# \#export **URL:** https://forum.qiime2.org/tag/export/24.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [.biom to .tsv is losing per-sample data from FeatureTable\[Frequency\]](https://forum.qiime2.org/t/biom-to-tsv-is-losing-per-sample-data-from-featuretable-frequency/34311)
**Author:** [@Emma\_Gardner](https://forum.qiime2.org/u/Emma_Gardner)\ **Replies:** 1\ **Last updated:** [September 3, 2026, 1:25pm UTC](https://forum.qiime2.org/t/biom-to-tsv-is-losing-per-sample-data-from-featuretable-frequency/34311 "2026-09-03T13:25:22Z")
.biom to .tsv is losing per-sample data from FeatureTable\[Frequency\] Hi! I'm trying to export my .qza files so that I can use some other analysis tools in R, and for some reason, it looks like I'm losing my per-sample fr… --- ## [Understanding the representative sequence output](https://forum.qiime2.org/t/understanding-the-representative-sequence-output/32717)
**Author:** [@ajithashokan123](https://forum.qiime2.org/u/ajithashokan123)\ **Replies:** 2\ **Last updated:** [March 10, 2025, 2:21pm UTC](https://forum.qiime2.org/t/understanding-the-representative-sequence-output/32717 "2025-03-10T14:21:08Z")
Hello, I exported the representative sequences after demultiplexing and denoising the forward reads from Illumina sequencing using the following command: ###DENOISING qiime dada2 denoise-single --i-demultiplexed-seq… --- ## [Corrupted BIOM export?](https://forum.qiime2.org/t/corrupted-biom-export/32605)
**Author:** [@raivo-otus](https://forum.qiime2.org/u/raivo-otus)\ **Replies:** 2\ **Last updated:** [February 25, 2025, 1:39pm UTC](https://forum.qiime2.org/t/corrupted-biom-export/32605 "2025-02-25T13:39:52Z")
Hey! I am experiencing some issues with trying to get my feature table out of Qiime2. The version of qiime2 I am using is 24.10-amplicon. The issue I am having is seemingly corrupted or flawed feature table file. I ha… --- ## [Exporting taxonomy with level columns](https://forum.qiime2.org/t/exporting-taxonomy-with-level-columns/29833)
**Author:** [@AdventureDavid](https://forum.qiime2.org/u/AdventureDavid)\ **Replies:** 2\ **Last updated:** [April 10, 2024, 6:41am UTC](https://forum.qiime2.org/t/exporting-taxonomy-with-level-columns/29833 "2024-04-10T06:41:50Z")
Hi, I am using QIIME2/2023.7 version. I use the "qiime tools export " function to export my taxonomy.qza into a tsv. My question, is there a way to export the file with the column identifiers for each of the levels of t… --- ## [Command line interface/tools to explore artifacts directly](https://forum.qiime2.org/t/command-line-interface-tools-to-explore-artifacts-directly/2779)
**Author:** [@cduvallet](https://forum.qiime2.org/u/cduvallet)\ **Replies:** 8\ **Last updated:** [March 25, 2024, 9:58pm UTC](https://forum.qiime2.org/t/command-line-interface-tools-to-explore-artifacts-directly/2779 "2024-03-25T21:58:01Z")
Not sure if this is feasible, but something that could dramatically improve the user experience with qiime2 would be to have a set of tools that can directly explore artifacts like OTU tables, sequences, etc. Basically a… --- ## [how can I export a FASTA file from QIIME 2?](https://forum.qiime2.org/t/how-can-i-export-a-fasta-file-from-qiime-2/28997)
**Author:** [@JHLee1](https://forum.qiime2.org/u/JHLee1)\ **Replies:** 4\ **Last updated:** [January 25, 2024, 12:24am UTC](https://forum.qiime2.org/t/how-can-i-export-a-fasta-file-from-qiime-2/28997 "2024-01-25T00:24:21Z")
Hi. Users I need Qiime2 data converted to fasta file for Picrust2 work. If you use the following command, only the biom file will be extracted. Please let me know how to solve this problem. Command : qiime tools expo… --- ## [Exporting：PermissionError: \[Errno 1\] Operation not permitted](https://forum.qiime2.org/t/exporting-permissionerror-errno-1-operation-not-permitted/28742)
