 (thread 0) f > STEP 445 / 899 (thread 0) f > STEP 446 / 899 (thread 0) f > STEP 447 / 899 (thread 0) f > STEP 448 / 899 (thread 0) f > STEP 449 / 899 (thread 0) f > STEP 450 / 899 (thread 0) f > STEP 451 / 899 (thread 0) f > STEP 452 / 899 (thread 0) f > STEP 453 / 899 (thread 0) f > STEP 454 / 899 (thread 0) f > STEP 455 / 899 (thread 0) f > STEP 456 / 899 (thread 0) f > STEP 457 / 899 (thread 0) f > STEP 458 / 899 (thread 0) f > STEP 459 / 899 (thread 0) f > STEP 460 / 899 (thread 0) f > STEP 461 / 899 (thread 0) f > STEP 462 / 899 (thread 0) f > STEP 463 / 899 (thread 0) f > STEP 464 / 899 (thread 0) f > STEP 465 / 899 (thread 0) f > STEP 466 / 899 (thread 0) f > STEP 467 / 899 (thread 0) f > STEP 468 / 899 (thread 0) f > STEP 469 / 899 (thread 0) f > STEP 470 / 899 (thread 0) f > STEP 471 / 899 (thread 0) f > STEP 472 / 899 (thread 0) f > STEP 473 / 899 (thread 0) f > STEP 474 / 899 (thread 0) f > STEP 475 / 899 (thread 0) f > STEP 476 / 899 (thread 0) f > STEP 477 / 899 (thread 0) f > STEP 478 / 899 (thread 0) f > STEP 479 / 899 (thread 0) f > STEP 480 / 899 (thread 0) f > STEP 481 / 899 (thread 0) f > STEP 482 / 899 (thread 0) f > STEP 483 / 899 (thread 0) f > STEP 484 / 899 (thread 0) f > STEP 485 / 899 (thread 0) f > STEP 486 / 899 (thread 0) f > STEP 487 / 899 (thread 0) f > STEP 488 / 899 (thread 0) f > STEP 489 / 899 (thread 0) f > STEP 490 / 899 (thread 0) f > STEP 491 / 899 (thread 0) f > STEP 492 / 899 (thread 0) f > STEP 493 / 899 (thread 0) f > STEP 494 / 899 (thread 0) f > STEP 495 / 899 (thread 0) f > STEP 496 / 899 (thread 0) f > STEP 497 / 899 (thread 0) f > STEP 498 / 899 (thread 0) f > STEP 499 / 899 (thread 0) f > STEP 500 / 899 (thread 0) f > STEP 501 / 899 (thread 0) f > STEP 601 / 899 (thread 0) f > STEP 701 / 899 (thread 0) f > STEP 801 / 899 (thread 0) f > Reallocating..done. \*alloclen = 1768 > > done. > > Making a distance matrix from msa.. > > ``` > 0 / 900 (thread 0) > > ``` > > 100 / 900 (thread 0) > 200 / 900 (thread 0) > 300 / 900 (thread 0) > 400 / 900 (thread 0) > 500 / 900 (thread 0) > 600 / 900 (thread 0) > 700 / 900 (thread 0) > 800 / 900 (thread 0) > done. > > Constructing a UPGMA tree (efffree=1) ... > > ``` > 0 / 900 > > ``` > > 10 / 900 > 20 / 900 > 30 / 900 > 40 / 900 > 50 / 900 > 60 / 900 > 70 / 900 > 80 / 900 > 90 / 900 > 100 / 900 > 110 / 900 > 120 / 900 > 130 / 900 > 140 / 900 > 150 / 900 > 160 / 900 > 170 / 900 > 180 / 900 > 190 / 900 > 200 / 900 > 210 / 900 > 220 / 900 > 230 / 900 > 240 / 900 > 250 / 900 > 260 / 900 > 270 / 900 > 280 / 900 > 290 / 900 > 300 / 900 > 310 / 900 > 320 / 900 > 330 / 900 > 340 / 900 > 350 / 900 > 360 / 900 > 370 / 900 > 380 / 900 > 390 / 900 > 400 / 900 > 410 / 900 > 420 / 900 > 430 / 900 > 440 / 900 > 450 / 900 > 460 / 900 > 470 / 900 > 480 / 900 > 490 / 900 > 500 / 900 > 510 / 900 > 520 / 900 > 530 / 900 > 540 / 900 > 550 / 900 > 560 / 900 > 570 / 900 > 580 / 900 > 590 / 900 > 600 / 900 > 610 / 900 > 620 / 900 > 630 / 900 > 640 / 900 > 650 / 900 > 660 / 900 > 670 / 900 > 680 / 900 > 690 / 900 > 700 / 900 > 710 / 900 > 720 / 900 > 730 / 900 > 740 / 900 > 750 / 900 > 760 / 900 > 770 / 900 > 780 / 900 > 790 / 900 > 800 / 900 > 810 / 900 > 820 / 900 > 830 / 900 > 840 / 900 > 850 / 900 > 860 / 900 > 870 / 900 > 880 / 900 > 890 / 900 > done. > > Progressive alignment 2/2... > > STEP 1 / 899 (thread 0) f > STEP 2 / 899 (thread 0) f > STEP 3 / 899 (thread 0) f > STEP 4 / 899 (thread 0) f > STEP 5 / 899 (thread 0) f > STEP 6 / 899 (thread 0) f > STEP 7 / 899 (thread 0) f > STEP 8 / 899 (thread 0) f > STEP 9 / 899 (thread 0) f > STEP 10 / 899 (thread 0) f > STEP 11 / 899 (thread 0) f > STEP 12 / 899 (thread 0) f > STEP 13 / 899 (thread 0) f > STEP 14 / 899 (thread 0) f > STEP 15 / 899 (thread 0) f > STEP 16 / 899 (thread 0) f > STEP 17 / 899 (thread 0) f > STEP 18 / 899 (thread 0) f > STEP 19 / 899 (thread 0) f > STEP 20 / 899 (thread 0) f > STEP 21 / 899 (thread 0) f > STEP 22 / 899 (thread 0) f > STEP 23 / 899 (thread 0) f > STEP 24 / 899 (thread 0) f > STEP 25 / 899 (thread 0) f > STEP 26 / 899 (thread 0) f > STEP 27 / 899 (thread 0) f > STEP 28 / 899 (thread 0) f > STEP 29 / 899 (thread 0) f > STEP 30 / 899 (thread 0) f > STEP 31 / 899 (thread 0) f > STEP 32 / 899 (thread 0) f > STEP 33 / 899 (thread 0) f > STEP 34 / 899 (thread 0) f > STEP 35 / 899 (thread 0) f > STEP 36 / 899 (thread 0) f > STEP 37 / 899 (thread 0) f > STEP 38 / 899 (thread 0) f > STEP 39 / 899 (thread 0) f > STEP 40 / 899 (thread 0) f > STEP 41 / 899 (thread 0) f > STEP 42 / 899 (thread 0) f > STEP 43 / 899 (thread 0) f > STEP 44 / 899 (thread 0) f > STEP 45 / 899 (thread 0) f > STEP 46 / 899 (thread 0) f > STEP 47 / 899 (thread 0) f > STEP 48 / 899 (thread 0) f > STEP 49 / 899 (thread 0) f > STEP 50 / 899 (thread 0) f > STEP 51 / 899 (thread 0) f > STEP 52 / 899 (thread 0) f > STEP 53 / 899 (thread 0) f > STEP 54 / 899 (thread 0) f > STEP 55 / 899 (thread 0) f > STEP 56 / 899 (thread 0) f > STEP 57 / 899 (thread 0) f > STEP 58 / 899 (thread 0) f > STEP 59 / 899 (thread 0) f > STEP 60 / 899 (thread 0) f > STEP 61 / 899 (thread 0) f > STEP 62 / 899 (thread 0) f > STEP 63 / 899 (thread 0) f > STEP 64 / 899 (thread 0) f > STEP 65 / 899 (thread 0) f > STEP 66 / 899 (thread 0) f > STEP 67 / 899 (thread 0) f > STEP 68 / 899 (thread 0) f > STEP 69 / 899 (thread 0) f > STEP 70 / 899 (thread 0) f > STEP 71 / 899 (thread 0) f > STEP 72 / 899 (thread 0) f > STEP 73 / 899 (thread 0) f > STEP 74 / 899 (thread 0) f > STEP 75 / 899 (thread 0) f > STEP 76 / 899 (thread 0) f > STEP 77 / 899 (thread 0) f > STEP 78 / 899 (thread 0) f > STEP 79 / 899 (thread 0) f > STEP 80 / 899 (thread 0) f > STEP 81 / 899 (thread 0) f > STEP 82 / 899 (thread 0) f > STEP 83 / 899 (thread 0) f > STEP 84 / 899 (thread 0) f > STEP 85 / 899 (thread 0) f > STEP 86 / 899 (thread 0) f > STEP 87 / 899 (thread 0) f > STEP 88 / 899 (thread 0) f > STEP 89 / 899 (thread 0) f > STEP 90 / 899 (thread 0) f > STEP 91 / 899 (thread 0) f > STEP 92 / 899 (thread 0) f > STEP 93 / 899 (thread 0) f > STEP 94 / 899 (thread 0) f > STEP 95 / 899 (thread 0) f > STEP 96 / 899 (thread 0) f > STEP 97 / 899 (thread 0) f > STEP 98 / 899 (thread 0) f > STEP 99 / 899 (thread 0) f > STEP 100 / 899 (thread 0) f > STEP 101 / 899 (thread 0) f > STEP 102 / 899 (thread 0) f > STEP 103 / 899 (thread 0) f > STEP 104 / 899 (thread 0) f > STEP 105 / 899 (thread 0) f > STEP 106 / 899 (thread 0) f > STEP 107 / 899 (thread 0) f > STEP 108 / 899 (thread 0) f > STEP 109 / 899 (thread 0) f > STEP 110 / 899 (thread 0) f > STEP 111 / 899 (thread 0) f > STEP 112 / 899 (thread 0) f > STEP 113 / 899 (thread 0) f > STEP 114 / 899 (thread 0) f > STEP 115 / 899 (thread 0) f > STEP 116 / 899 (thread 0) f > STEP 117 / 899 (thread 0) f > STEP 118 / 899 (thread 0) f > STEP 119 / 899 (thread 0) f > STEP 120 / 899 (thread 0) f > STEP 121 / 899 (thread 0) f > STEP 122 / 899 (thread 0) f > STEP 123 / 899 (thread 0) f > STEP 124 / 899 (thread 0) f > STEP 125 / 899 (thread 0) f > STEP 126 / 899 (thread 0) f > STEP 127 / 899 (thread 0) f > STEP 128 / 899 (thread 0) f > STEP 129 / 899 (thread 0) f > STEP 130 / 899 (thread 0) f > STEP 131 / 899 (thread 0) f > STEP 132 / 899 (thread 0) f > STEP 133 / 899 (thread 0) f > STEP 134 / 899 (thread 0) f > STEP 135 / 899 (thread 0) f > STEP 136 / 899 (thread 0) f > STEP 137 / 899 (thread 0) f > STEP 138 / 899 (thread 0) f > STEP 139 / 899 (thread 0) f > STEP 140 / 899 (thread 0) f > STEP 141 / 899 (thread 0) f > STEP 142 / 899 (thread 0) f > STEP 143 / 899 (thread 0) f > STEP 144 / 899 (thread 0) f > STEP 145 / 899 (thread 0) f > STEP 146 / 899 (thread 0) f > STEP 147 / 899 (thread 0) f > STEP 148 / 899 (thread 0) f > STEP 149 / 899 (thread 0) f > STEP 150 / 899 (thread 0) f > STEP 151 / 899 (thread 0) f > STEP 152 / 899 (thread 0) f > STEP 153 / 899 (thread 0) f > STEP 154 / 899 (thread 0) f > STEP 155 / 899 (thread 0) f > STEP 156 / 899 (thread 0) f > STEP 157 / 899 (thread 0) f > STEP 158 / 899 (thread 0) f > STEP 159 / 899 (thread 0) f > STEP 160 / 899 (thread 0) f > STEP 161 / 899 (thread 0) f > STEP 162 / 899 (thread 0) f > STEP 163 / 899 (thread 0) f > STEP 164 / 899 (thread 0) f > STEP 165 / 899 (thread 0) f > STEP 166 / 899 (thread 0) f > STEP 167 / 899 (thread 0) f > STEP 168 / 899 (thread 0) f > STEP 169 / 899 (thread 0) f > STEP 170 / 899 (thread 0) f > STEP 171 / 899 (thread 0) f > STEP 172 / 899 (thread 0) f > STEP 173 / 899 (thread 0) f > STEP 174 / 899 (thread 0) f > STEP 175 / 899 (thread 0) f > STEP 176 / 899 (thread 0) f > STEP 177 / 899 (thread 0) f > STEP 178 / 899 (thread 0) f > STEP 179 / 899 (thread 0) f > STEP 180 / 899 (thread 0) f > STEP 181 / 899 (thread 0) f > STEP 182 / 899 (thread 0) f > STEP 183 / 899 (thread 0) f > STEP 184 / 899 (thread 0) f > STEP 185 / 899 (thread 0) f > STEP 186 / 899 (thread 0) f > STEP 187 / 899 (thread 0) f > STEP 188 / 899 (thread 0) f > STEP 189 / 899 (thread 0) f > STEP 190 / 899 (thread 0) f > STEP 191 / 899 (thread 0) f > STEP 192 / 899 (thread 0) f > STEP 193 / 899 (thread 0) f > STEP 194 / 899 (thread 0) f > STEP 195 / 899 (thread 0) f > STEP 196 / 899 (thread 0) f > STEP 197 / 899 (thread 0) f > STEP 