# \#mafft **URL:** https://forum.qiime2.org/tag/mafft/53.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [qiime alignment mafft error](https://forum.qiime2.org/t/qiime-alignment-mafft-error/33143)
**Author:** [@Sue](https://forum.qiime2.org/u/Sue)\ **Replies:** 2\ **Last updated:** [May 15, 2025, 2:13pm UTC](https://forum.qiime2.org/t/qiime-alignment-mafft-error/33143 "2025-05-15T14:13:38Z")
Hello, I have the same issue as described in this post: ERROR: Qiime 2 alignment mafft My question is: can I use the --p-parttree parameter even when the number of sequences being aligned is less than 1,000,000? I wan… --- ## [MAFFT parameters - reproducability](https://forum.qiime2.org/t/mafft-parameters-reproducability/32365)
**Author:** [@arwqiime](https://forum.qiime2.org/u/arwqiime)\ **Replies:** 3\ **Last updated:** [January 22, 2025, 11:33am UTC](https://forum.qiime2.org/t/mafft-parameters-reproducability/32365 "2025-01-22T11:33:46Z")
Hello, I used the qiime phylogeny align-to-tree-mafft-fasttree pipeline to construct phylogenetic trees from fungal ITS1 ASVs (trimmed by ITSxpress). I opened the resulting MAFFT alignment in a third-party sequence anal… --- ## [MAFFT crashes after about 1 hour](https://forum.qiime2.org/t/mafft-crashes-after-about-1-hour/28483)
**Author:** [@marty\_pl](https://forum.qiime2.org/u/marty_pl)\ **Replies:** 4\ **Last updated:** [December 4, 2023, 9:12pm UTC](https://forum.qiime2.org/t/mafft-crashes-after-about-1-hour/28483 "2023-12-04T21:12:00Z")
I am running the latest version of QIIME2 (2023.09) in WSL. My 16S V3V4 data file (after quality check) contains \>2M reads from 50 samples. To build the phylogenetic tree I've run the following command set: qiime phylog… --- ## [plugin error from phylogeny - no such file or directory: mafft](https://forum.qiime2.org/t/plugin-error-from-phylogeny-no-such-file-or-directory-mafft/26349)
**Author:** [@fdebus](https://forum.qiime2.org/u/fdebus)\ **Replies:** 4\ **Last updated:** [May 10, 2023, 1:22pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-no-such-file-or-directory-mafft/26349 "2023-05-10T13:22:11Z")
Hello! I'm new to the use of Qiime2 and am trying to get the hang of if by following the Moving Pictures Tutorial. This forum has been a great help, so I first wanted to thank all of you already! The problem I face is … --- ## [Having trouble with alignment: mafft, SEPP, & SINA](https://forum.qiime2.org/t/having-trouble-with-alignment-mafft-sepp-sina/20732)
**Author:** [@BeckWehrle](https://forum.qiime2.org/u/BeckWehrle)\ **Replies:** 7\ **Last updated:** [October 11, 2021, 2:45am UTC](https://forum.qiime2.org/t/having-trouble-with-alignment-mafft-sepp-sina/20732 "2021-10-11T02:45:16Z")
Hello QIIME users, I’m trying to analyze sequences with QIIME2 that a collaborator previously analyzed with QIIME1, but I’m having trouble with alignment. I’m starting out with file.fna that contains ~1.5 million sequen… --- ## [mafft does not work inside my Qiime2 environment](https://forum.qiime2.org/t/mafft-does-not-work-inside-my-qiime2-environment/19267)
**Author:** [@kathrine-mcaulay](https://forum.qiime2.org/u/kathrine-mcaulay)\ **Replies:** 6\ **Last updated:** [April 22, 2021, 4:59pm UTC](https://forum.qiime2.org/t/mafft-does-not-work-inside-my-qiime2-environment/19267 "2021-04-22T16:59:24Z")
Hello, I am running q2cli version 2021.2.0, installed using conda, on MacOS Mojave 10.14.6. I am having issues with mafft but it doesn't seem to be related to the memory/large file issues covered in posts like this one.… --- ## [Re: Alignment error message](https://forum.qiime2.org/t/re-alignment-error-message/19002)