**Author:** [@Chnyng](https://forum.qiime2.org/u/Chnyng)\ **Replies:** 1\ **Last updated:** [December 28, 2023, 5:51pm UTC](https://forum.qiime2.org/t/exporting-permissionerror-errno-1-operation-not-permitted/28742 "2023-12-28T17:51:24Z")
Hellow everyone! I would like to export my data, but when I run qiime2, It seems like there is a error"PermissionError: \[Errno 1\] Operation not permitted". It means that I have no permission the do the command. So how … --- ## [Convert qza file to xls or csv](https://forum.qiime2.org/t/convert-qza-file-to-xls-or-csv/28244)
**Author:** [@miguel\_lopez](https://forum.qiime2.org/u/miguel_lopez)\ **Replies:** 2\ **Last updated:** [November 13, 2023, 4:24pm UTC](https://forum.qiime2.org/t/convert-qza-file-to-xls-or-csv/28244 "2023-11-13T16:24:57Z")
Hi, I'm trying to export my table frequency file table.qza to xls or csv, I followed this command: qiime tools export --input-path feature-table.qza --output-path exported-feature-table but it exports them as a biom… --- ## [Feature table export to BIOM](https://forum.qiime2.org/t/feature-table-export-to-biom/28150)
**Author:** [@Parikrama\_Sapkota](https://forum.qiime2.org/u/Parikrama_Sapkota)\ **Replies:** 3\ **Last updated:** [November 3, 2023, 4:56pm UTC](https://forum.qiime2.org/t/feature-table-export-to-biom/28150 "2023-11-03T16:56:45Z")
While running this code: qiime tools export /DATA/scratch/psapkota/GH/dada2\_table\_16S.qza --output-dir /DATA/scratch/psapkota/GH/extracted-feature-table I get this error " (1/1?) No such option: --output-dir" Any help… --- ## ["ValueError: Path: 'None' already exists and is not a cache" when converting file formats](https://forum.qiime2.org/t/valueerror-path-none-already-exists-and-is-not-a-cache-when-converting-file-formats/27365)
**Author:** [@jolespin](https://forum.qiime2.org/u/jolespin)\ **Replies:** 5\ **Last updated:** [August 14, 2023, 1:26pm UTC](https://forum.qiime2.org/t/valueerror-path-none-already-exists-and-is-not-a-cache-when-converting-file-formats/27365 "2023-08-14T13:26:36Z")
Here's my command: qiime tools export --input-path dada2-ccs\_table\_merged.qza --output-path . Here's my error: Traceback (most recent call last): File "/Users/jespinoz/anaconda3/envs/qiime2\_env/bin/qiime", line 11, … --- ## [adding taxonomy data to a feature-table.biom file](https://forum.qiime2.org/t/adding-taxonomy-data-to-a-feature-table-biom-file/25488)
**Author:** [@nietof](https://forum.qiime2.org/u/nietof)\ **Replies:** 3\ **Last updated:** [February 14, 2023, 2:27pm UTC](https://forum.qiime2.org/t/adding-taxonomy-data-to-a-feature-table-biom-file/25488 "2023-02-14T14:27:25Z")
Hi I am using natively installed qiime2 on a Big Sur 11.3.1 macbook pro. I tried to use a script recommended on a previous post by @jairideout to add the taxonomy data to a feature-table.biom file using the following sc… --- ## [Multiple Samples](https://forum.qiime2.org/t/multiple-samples/24948)
**Author:** [@NMDG](https://forum.qiime2.org/u/NMDG)\ **Replies:** 5\ **Last updated:** [December 8, 2022, 2:03pm UTC](https://forum.qiime2.org/t/multiple-samples/24948 "2022-12-08T14:03:21Z")
Hi, I'm trying to process multiple samples using Qiime2. I imported all samples as one .qza file and went through the pipeline to process them. When I output the files, there's no indication of what sample the DNA origi… --- ## [qiime tools import or export altering fastq names?](https://forum.qiime2.org/t/qiime-tools-import-or-export-altering-fastq-names/23742)