198 / 899 (thread 0) f > STEP 199 / 899 (thread 0) f > STEP 200 / 899 (thread 0) f > STEP 201 / 899 (thread 0) f > STEP 202 / 899 (thread 0) f > STEP 203 / 899 (thread 0) f > STEP 204 / 899 (thread 0) f > STEP 205 / 899 (thread 0) f > STEP 206 / 899 (thread 0) f > STEP 207 / 899 (thread 0) f > STEP 208 / 899 (thread 0) f > STEP 209 / 899 (thread 0) f > STEP 210 / 899 (thread 0) f > STEP 211 / 899 (thread 0) f > STEP 212 / 899 (thread 0) f > STEP 213 / 899 (thread 0) f > STEP 214 / 899 (thread 0) f > STEP 215 / 899 (thread 0) f > STEP 216 / 899 (thread 0) f > STEP 217 / 899 (thread 0) f > STEP 218 / 899 (thread 0) f > STEP 219 / 899 (thread 0) f > STEP 220 / 899 (thread 0) f > STEP 221 / 899 (thread 0) f > STEP 222 / 899 (thread 0) f > STEP 223 / 899 (thread 0) f > STEP 224 / 899 (thread 0) f > STEP 225 / 899 (thread 0) f > STEP 226 / 899 (thread 0) f > STEP 227 / 899 (thread 0) f > STEP 228 / 899 (thread 0) f > STEP 229 / 899 (thread 0) f > STEP 230 / 899 (thread 0) f > STEP 231 / 899 (thread 0) f > STEP 232 / 899 (thread 0) f > STEP 233 / 899 (thread 0) f > STEP 234 / 899 (thread 0) f > STEP 235 / 899 (thread 0) f > STEP 236 / 899 (thread 0) f > STEP 237 / 899 (thread 0) f > STEP 238 / 899 (thread 0) f > STEP 239 / 899 (thread 0) f > STEP 240 / 899 (thread 0) f > STEP 241 / 899 (thread 0) f > STEP 242 / 899 (thread 0) f > STEP 243 / 899 (thread 0) f > STEP 244 / 899 (thread 0) f > STEP 245 / 899 (thread 0) f > STEP 246 / 899 (thread 0) f > STEP 247 / 899 (thread 0) f > STEP 248 / 899 (thread 0) f > STEP 249 / 899 (thread 0) f > STEP 250 / 899 (thread 0) f > STEP 251 / 899 (thread 0) f > STEP 252 / 899 (thread 0) f > STEP 253 / 899 (thread 0) f > STEP 254 / 899 (thread 0) f > STEP 255 / 899 (thread 0) f > STEP 256 / 899 (thread 0) f > STEP 257 / 899 (thread 0) f > STEP 258 / 899 (thread 0) f > STEP 259 / 899 (thread 0) f > STEP 260 / 899 (thread 0) f > STEP 261 / 899 (thread 0) f > STEP 262 / 899 (thread 0) f > STEP 263 / 899 (thread 0) f > STEP 264 / 899 (thread 0) f > STEP 265 / 899 (thread 0) f > STEP 266 / 899 (thread 0) f > STEP 267 / 899 (thread 0) f > STEP 268 / 899 (thread 0) f > STEP 269 / 899 (thread 0) f > STEP 270 / 899 (thread 0) f > STEP 271 / 899 (thread 0) f > STEP 272 / 899 (thread 0) f > STEP 273 / 899 (thread 0) f > STEP 274 / 899 (thread 0) f > STEP 275 / 899 (thread 0) f > STEP 276 / 899 (thread 0) f > STEP 277 / 899 (thread 0) f > STEP 278 / 899 (thread 0) f > STEP 279 / 899 (thread 0) f > STEP 280 / 899 (thread 0) f > STEP 281 / 899 (thread 0) f > STEP 282 / 899 (thread 0) f > STEP 283 / 899 (thread 0) f > STEP 284 / 899 (thread 0) f > STEP 285 / 899 (thread 0) f > STEP 286 / 899 (thread 0) f > STEP 287 / 899 (thread 0) f > STEP 288 / 899 (thread 0) f > STEP 289 / 899 (thread 0) f > STEP 290 / 899 (thread 0) f > STEP 291 / 899 (thread 0) f > STEP 292 / 899 (thread 0) f > STEP 293 / 899 (thread 0) f > STEP 294 / 899 (thread 0) f > STEP 295 / 899 (thread 0) f > STEP 296 / 899 (thread 0) f > STEP 297 / 899 (thread 0) f > STEP 298 / 899 (thread 0) f > STEP 299 / 899 (thread 0) f > STEP 300 / 899 (thread 0) f > STEP 301 / 899 (thread 0) f > STEP 302 / 899 (thread 0) f > STEP 303 / 899 (thread 0) f > STEP 304 / 899 (thread 0) f > STEP 305 / 899 (thread 0) f > STEP 306 / 899 (thread 0) f > STEP 307 / 899 (thread 0) f > STEP 308 / 899 (thread 0) f > STEP 309 / 899 (thread 0) f > STEP 310 / 899 (thread 0) f > STEP 311 / 899 (thread 0) f > STEP 312 / 899 (thread 0) f > STEP 313 / 899 (thread 0) f > STEP 314 / 899 (thread 0) f > STEP 315 / 899 (thread 0) f > STEP 316 / 899 (thread 0) f > STEP 317 / 899 (thread 0) f > STEP 318 / 899 (thread 0) f > STEP 319 / 899 (thread 0) f > STEP 320 / 899 (thread 0) f > STEP 321 / 899 (thread 0) f > STEP 322 / 899 (thread 0) f > STEP 323 / 899 (thread 0) f > STEP 324 / 899 (thread 0) f > STEP 325 / 899 (thread 0) f > STEP 326 / 899 (thread 0) f > STEP 327 / 899 (thread 0) f > STEP 328 / 899 (thread 0) f > STEP 329 / 899 (thread 0) f > STEP 330 / 899 (thread 0) f > STEP 331 / 899 (thread 0) f > STEP 332 / 899 (thread 0) f > STEP 333 / 899 (thread 0) f > STEP 334 / 899 (thread 0) f > STEP 335 / 899 (thread 0) f > STEP 336 / 899 (thread 0) f > STEP 337 / 899 (thread 0) f > STEP 338 / 899 (thread 0) f > STEP 339 / 899 (thread 0) f > STEP 340 / 899 (thread 0) f > STEP 341 / 899 (thread 0) f > STEP 342 / 899 (thread 0) f > STEP 343 / 899 (thread 0) f > STEP 344 / 899 (thread 0) f > STEP 345 / 899 (thread 0) f > STEP 346 / 899 (thread 0) f > STEP 347 / 899 (thread 0) f > STEP 348 / 899 (thread 0) f > STEP 349 / 899 (thread 0) f > STEP 