**Author:** [@Willm\_Martens-Habben](https://forum.qiime2.org/u/Willm_Martens-Habben)\ **Replies:** 0\ **Last updated:** [March 27, 2021, 4:43am UTC](https://forum.qiime2.org/t/re-alignment-error-message/19002 "2021-03-27T04:43:54Z")
this might be a little outdated, but just for the record: In response to @coralgal's post regarding an error message when running qiime alignment mafft --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs.qza in e… --- ## [Info on qiime phylogeny align-to-tree-mafft-fasttree algorithm](https://forum.qiime2.org/t/info-on-qiime-phylogeny-align-to-tree-mafft-fasttree-algorithm/15256)
**Author:** [@Maider](https://forum.qiime2.org/u/Maider)\ **Replies:** 1\ **Last updated:** [June 5, 2020, 2:50pm UTC](https://forum.qiime2.org/t/info-on-qiime-phylogeny-align-to-tree-mafft-fasttree-algorithm/15256 "2020-06-05T14:50:55Z")
Hi, I would like to play more with the phylogeny of sequences, by selecting / removing some of the rep-seqs from the tree. I know Qiime2 doesn't support this kind of analysis, I work mainly on Geneious. My question … --- ## [mafft --large argument support](https://forum.qiime2.org/t/mafft-large-argument-support/14564)
**Author:** [@Deni\_Ribicic](https://forum.qiime2.org/u/Deni_Ribicic)\ **Replies:** 2\ **Last updated:** [April 20, 2020, 9:46pm UTC](https://forum.qiime2.org/t/mafft-large-argument-support/14564 "2020-04-20T21:46:32Z")
Dear developers, I think it would be handy to have mafft --large option available. Many people, including myself are taking advantage of q2 pipeline to process long 16S rRNA reads generated by Oxford Nanopore technolog… --- ## [Question about 'masked' alignment- how do I acquire details of alignment?](https://forum.qiime2.org/t/question-about-masked-alignment-how-do-i-acquire-details-of-alignment/12965)
**Author:** [@nvtravan](https://forum.qiime2.org/u/nvtravan)\ **Replies:** 2\ **Last updated:** [December 20, 2019, 8:07pm UTC](https://forum.qiime2.org/t/question-about-masked-alignment-how-do-i-acquire-details-of-alignment/12965 "2019-12-20T20:07:43Z")
I am using Qiime2 2019.4; I can update if necessary. I have put some 16S sequencing data into alignment via mafft alignment algorithm prior to diversity analyses. The data includes V4 amplicons (515-806) and V3V4 ampli… --- ## [Aligning large numbers of reads](https://forum.qiime2.org/t/aligning-large-numbers-of-reads/12598)
**Author:** [@Maxy](https://forum.qiime2.org/u/Maxy)\ **Replies:** 1\ **Last updated:** [November 23, 2019, 9:27pm UTC](https://forum.qiime2.org/t/aligning-large-numbers-of-reads/12598 "2019-11-23T21:27:14Z")
Hello all. I have been working with the results of a minION experiment with ~30 samples. The result of this experiment is ~2 million reads each around 350bp spread across the 30 samples fairly evenly (humble brag). I wor… --- ## [Mafft /dev/stderr permission denied under jupyter](https://forum.qiime2.org/t/mafft-dev-stderr-permission-denied-under-jupyter/8114)
**Author:** [@jamesabbott](https://forum.qiime2.org/u/jamesabbott)\ **Replies:** 5\ **Last updated:** [February 13, 2019, 5:33pm UTC](https://forum.qiime2.org/t/mafft-dev-stderr-permission-denied-under-jupyter/8114 "2019-02-13T17:33:48Z")
I'm having trouble running the align\_to\_tree\_mafft\_fasttree pipeline using the artefact API in a jupyter notebook. Here is a minimal example using the moving pictures example data which demonstrates the problem. import… --- ## [MAFFT Error: non-zero exit status 1](https://forum.qiime2.org/t/mafft-error-non-zero-exit-status-1/6345)
**Author:** [@Purrsia\_Felidae](https://forum.qiime2.org/u/Purrsia_Felidae)\ **Replies:** 6\ **Last updated:** [November 2, 2018, 11:15am UTC](https://forum.qiime2.org/t/mafft-error-non-zero-exit-status-1/6345 "2018-11-02T11:15:56Z")
Dear Qiime2 White Wizards: I thought I would follow up with my previous post: Mafft 'returned non-zero exit status 1' ERROR - #9 First of all, THANK you for putting the --parttree option for the mafft alignment. I thou… --- ## [Problem running Mafft alignment](https://forum.qiime2.org/t/problem-running-mafft-alignment/6193)