**Author:** [@M\_R](https://forum.qiime2.org/u/M_R)\ **Replies:** 3\ **Last updated:** [August 15, 2022, 10:10pm UTC](https://forum.qiime2.org/t/qiime-tools-import-or-export-altering-fastq-names/23742 "2022-08-15T22:10:32Z")
Hi fellow qiime2 users, So, i'm having this small issue in which my fastq-files names come out different from what is in the manifest file. Example Manifest file (I replaced part of the path with ... to make it a bit m… --- ## [Exporting feature table with taxonomy added not working](https://forum.qiime2.org/t/exporting-feature-table-with-taxonomy-added-not-working/23373)
**Author:** [@jnarv](https://forum.qiime2.org/u/jnarv)\ **Replies:** 2\ **Last updated:** [June 22, 2022, 5:06pm UTC](https://forum.qiime2.org/t/exporting-feature-table-with-taxonomy-added-not-working/23373 "2022-06-22T17:06:49Z")
Hello! I am a newbie on the qiime2 world and I am having isues exporting the feature table with the taxonomy annotations added for my data. I have followed the Exporting and modifying BIOM tables (e.g. adding taxonomy … --- ## [qiime tools export TEXT file format](https://forum.qiime2.org/t/qiime-tools-export-text-file-format/22463)
**Author:** [@arwqiime](https://forum.qiime2.org/u/arwqiime)\ **Replies:** 1\ **Last updated:** [March 15, 2022, 9:30pm UTC](https://forum.qiime2.org/t/qiime-tools-export-text-file-format/22463 "2022-03-15T21:30:11Z")
Hi, I am using 'q2 tools export' to export data to biom format (using version 2021.11). What are the allowed formats for TEXT when using '--output-format TEXT'? Best, --- ## [Customized file naming convention for qiime tools export](https://forum.qiime2.org/t/customized-file-naming-convention-for-qiime-tools-export/2294)
**Author:** [@kparke10](https://forum.qiime2.org/u/kparke10)\ **Replies:** 1\ **Last updated:** [December 22, 2017, 7:25pm UTC](https://forum.qiime2.org/t/customized-file-naming-convention-for-qiime-tools-export/2294 "2017-12-22T19:25:15Z")
We are able provide a custom name to --output-dir . For instance: qiime tools export \\ core-metrics-results/unweighted\_unifrac\_distance\_matrix.qza --output-dir uw\_unifrac However, rather than have several directories f… --- ## [Obtain normalized data - ANCOM](https://forum.qiime2.org/t/obtain-normalized-data-ancom/22021)
**Author:** [@JeremyTournayre](https://forum.qiime2.org/u/JeremyTournayre)\ **Replies:** 5\ **Last updated:** [February 4, 2022, 2:58pm UTC](https://forum.qiime2.org/t/obtain-normalized-data-ancom/22021 "2022-02-04T14:58:35Z")
Hello, Is it possible to get the normalized data after the normalization by ANCOM please? Thanks in advance, Jérémy Tournayre --- ## [Is there a way to export statisti overview results](https://forum.qiime2.org/t/is-there-a-way-to-export-statisti-overview-results/22047)
**Author:** [@Viktor](https://forum.qiime2.org/u/Viktor)\ **Replies:** 1\ **Last updated:** [February 3, 2022, 2:27pm UTC](https://forum.qiime2.org/t/is-there-a-way-to-export-statisti-overview-results/22047 "2022-02-03T14:27:52Z")
I have run an ANOSIM test on my data and I am now trying to export the results. When the statistics are visualized I get an overview of the ANOSIM results (see image below), some boxplots, and statistics for pairwise com… --- ## [Issue with using summarize\_otu\_distributions.py (from Earth Microbiome Project) on biom table exported from Qiime2](https://forum.qiime2.org/t/issue-with-using-summarize-otu-distributions-py-from-earth-microbiome-project-on-biom-table-exported-from-qiime2/21205)