350 / 899 (thread 0) f > STEP 351 / 899 (thread 0) f > STEP 352 / 899 (thread 0) f > STEP 353 / 899 (thread 0) f > STEP 354 / 899 (thread 0) f > STEP 355 / 899 (thread 0) f > STEP 356 / 899 (thread 0) f > STEP 357 / 899 (thread 0) f > STEP 358 / 899 (thread 0) f > STEP 359 / 899 (thread 0) f > STEP 360 / 899 (thread 0) f > STEP 361 / 899 (thread 0) f > STEP 362 / 899 (thread 0) f > STEP 363 / 899 (thread 0) f > STEP 364 / 899 (thread 0) f > STEP 365 / 899 (thread 0) f > STEP 366 / 899 (thread 0) f > STEP 367 / 899 (thread 0) f > STEP 368 / 899 (thread 0) f > STEP 369 / 899 (thread 0) f > STEP 370 / 899 (thread 0) f > STEP 371 / 899 (thread 0) f > STEP 372 / 899 (thread 0) f > STEP 373 / 899 (thread 0) f > STEP 374 / 899 (thread 0) f > STEP 375 / 899 (thread 0) f > STEP 376 / 899 (thread 0) f > STEP 377 / 899 (thread 0) f > STEP 378 / 899 (thread 0) f > STEP 379 / 899 (thread 0) f > STEP 380 / 899 (thread 0) f > STEP 381 / 899 (thread 0) f > STEP 382 / 899 (thread 0) f > STEP 383 / 899 (thread 0) f > STEP 384 / 899 (thread 0) f > STEP 385 / 899 (thread 0) f > STEP 386 / 899 (thread 0) f > STEP 387 / 899 (thread 0) f > STEP 388 / 899 (thread 0) f > STEP 389 / 899 (thread 0) f > STEP 390 / 899 (thread 0) f > STEP 391 / 899 (thread 0) f > STEP 392 / 899 (thread 0) f > STEP 393 / 899 (thread 0) f > STEP 394 / 899 (thread 0) f > STEP 395 / 899 (thread 0) f > STEP 396 / 899 (thread 0) f > STEP 397 / 899 (thread 0) f > STEP 398 / 899 (thread 0) f > STEP 399 / 899 (thread 0) f > STEP 400 / 899 (thread 0) f > STEP 401 / 899 (thread 0) f > STEP 402 / 899 (thread 0) f > STEP 403 / 899 (thread 0) f > STEP 404 / 899 (thread 0) f > STEP 405 / 899 (thread 0) f > STEP 406 / 899 (thread 0) f > STEP 407 / 899 (thread 0) f > STEP 408 / 899 (thread 0) f > STEP 409 / 899 (thread 0) f > STEP 410 / 899 (thread 0) f > STEP 411 / 899 (thread 0) f > STEP 412 / 899 (thread 0) f > STEP 413 / 899 (thread 0) f > STEP 414 / 899 (thread 0) f > STEP 415 / 899 (thread 0) f > STEP 416 / 899 (thread 0) f > STEP 417 / 899 (thread 0) f > STEP 418 / 899 (thread 0) f > STEP 419 / 899 (thread 0) f > STEP 420 / 899 (thread 0) f > STEP 421 / 899 (thread 0) f > STEP 422 / 899 (thread 0) f > STEP 423 / 899 (thread 0) f > STEP 424 / 899 (thread 0) f > STEP 425 / 899 (thread 0) f > STEP 426 / 899 (thread 0) f > STEP 427 / 899 (thread 0) f > STEP 428 / 899 (thread 0) f > STEP 429 / 899 (thread 0) f > STEP 430 / 899 (thread 0) f > STEP 431 / 899 (thread 0) f > STEP 432 / 899 (thread 0) f > STEP 433 / 899 (thread 0) f > STEP 434 / 899 (thread 0) f > STEP 435 / 899 (thread 0) f > STEP 436 / 899 (thread 0) f > STEP 437 / 899 (thread 0) f > STEP 438 / 899 (thread 0) f > STEP 439 / 899 (thread 0) f > STEP 440 / 899 (thread 0) f > STEP 441 / 899 (thread 0) f > STEP 442 / 899 (thread 0) f > STEP 443 / 899 (thread 0) f > STEP 444 / 899 (thread 0) f > STEP 445 / 899 (thread 0) f > STEP 446 / 899 (thread 0) f > STEP 447 / 899 (thread 0) f > STEP 448 / 899 (thread 0) f > STEP 449 / 899 (thread 0) f > STEP 450 / 899 (thread 0) f > STEP 451 / 899 (thread 0) f > STEP 452 / 899 (thread 0) f > STEP 453 / 899 (thread 0) f > STEP 454 / 899 (thread 0) f > STEP 455 / 899 (thread 0) f > STEP 456 / 899 (thread 0) f > STEP 457 / 899 (thread 0) f > STEP 458 / 899 (thread 0) f > STEP 459 / 899 (thread 0) f > STEP 460 / 899 (thread 0) f > STEP 461 / 899 (thread 0) f > STEP 462 / 899 (thread 0) f > STEP 463 / 899 (thread 0) f > STEP 464 / 899 (thread 0) f > STEP 465 / 899 (thread 0) f > STEP 466 / 899 (thread 0) f > STEP 467 / 899 (thread 0) f > STEP 468 / 899 (thread 0) f > STEP 469 / 899 (thread 0) f > STEP 470 / 899 (thread 0) f > STEP 471 / 899 (thread 0) f > STEP 472 / 899 (thread 0) f > STEP 473 / 899 (thread 0) f > STEP 474 / 899 (thread 0) f > STEP 475 / 899 (thread 0) f > STEP 476 / 899 (thread 0) f > STEP 477 / 899 (thread 0) f > STEP 478 / 899 (thread 0) f > STEP 479 / 899 (thread 0) f > STEP 480 / 899 (thread 0) f > STEP 481 / 899 (thread 0) f > STEP 482 / 899 (thread 0) f > STEP 483 / 899 (thread 0) f > STEP 484 / 899 (thread 0) f > STEP 485 / 899 (thread 0) f > STEP 486 / 899 (thread 0) f > STEP 487 / 899 (thread 0) f > STEP 488 / 899 (thread 0) f > STEP 489 / 899 (thread 0) f > STEP 490 / 899 (thread 0) f > STEP 491 / 899 (thread 0) f > STEP 492 / 899 (thread 0) f > STEP 493 / 899 (thread 0) f > STEP 494 / 899 (thread 0) f > STEP 495 / 899 (thread 0) f > STEP 496 / 899 (thread 0) f > STEP 497 / 899 (thread 0) f > STEP 498 / 899 (thread 0) f > STEP 499 / 899 (thread 0) f > STEP 500 / 899 (thread 0) f > STEP 501 / 899 (thread 0) f > STEP 