**Author:** [@Vorthon](https://forum.qiime2.org/u/Vorthon)\ **Replies:** 6\ **Last updated:** [October 2, 2018, 4:10am UTC](https://forum.qiime2.org/t/problem-running-mafft-alignment/6193 "2018-10-02T04:10:25Z")
Hello, I just ran the mafft alignment and it failed. I got the massage below. Could any one please inform me why it failed? Thank you. Plugin error from alignment: Command '\['mafft', '--preservecase', '--inputorder', … --- ## [Qiime alignment mafft threads error](https://forum.qiime2.org/t/qiime-alignment-mafft-threads-error/5026)
**Author:** [@arwqiime](https://forum.qiime2.org/u/arwqiime)\ **Replies:** 1\ **Last updated:** [July 13, 2018, 5:43pm UTC](https://forum.qiime2.org/t/qiime-alignment-mafft-threads-error/5026 "2018-07-13T17:43:40Z")
Hello, a value of -1 (automatically useall cores) should be available in the following step, but I get an error message. If I specify it manually (e.g. 12), it works. $ qiime alignment mafft \\ --i-sequences 2b\_BF1u2-… --- ## [What Algorithm does Qiime use by Default for Multiple Sequence Alignment When Using MAFFT?](https://forum.qiime2.org/t/what-algorithm-does-qiime-use-by-default-for-multiple-sequence-alignment-when-using-mafft/4290)
**Author:** [@AlfalfaResearcher](https://forum.qiime2.org/u/AlfalfaResearcher)\ **Replies:** 2\ **Last updated:** [May 29, 2018, 8:08pm UTC](https://forum.qiime2.org/t/what-algorithm-does-qiime-use-by-default-for-multiple-sequence-alignment-when-using-mafft/4290 "2018-05-29T20:08:06Z")
Hi everyone, I am curious about which strategy is used to perform multiple sequence alignment in Qiime 2. For example on MAFFT's website they list multiple progressive and iterative methods that can be used to align seq… --- ## [Mafft error with virtual box](https://forum.qiime2.org/t/mafft-error-with-virtual-box/4285)
**Author:** [@mshelomi1](https://forum.qiime2.org/u/mshelomi1)\ **Replies:** 2\ **Last updated:** [May 28, 2018, 2:32am UTC](https://forum.qiime2.org/t/mafft-error-with-virtual-box/4285 "2018-05-28T02:32:50Z")
Hello. I have successfully installed Qiime2-2018.4 on my virtual box running Ubuntu. When attempting to run alignment mafft with the verbose setting, I get the following output. qiime alignment mafft --verbose --i- se… --- ## [Mafft error for alignment of rep-seqs](https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915)
**Author:** [@gilberto\_solano](https://forum.qiime2.org/u/gilberto_solano)\ **Replies:** 4\ **Last updated:** [May 1, 2018, 2:26pm UTC](https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915 "2018-05-01T14:26:31Z")
Hi. I am trying to align some sequences following the steps given in the "Moving pictures" tutorial to create a phylogenetic tree; I am using : \*\*$ qiime alignment mafft \*\* \*\*--i-sequences rawmilk\_rep-seqs.qza \*\* --o… --- ## [Alignment error message](https://forum.qiime2.org/t/alignment-error-message/2383)
**Author:** [@coralgal](https://forum.qiime2.org/u/coralgal)\ **Replies:** 18\ **Last updated:** [April 10, 2018, 5:04pm UTC](https://forum.qiime2.org/t/alignment-error-message/2383 "2018-04-10T17:04:56Z")
Hi there, I have been trying to align my sequences by running the maaft command. It crops up with this error. (qiime2-2017.11) qiime2@qiime2core2017-11:~/gbstrial2$ qiime alignment mafft \\ \> --i-sequences rep-seqs.qz… --- ## [Diversity plugin error](https://forum.qiime2.org/t/diversity-plugin-error/2976)
**Author:** [@LauraMason](https://forum.qiime2.org/u/LauraMason)\ **Replies:** 11\ **Last updated:** [February 19, 2018, 5:25pm UTC](https://forum.qiime2.org/t/diversity-plugin-error/2976 "2018-02-19T17:25:20Z")
Continuing the discussion from Alignment error message: Hello I am trying to generate a tree for phylogenetic diversity analyses using the command: qiime alignment mafft. And I am receiving the same error as the user l… --- ## [Parameters in phylogenetic tree creation](https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998)