**Author:** [@dinhe878](https://forum.qiime2.org/u/dinhe878)\ **Replies:** 4\ **Last updated:** [October 29, 2021, 12:30pm UTC](https://forum.qiime2.org/t/issue-with-using-summarize-otu-distributions-py-from-earth-microbiome-project-on-biom-table-exported-from-qiime2/21205 "2021-10-29T12:30:27Z")
Hi all, I am trying to run a python script from Earth Microbiome Project (EMP), summarize\_otu\_distributions.py, to produce otu distribution data from a biom table exported from Qiime2 (2021.2) feature table artifact (da… --- ## [Extracting representative sequences from table](https://forum.qiime2.org/t/extracting-representative-sequences-from-table/20781)
**Author:** [@bkramer](https://forum.qiime2.org/u/bkramer)\ **Replies:** 1\ **Last updated:** [September 21, 2021, 11:43pm UTC](https://forum.qiime2.org/t/extracting-representative-sequences-from-table/20781 "2021-09-21T23:43:19Z")
Hello, I have filtered my table.qza file containing all of my sequences based on those sequences found in a single sample using the qiime feature-table filter-samples command, but I was wondering if it was possible to e… --- ## [Exporting processed .qza reads into separate .fasta files for each sample](https://forum.qiime2.org/t/exporting-processed-qza-reads-into-separate-fasta-files-for-each-sample/19327)
**Author:** [@sjcochran](https://forum.qiime2.org/u/sjcochran)\ **Replies:** 2\ **Last updated:** [April 24, 2021, 4:57pm UTC](https://forum.qiime2.org/t/exporting-processed-qza-reads-into-separate-fasta-files-for-each-sample/19327 "2021-04-24T16:57:11Z")
Hello! I am looking for help with processing my data from Fungal ITS1 amplicon sequencing. I have demultiplexed, paired-end reads in .fastq format. I imported my data into QIIME2 (installed on a VirtualBox), cut the pri… --- ## [How to produce a merged feature table?](https://forum.qiime2.org/t/how-to-produce-a-merged-feature-table/19091)
**Author:** [@wburgess](https://forum.qiime2.org/u/wburgess)\ **Replies:** 4\ **Last updated:** [April 20, 2021, 4:39pm UTC](https://forum.qiime2.org/t/how-to-produce-a-merged-feature-table/19091 "2021-04-20T16:39:32Z")
wlb\_merging\_help\_code.txt (2.2 KB) feature-table\_w\_tax.txt (219 Bytes) merged0.qza (59.0 KB) merged\_data0.qza (59.6 KB) Summary: I am searching for a generalizeable way to merge samples for downstream analysis and have… --- ## [Exporting data question](https://forum.qiime2.org/t/exporting-data-question/18549)
**Author:** [@Matesla1](https://forum.qiime2.org/u/Matesla1)\ **Replies:** 12\ **Last updated:** [March 17, 2021, 2:30pm UTC](https://forum.qiime2.org/t/exporting-data-question/18549 "2021-03-17T14:30:10Z")
Hi! It is possiblle change a file .qza to a new file .fasta? Thanks! Hi! It is possiblle change a file .qza to a new file .fasta? Thanks! --- ## [Export merged paired-end fastq files](https://forum.qiime2.org/t/export-merged-paired-end-fastq-files/18052)
**Author:** [@kms285](https://forum.qiime2.org/u/kms285)\ **Replies:** 2\ **Last updated:** [January 14, 2021, 7:41pm UTC](https://forum.qiime2.org/t/export-merged-paired-end-fastq-files/18052 "2021-01-14T19:41:53Z")
I need to merge demultiplexed paired-end reads to a single fastq file for each sample for uploading to a repository. Is there a way to obtain these files from QIIME2, rather than using a completely separate tool like FLA… --- ## [Biom export option that appends taxonomic assignments to the feature table](https://forum.qiime2.org/t/biom-export-option-that-appends-taxonomic-assignments-to-the-feature-table/1530)