601 / 899 (thread 0) f > STEP 701 / 899 (thread 0) f > STEP 801 / 899 (thread 0) f > Reallocating..done. \*alloclen = 1773 > > done. > > disttbfast (nuc) Version 7.505 > alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 > 1 thread(s) > > Strategy: > FFT-NS-2 (Fast but rough) > Progressive method (guide trees were built 2 times.) > > If unsure which option to use, try 'mafft --auto input \> output'. > For more information, see 'mafft --help', 'mafft --man' and the mafft page. > > The default gap scoring scheme has been changed in version 7.110 (2013 Oct). > It tends to insert more gaps into gap-rich regions than previous versions. > To disable this change, add the --leavegappyregion option. > > Running external command line application. This may print messages to stdout and/or stderr. > The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. > > Command: raxmlHPC -m GTRGAMMA -p 6913 -N 1 -s /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta -w /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/tmpfqmrssqb -n q2 > > Warning, you specified a working directory via "-w" > Keep in mind that RAxML only accepts absolute path names, not relative ones! > > RAxML can't, parse the alignment file as phylip file > it will now try to parse it as FASTA file > > IMPORTANT WARNING: Sequences 56b08b3fbdf6bf8b41c0864c5c53c524 and abfd1bd8714a1e8a9f7c4b56c292128d are exactly identical > > IMPORTANT WARNING: Sequences defa302fbc7847b6b5074d0d0b89a917 and 76677892a4dd300bba8b7b441734111b are exactly identical > > IMPORTANT WARNING: Sequences 7c821085a5548386a8d91fe359fa3ff3 and 71c5d0ca8455f4647b0e9cf8a6f4818c are exactly identical > > IMPORTANT WARNING: Sequences 37d30f8109745b8f48bc05352fdb0b43 and e345298fe5d27dc5160d41b1744fc841 are exactly identical > > IMPORTANT WARNING: Sequences 860379b0caea95824ac8035507127cb1 and 3e903410685ad9651f779ce5871f25d9 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and 25be8565bb6d4b0ebcfc117225491be2 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and e924271260411e885401de5355fc6814 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and 9c7b78c7bd978735f1b2d363cb7c54be are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and 091a6fe437c9cd2484dd25e69c690bf6 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and 84143a32a142a2e05f3584b3efc8a96f are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and 6985cade0eb836e21f149f8dbf0b2bc6 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and ca369886ea9ac3b7f46e4b689d923412 are exactly identical > > IMPORTANT WARNING: Sequences 0f898170dbe4592000abdcde0dd2ba2e and d7a0a47542fa7ec651499db41a8608b5 are exactly identical > > IMPORTANT WARNING: Sequences e0b0817162b44d0e17a1c50486839924 and c24cc4827ae046cfc1903fade9a593aa are exactly identical > > IMPORTANT WARNING: Sequences 5431c93e93b57f0b74748eb702ea1e72 and 34f408f4631912dd38ff03bb337542bf are exactly identical > > IMPORTANT WARNING: Sequences 36f00e24a741c19a5ee20f58919004ad and 0560198302010f9b110d4ec9897e14d0 are exactly identical > > IMPORTANT WARNING: Sequences 95251fbafeb9956f566a3da93d145d63 and 982b9f926209fcf5e48d1b95afe44519 are exactly identical > > IMPORTANT WARNING: Sequences b40fb9f5f4e91452a7a60c1caa527513 and 3bf45ac921f4f036db87cf2602a76225 are exactly identical > > IMPORTANT WARNING: Sequences 1cd30fcbf9157649a8933f4b41240f95 and 50ae94daff8a1af26ebd92449801ec5f are exactly identical > > IMPORTANT WARNING: Sequences 6a49b0df18b1abfe220ecc00d5cbf296 and dd826da2c2da9ebff4cbf9b2d5a15794 are exactly identical > > IMPORTANT WARNING: Sequences eded7214e8c99bcaeed92cae1b849d42 and 1e5db7fe2844640a3a5a978ece66e8b3 are exactly identical > > IMPORTANT WARNING: Sequences eded7214e8c99bcaeed92cae1b849d42 and 84eade1f1e5832f039e3d4e7ccdc132b are exactly identical > > IMPORTANT WARNING: Sequences b3e560c415dd505b1e13ba0ba5dba6ba and a2f39bc23de50b91c6a65d69f7870f3f are exactly identical > > IMPORTANT WARNING: Sequences aeb7c3b23850fabd43d8f27125df5efa and 1982d602ae789aa6922c84379e82f28a are exactly identical > > IMPORTANT WARNING: Sequences c7724cd29323e7cdbcf29601a5a6558a and 64847e8d761ac2ee605b4968afa45012 are exactly identical > > IMPORTANT WARNING: Sequences 3dde63a29d5649dd61c8ce85e2a82f64 and 44cdc9c06c86362c29a54813aefd2f39 are exactly identical > > IMPORTANT WARNING: Sequences 820d3c5095323f85949bc959fd15d1b7 and 4d626567fc7b7136eed52c3f093c6ce9 are exactly identical > > IMPORTANT WARNING: Sequences 13e3b1b496b1af3160c30eca62df9661 and 1f016ec26e4774c86f029301b556de28 are exactly identical > > IMPORTANT