**Author:** [@Matilda\_H-D](https://forum.qiime2.org/u/Matilda_H-D)\ **Replies:** 1\ **Last updated:** [February 13, 2018, 6:36pm UTC](https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998 "2018-02-13T18:36:30Z")
Hi there, When we are creating a phylogenetic tree for use in phylogenetic diversity analysis, there is a step, qiime alignment mask, where we mask unconserved or highly gapped columns from our multiple sequence alignme… --- ## [Alignment error message when input sequences over 1000000](https://forum.qiime2.org/t/alignment-error-message-when-input-sequences-over-1000000/2922)
**Author:** [@yiwen](https://forum.qiime2.org/u/yiwen)\ **Replies:** 7\ **Last updated:** [February 12, 2018, 6:02pm UTC](https://forum.qiime2.org/t/alignment-error-message-when-input-sequences-over-1000000/2922 "2018-02-12T18:02:09Z")
Hi, I am trying to align my sequences through running the mafft command. It comes out with this error. inputfile = orig 1108985 x 392 - 150 d nthread = 10 The number of sequences must be \< 1000000 Please try the --p… --- ## [Error when trying to do multiple alignment](https://forum.qiime2.org/t/error-when-trying-to-do-multiple-alignment/2473)
**Author:** [@Qianhao\_Li](https://forum.qiime2.org/u/Qianhao_Li)\ **Replies:** 4\ **Last updated:** [January 9, 2018, 8:10pm UTC](https://forum.qiime2.org/t/error-when-trying-to-do-multiple-alignment/2473 "2018-01-09T20:10:33Z")
Hi all, I tried to do the multiple sequence alignment with mafft this morning for phylogenetic tree but got the error saying: . I used the latest version of QIIME2 which has the dada2 error fixed. Any idea about this … --- ## [MAFFT input in open-reference OTU picking workflow](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082)
**Author:** [@steff1088](https://forum.qiime2.org/u/steff1088)\ **Replies:** 2\ **Last updated:** [December 4, 2017, 5:32pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082 "2017-12-04T17:32:27Z")
@Nicholas\_Bokulich thanks a lot. From my workflow up to the classification and plotting, what intermediate file would I use as input to MAFFT in order to work on getting a rooted tree? -steffen --- ## [Is mafft issue solved?](https://forum.qiime2.org/t/is-mafft-issue-solved/1482)
**Author:** [@yeojuny](https://forum.qiime2.org/u/yeojuny)\ **Replies:** 10\ **Last updated:** [October 31, 2017, 11:32pm UTC](https://forum.qiime2.org/t/is-mafft-issue-solved/1482 "2017-10-31T23:32:57Z")
Continuing the discussion from Alignment Problem: I had exactly same error massage with this. and I search the answer but I couldn't find the solution. actually my rep-sea.qza file is quite big 32M. so even though I us… --- ## [Alignment Problem](https://forum.qiime2.org/t/alignment-problem/708)
**Author:** [@akknight216](https://forum.qiime2.org/u/akknight216)\ **Replies:** 16\ **Last updated:** [October 27, 2017, 6:41pm UTC](https://forum.qiime2.org/t/alignment-problem/708 "2017-10-27T18:41:43Z")
Hi, I'm trying to use alignment mafft as follows: qiime alignment mafft --i-sequences rep-seqsMerged\_060817\_250.qza --o-alignment aligned-rep-seqsMerged.qza And am getting this error: Plugin error from alignment: … --- ## [Which alignment algorithm should I use](https://forum.qiime2.org/t/which-alignment-algorithm-should-i-use/997)
**Author:** [@lindd](https://forum.qiime2.org/u/lindd)\ **Replies:** 1\ **Last updated:** [August 14, 2017, 3:03pm UTC](https://forum.qiime2.org/t/which-alignment-algorithm-should-i-use/997 "2017-08-14T15:03:22Z")
Hi, I am a beginner of microbiome data preprocessing and qiime2. I have done the quality control by DADA2 and want to build a phylogenetic tree to calculate diversity. According to moving picture tutorial, I need to ali…