plugin error from phylogeny raxml (default): returned non-zero exit status 255

Shuqi · December 7, 2022, 3:18pm

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. 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
--2022-12-07 09:33:45-- https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml
Resolving 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 [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
Resolving 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 ..
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done.

Constructing a UPGMA tree (efffree=0) ...
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done.

Progressive alignment 1/2...

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Reallocating..done. *alloclen = 1768

done.

Making a distance matrix from msa..
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done.

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done.

Progressive alignment 2/2...

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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