WARNING: Sequences 369fbaf59b969dfaa6af5bc7f769fd49 and 1a117227cfb94f3196ec36c6f4bc8bf1 are exactly identical > > IMPORTANT WARNING: Sequences 369fbaf59b969dfaa6af5bc7f769fd49 and 1d645c234614ddbf579edb05c466abfe are exactly identical > > IMPORTANT WARNING: Sequences 369fbaf59b969dfaa6af5bc7f769fd49 and b6597ed0ca2addf7349b5e40cf56bea4 are exactly identical > > IMPORTANT WARNING: Sequences 369fbaf59b969dfaa6af5bc7f769fd49 and 27cde56ed3c632a6ae4550ba464ebc5f are exactly identical > > IMPORTANT WARNING: Sequences 95c08da59378a0eb674c2b7dab943428 and a9db3c72585614b1e07373db125bc5f9 are exactly identical > > IMPORTANT WARNING: Sequences 4679cc695527888b23df9e041b1e7465 and 24297865aada8ebdda6cd290a70df0bc are exactly identical > > IMPORTANT WARNING: Sequences 81b95cf5e2e0e3f7579b7dfa4b2ebed0 and fd691ed5101bc4f5dc40691f13cb26d3 are exactly identical > > IMPORTANT WARNING: Sequences e7ef92a29e265a3f616b477f54e462dd and 6b765d5bd94a919b64ca182d3e71a0da are exactly identical > > IMPORTANT WARNING: Sequences fb8ddfb6886f3b08315ca8bbab50a788 and 1dca3770a40e64a30c54e82b832e378d are exactly identical > > IMPORTANT WARNING: Sequences c331094ff01669229c8ec91820f9b536 and 56ce7d1a65fdef6654e4e2e83040f18e are exactly identical > > IMPORTANT WARNING: Sequences c331094ff01669229c8ec91820f9b536 and 369c157e59f4d1e769b6e66991339093 are exactly identical > > IMPORTANT WARNING: Sequences c331094ff01669229c8ec91820f9b536 and 6bd02355d7dbd3cf6d1c40a4aeefb6ff are exactly identical > > IMPORTANT WARNING: Sequences c331094ff01669229c8ec91820f9b536 and 30c9be8d7dac583f199f3268f5341eda are exactly identical > > IMPORTANT WARNING: Sequences 2ddd18d49a8163e0fc79e28ea6273254 and 408c2bd27f98e4b798457f7d67fd7234 are exactly identical > > IMPORTANT WARNING: Sequences 63cec1d17b18ade410571d03ed172605 and 045158fe88c15a26d9626d6eb7128c8e are exactly identical > > IMPORTANT WARNING: Sequences a1d1764926bb0e83c87746990041fafe and dd3dab0f0d0f36f2e91105fd647cd8b9 are exactly identical > > IMPORTANT WARNING: Sequences 2128aa4b835441846a28f543aeb54ea4 and cb9b36e0f9f537ad74c7fa25b8595b84 are exactly identical > > IMPORTANT WARNING: Sequences ecd7a4f5f3d286321123fbf1a6eb3c11 and 475b82228fdf19f8a1dc65a0b403b160 are exactly identical > > IMPORTANT WARNING: Sequences 9f109dfcb2f1ff4857ecdc77e42a739b and 3828275767b4aa264369f5af06950b60 are exactly identical > > IMPORTANT WARNING: Sequences 1ce0d1cfa2c68160f70e20616d2d4bc2 and 611cf20c9875f7aa3c89a01734905263 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and fa1db397af8990ba41f0ecdbb3edb893 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and 50c416538130a88592deadbbbf2437b3 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and a1eb68b0d24005ba889e3b7b371153ec are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and 388b693c2fd21798432bcf24725efba4 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and 154698c357bf4466181d2a3750dfd74d are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and 4c207c46ef44b1840fb75bec0fea73c4 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and 661bf53da30db92d530906d70f72fbb7 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and e1c330afdd7d0e11de5686828f0e5dd6 are exactly identical > > IMPORTANT WARNING: Sequences 51a99ed82e9ae5a91d506be3c7df8845 and f1b052555500eab00b804e0d4251e8e0 are exactly identical > > IMPORTANT WARNING: Sequences 01491b7ad3b35c7e644dd24ae831bee2 and 38333c02930f4256040f869cc1e3e282 are exactly identical > > IMPORTANT WARNING: Sequences b73f55184aea80b446bc758a3235b976 and 3d81f09eebdb4e0b350dee6991bd318b are exactly identical > > IMPORTANT WARNING: Sequences a550440c07634d574b0478021376109c and 28c8b117cb81940713732fc6f39564fd are exactly identical > > IMPORTANT WARNING: Sequences a550440c07634d574b0478021376109c and 23c51a6b56ae6b5971e275a5a713f475 are exactly identical > > IMPORTANT WARNING: Sequences 64286fb19f06c675804bd7625474554b and 2b41d91bf6051ad4803f21482b853443 are exactly identical > > IMPORTANT WARNING: Sequences d6dd3e31efb998491ac861a748c7ee7d and 57aac4fa7b17d1e4a7e15e6cb3e3bea9 are exactly identical > > IMPORTANT WARNING: Sequences 64baf54b2d5d3f420bab293912167c6a and 54716b25978a46bb2be2690b4e75b92e are exactly identical > > IMPORTANT WARNING: Sequences 8ec58a12417250f652a8b3329977e0a6 and bfd0937806ac4e67ffa5540c6bd14f13 are exactly identical > > IMPORTANT WARNING: Sequences 26de4690cd2c89c490c37a8d1418d67a and 5733aa5932117f674b51857ab7817f3c are exactly identical > > IMPORTANT WARNING: Sequences 43349a8c681162a58bd1691609e282ee and 035d7c40336a485a1b7afdad13a75eec