**Author:** [@vrbana](https://forum.qiime2.org/u/vrbana)\ **Replies:** 4\ **Last updated:** [October 24, 2017, 4:19pm UTC](https://forum.qiime2.org/t/biom-export-option-that-appends-taxonomic-assignments-to-the-feature-table/1530 "2017-10-24T16:19:22Z")
Would it be possible to have this? --- ## [Absolute read count after classification](https://forum.qiime2.org/t/absolute-read-count-after-classification/17689)
**Author:** [@Saptarathi\_Deb](https://forum.qiime2.org/u/Saptarathi_Deb)\ **Replies:** 1\ **Last updated:** [December 4, 2020, 4:03pm UTC](https://forum.qiime2.org/t/absolute-read-count-after-classification/17689 "2020-12-04T16:03:36Z")
Hello Qiime users, I wanted to know if there is any straight forward way to get absolute read count per taxa, just like the relative abundance table. I am a little confused about how the relative abundance table is cal… --- ## [Creating & Exporting ASV tables](https://forum.qiime2.org/t/creating-exporting-asv-tables/17478)
**Author:** [@fabipc](https://forum.qiime2.org/u/fabipc)\ **Replies:** 4\ **Last updated:** [November 17, 2020, 8:31pm UTC](https://forum.qiime2.org/t/creating-exporting-asv-tables/17478 "2020-11-17T20:31:23Z")
Hello, I have a quick question, or more like a confirmation of my analysis. I had previously followed a tutorial on how to create and export an ASV table and I feel like I did it correctly, however, after a request from… --- ## [Batch export-2020](https://forum.qiime2.org/t/batch-export-2020/17260)
**Author:** [@shira](https://forum.qiime2.org/u/shira)\ **Replies:** 8\ **Last updated:** [November 4, 2020, 2:53pm UTC](https://forum.qiime2.org/t/batch-export-2020/17260 "2020-11-04T14:53:10Z")
Continuing the discussion from Batch export for files: The useful script described previously seems to be incompatible with newer versions of qiime. The following line needs to be adapted - qiime tools export ${i} --ou… --- ## [Importing trained sample-classifier in python/R in order to access feature importance "orientation"](https://forum.qiime2.org/t/importing-trained-sample-classifier-in-python-r-in-order-to-access-feature-importance-orientation/17297)
**Author:** [@ncaramello](https://forum.qiime2.org/u/ncaramello)\ **Replies:** 4\ **Last updated:** [November 3, 2020, 2:18pm UTC](https://forum.qiime2.org/t/importing-trained-sample-classifier-in-python-r-in-order-to-access-feature-importance-orientation/17297 "2020-11-03T14:18:34Z")
Dear all, I used regress-samples (with RandomForest as the estimator) in order to identify the features contributing the most to a given Behavioral Score (Time spent in social contact). " qiime sample-classifier regre… --- ## [Creation of barplot with excel](https://forum.qiime2.org/t/creation-of-barplot-with-excel/17245)
**Author:** [@cortegas](https://forum.qiime2.org/u/cortegas)\ **Replies:** 11\ **Last updated:** [October 29, 2020, 5:09pm UTC](https://forum.qiime2.org/t/creation-of-barplot-with-excel/17245 "2020-10-29T17:09:00Z")
Hi everyone, I exported my taxa-bar-plot data as a CSV file to my computer to create a barplot by groups rather than by sample ID. I am having trouble creating the same type of barplots that we get in QIIME2 on excel. D… [Next page](https://forum.qiime2.org/tag/export/24.md?match_all_tags=true&page=1&tags%5B%5D=export)