are exactly identical > > IMPORTANT WARNING: Sequences 43349a8c681162a58bd1691609e282ee and 00692849e6965c897ed15b7c483efcaf are exactly identical > > IMPORTANT WARNING: Sequences f720e80bee7ec3ae14d40c1a13894474 and b750e8f98f7b783b27434636ab4627bd are exactly identical > > IMPORTANT WARNING: Sequences c5bd025300b4ef0c652dd11cef56ac29 and f92271ec21793f18a2e0ee39b5abc693 are exactly identical > > IMPORTANT WARNING: Sequences bd67c391458925fcc54d3f9590a94d25 and 6eee0ca5b27e89ca22956429494be0ad are exactly identical > > IMPORTANT WARNING: Sequences c8571516114b6d099f2896c28934ffff and 2f1f7e86925baf19bd1feefec5c385fd are exactly identical > > IMPORTANT WARNING: Sequences 82465f2440c4d9519be367dec4ce0d87 and b0fa0b77c514f623055b10b51adc4ab4 are exactly identical > > IMPORTANT WARNING: Sequences 029f486bbaf9b9c6f987293c831b894e and 06b25349b04a18c9de6b7bd4a35e67b2 are exactly identical > > IMPORTANT WARNING: Sequences 5b566831834a36a716c12800e67c01b2 and fadee5c13d2199a94673bf806721d047 are exactly identical > > IMPORTANT WARNING: Sequences ba4cd9813ef84446b4d39b3b2f7967fd and c0a220e90a423d039e85bd49c6b0f7a2 are exactly identical > > IMPORTANT WARNING: Sequences 8785b6b428428e85223da6a99fbde584 and 530e1c9b76907cc0d304476801782ca0 are exactly identical > > IMPORTANT WARNING: Sequences dc2e050d5552654a8ffcd9cbd4123e63 and bbbfb1dd6ca14c290b4818dab7e881e2 are exactly identical > > IMPORTANT WARNING: Sequences d0f4e1ddbaf535c45acc903ca3367ce0 and 8a4c89e991253889f8e6a2df90cad481 are exactly identical > > IMPORTANT WARNING: Sequences 89879e3f6e9a406d9ddd9180b5619eee and 3cf7841f8f276e0e45caadac3b1d3e74 are exactly identical > > IMPORTANT WARNING: Sequences 2d01eed9043038bed06aebde72fe5fa8 and 7a3d69b78dbc97a921dac98cbf437b56 are exactly identical > > IMPORTANT WARNING: Sequences 74513c723bd0d320e052ee542a8af469 and 6a2fbbfe46018e5a3c4c6315e3eb9b38 are exactly identical > > IMPORTANT WARNING: Sequences 74513c723bd0d320e052ee542a8af469 and fb8bec35fb92be4b6def09e40c837279 are exactly identical > > IMPORTANT WARNING: Sequences e4d94f7a630123fef47db4f8f3395bc4 and b8194f88a401a9d3f3adddd6742b0adb are exactly identical > > IMPORTANT WARNING: Sequences a15a640856f36e99e54dacfb3c65aa6f and 12d2cccb74d30b7631d861a132944d50 are exactly identical > > IMPORTANT WARNING: Sequences d5d8e2716a11844a2026bb0722de1073 and ab6e0cad1e50436eefb43c3766ebb885 are exactly identical > > IMPORTANT WARNING: Sequences eadcb68ceb94c198335f64abd7f442a0 and f661a24ced70e93b301d151e61fd2cd0 are exactly identical > > IMPORTANT WARNING: Sequences 165ff3bd67edc9d3e7b3802ee3254c74 and 90ea6a57c53b9e8d47dd56ca8f0b55f8 are exactly identical > > IMPORTANT WARNING: Sequences f28d813d7bdd596b5208205e93b4d0de and d27cf6736e4217840a81efcd66de0502 are exactly identical > > IMPORTANT WARNING: Sequences a527568bad8ed46421c84221e4a1f6ea and 118b4ed36493d6419ce11a1731c0f5c3 are exactly identical > > IMPORTANT WARNING: Sequences a527568bad8ed46421c84221e4a1f6ea and ea826da5239889531837d17bf5cea03c are exactly identical > > IMPORTANT WARNING: Sequences e7e7687f1f2196ab6ea2ad9f93e858e9 and ffb9eb8907b450fc45f9451a74493e03 are exactly identical > > IMPORTANT WARNING: Sequences 6a5bebbb82a396467e373f1d294a8474 and 1e110acb6cd66c3519c0d0bc17f80e17 are exactly identical > > IMPORTANT WARNING: Sequences f0ff31de7aa89dcc62090a965991acd2 and a7cbba613e43e338f8b433805d581536 are exactly identical > > IMPORTANT WARNING: Sequences f9748a9a5a7635bff0a321c3ba5f506e and 4265ddc064ddf30efc554504d9d200e3 are exactly identical > > IMPORTANT WARNING: Sequences 0177862b3ff620d642fc6c8f610d6ed4 and dc7779efdb0b987bcfad3b4a87f1b1c3 are exactly identical > > IMPORTANT WARNING: Sequences 7b3a9220fe8f085aeb72063818d61080 and 5caca6838f9cd757767d518b1816c742 are exactly identical > > IMPORTANT WARNING: Sequences 3c397d9e1cf3c44c6414ae77b866cd88 and d52af2ab32fe93301f13cfcc445514c8 are exactly identical > > IMPORTANT WARNING: Sequences af889321b2a6c6d991d6b51489ac6e74 and 55c356462ebcca0add5ed19fd952109e are exactly identical > > IMPORTANT WARNING: Sequences 5285ecfd3f4b901925ebedcae9f0f80a and 7b8b61ef907be54ea7285715890d4f7d are exactly identical > > IMPORTANT WARNING: Sequences 38f8d31bd82cd56461994a4f95ec8b86 and 7cee37cbbb44a1e20df80e7ef2e8c50b are exactly identical > > IMPORTANT WARNING: Sequences a5b5df21001bc4f508e1af15f74902d7 and 6ca238a15fe2265bcc87080c89d73bff are exactly identical > > IMPORTANT WARNING: Sequences c61de01b08d6c8598f7047abdd0c8964 and 88cd36875bffad28a3043978afbdb598 are exactly identical > > IMPORTANT WARNING: Sequences c61de01b08d6c8598f7047abdd0c8964 and a91b0a587170005bb7bf76bad098761f are exactly identical > > IMPORTANT WARNING: Sequences 1a0af30873d72b80e3fe80985a24f924 and 5792b7eecdfef35db420f3ffaba4deff are exactly identical > > IMPORTANT WARNING: Sequences 6b6544b1bea60f490b571296f1b651d9 and 6ef5e55e8ccb3f1af9fcc32c61428348 are exactly identical > > IMPORTANT WARNING: Sequences b0112f1e997c6422c13cb46a59303c72 and 32b61a09609737680ce2e05dad2b299c are exactly identical > > IMPORTANT WARNING: Sequences be1b3fb43dd62142f7bed00000ba0e45 and ee31afc894855f8be8a66bec0631c979 are exactly identical > > IMPORTANT WARNING: Sequences 3d79308fb7308a3bc85e7118867ef58e and 300e374bcaabbbee6af6cd64610b678a are exactly identical > > IMPORTANT WARNING: Sequences 4ec9e2702a0524c29881be195a38c685 and 213735bd18357eded895708efff28030 are exactly identical > > IMPORTANT WARNING: Sequences 64c062cc30c6527ff9983d28a21b5524 and 622ce1852e94eca7a65c8826fe5c4c09 are exactly identical > > IMPORTANT WARNING: Sequences 14c917d7fe9555ccf48d7d3d997cc5ec and f73d3c8ec084708e5a32e515a21baf4b are exactly identical > > IMPORTANT WARNING > Found 112 sequences that are exactly identical to other sequences in the alignment. > Normally they should be excluded from the analysis. > > Just in case you might need it, an alignment file with > sequence duplicates removed is printed to file /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta.reduced > The file /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta.reduced RAxML wants to open for writing or appending can not be opened [mode: wb], exiting ... > Traceback (most recent call last): > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in **call** > results = action(\*\*arguments) > File "", line 2, in align\_to\_tree\_mafft\_raxml > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound\_callable > outputs = self._callable\_executor_(scope, callable\_args, > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 475, in _callable\_executor_ > outputs = self.\_callable(scope.ctx, \*\*view\_args) > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2\_phylogeny/\_align\_to\_tree\_mafft\_raxml.py", line 26, in align\_to\_tree\_mafft\_raxml > unrooted\_tree, = raxml(alignment=masked\_seq, n\_threads=n\_threads, > File "", line 2, in raxml > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound\_callable > outputs = self._callable\_executor_(scope, callable\_args, > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable\_executor_ > output\_views = self.\_callable(\*\*view\_args) > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2\_phylogeny/\_raxml.py", line 68, in raxml > run\_command(cmd) > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2\_phylogeny/\_raxml.py", line 34, in run\_command > subprocess.run(cmd, check=True) > File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run > raise CalledProcessError(retcode, process.args, > subprocess.CalledProcessError: Command '['raxmlHPC', '-m', 'GTRGAMMA', '-p', '6913', '-N', '1', '-s', '/var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta', '-w', '/var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/tmpfqmrssqb', '-n', 'q2']' returned non-zero exit status 255. I have also checked the alignment file with seq duplicates removed using the path printed, however, there was actually no data files in the qiime2/sl/data folder: > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % ls /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta.reduced > ls: /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/aligned-dna-sequences.fasta.reduced: No such file or directory > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % ls /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/ > ls: /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a/data/: No such file or directory > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % ls /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a > ls: /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/74f2680f-69ca-4db8-b97a-8fb90085c13a: No such file or directory > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % ls /var/folders/wr/wy2g8g411gd5l7rzddpf7f8r0000gn/T/qiime2/sl/data/ > (qiime2-2022.8) sl@SHUQI-only-one-U CL-04-NOMMS % This made me very confused, how come it generated a fasta file but the file is missing? Any suggestions/ideas will be appreciated. Thank you so much! PS. the re-installation, running raxml were all completed today. Best, Shuqi --- _[View the full topic](https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765)._