# \#fastq-manifest **URL:** https://forum.qiime2.org/tag/fastq-manifest/47.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [removing text before the sample id using fq-manifestor](https://forum.qiime2.org/t/removing-text-before-the-sample-id-using-fq-manifestor/34167)
**Author:** [@XandraS](https://forum.qiime2.org/u/XandraS)\ **Replies:** 3\ **Last updated:** [May 7, 2026, 6:25pm UTC](https://forum.qiime2.org/t/removing-text-before-the-sample-id-using-fq-manifestor/34167 "2026-05-07T18:25:44Z")
Hi Greg, This looks like a great tool, but for some reason only one forward and one reverse of my 96 files are being recognized and the two are from different samples. Nor is the sample ID recognized. I will paste a scre… --- ## [Error importing manifest.tsv. "No transformation from \ to \"](https://forum.qiime2.org/t/error-importing-manifest-tsv-no-transformation-from-x-class-to-y-class/28902)
**Author:** [@alex\_bt](https://forum.qiime2.org/u/alex_bt)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 5:55pm UTC](https://forum.qiime2.org/t/error-importing-manifest-tsv-no-transformation-from-x-class-to-y-class/28902 "2024-01-16T17:55:30Z")
I was trying to import my fastq reads through a manifest file in WSL, q2cli version 2023.7.0 This is my manifest file "sample-id forward-absolute-filepath reverse-absolute-filepath E1T1 /home/alfa\_ley/TFG/qiimefile/ma… --- ## [Error in importing data using manifest](https://forum.qiime2.org/t/error-in-importing-data-using-manifest/26424)
**Author:** [@gspazmino](https://forum.qiime2.org/u/gspazmino)\ **Replies:** 3\ **Last updated:** [May 13, 2023, 11:28pm UTC](https://forum.qiime2.org/t/error-in-importing-data-using-manifest/26424 "2023-05-13T23:28:10Z")
Hi! I am trying to import a data base using manifest. But everytime I try to run the code, the following message appears: There was a problem importing /Users/giulianapazmino/Desktop/manifestgz.txt: /Users/giulianapazm… --- ## [Help! Creating a directory for a manifest](https://forum.qiime2.org/t/help-creating-a-directory-for-a-manifest/26412)
**Author:** [@RiparianForest](https://forum.qiime2.org/u/RiparianForest)\ **Replies:** 3\ **Last updated:** [May 11, 2023, 5:49pm UTC](https://forum.qiime2.org/t/help-creating-a-directory-for-a-manifest/26412 "2023-05-11T17:49:10Z")
Hey, I'm running qiime2 on Ubuntu 20.04.6 and on anaconda3. I'm trying to import data according to the tutorial that is available on qiime2. (Importing data — QIIME 2 2022.8.3 documentation). I'm working with PairedEn… --- ## [Importing data - Manifest errors - absolute-file path not found](https://forum.qiime2.org/t/importing-data-manifest-errors-absolute-file-path-not-found/25891)
**Author:** [@xicesam](https://forum.qiime2.org/u/xicesam)\ **Replies:** 2\ **Last updated:** [March 26, 2023, 4:19pm UTC](https://forum.qiime2.org/t/importing-data-manifest-errors-absolute-file-path-not-found/25891 "2023-03-26T16:19:12Z")
Hello, I have gone through every forum that have already had similar issues, but nothing has worked. I believe my issue stems from the file path being wrong somewhere. I am using qiime2-2022.11 through Ubuntu on a Windo… --- ## [Manifest file error - ascii character?](https://forum.qiime2.org/t/manifest-file-error-ascii-character/25630)
**Author:** [@Alessandra\_Dupont](https://forum.qiime2.org/u/Alessandra_Dupont)\ **Replies:** 2\ **Last updated:** [March 2, 2023, 9:11am UTC](https://forum.qiime2.org/t/manifest-file-error-ascii-character/25630 "2023-03-02T09:11:56Z")
Hello Qiime team! The last time I posted in the forum I was running Qiime1, and had it working smooth until now :slight\_smile: I have obtained MiSeq data from LGC genomics in fastq.bz2 format, with barcodes and adapter… --- ## [Manifest preparation + Error import](https://forum.qiime2.org/t/manifest-preparation-error-import/24187)
**Author:** [@cortegas](https://forum.qiime2.org/u/cortegas)\ **Replies:** 1\ **Last updated:** [September 19, 2022, 2:41pm UTC](https://forum.qiime2.org/t/manifest-preparation-error-import/24187 "2022-09-19T14:41:13Z")
Hi everyone, I am working with a new sequencing center and I run into the problem that I never worked on a manifest document. I review the documents available on qiime and validate my manifest at keeime. Carmen:FASTQ C… --- ## [Importing fastq sequences that were previously transformed from ab1 files (Sanger Sequencing)](https://forum.qiime2.org/t/importing-fastq-sequences-that-were-previously-transformed-from-ab1-files-sanger-sequencing/22416)
**Author:** [@diegorg](https://forum.qiime2.org/u/diegorg)\ **Replies:** 2\ **Last updated:** [March 12, 2022, 5:00pm UTC](https://forum.qiime2.org/t/importing-fastq-sequences-that-were-previously-transformed-from-ab1-files-sanger-sequencing/22416 "2022-03-12T17:00:13Z")
I have extracted the 16S rRNA from single cultured bacteria and then performed Sanger sequencing for identification purposes (Ihad both forward and reverse sequences for each one.). Therefore, I had ab1 files. After foll… --- ## [Issue importing Paired end sequences with quality](https://forum.qiime2.org/t/issue-importing-paired-end-sequences-with-quality/21256)
**Author:** [@lautaro.rostoll](https://forum.qiime2.org/u/lautaro.rostoll)\ **Replies:** 10\ **Last updated:** [November 7, 2021, 5:26pm UTC](https://forum.qiime2.org/t/issue-importing-paired-end-sequences-with-quality/21256 "2021-11-07T17:26:09Z")
Hello Everyone, I am trying to import Paired end sequences with quality using a manifest (attached here an example with just a few files. Manifest.txt (547 Bytes) I am using putty to access the server from my universit… --- ## [Error importing manifest file](https://forum.qiime2.org/t/error-importing-manifest-file/18058)
**Author:** [@Newt](https://forum.qiime2.org/u/Newt)\ **Replies:** 2\ **Last updated:** [January 14, 2021, 5:59pm UTC](https://forum.qiime2.org/t/error-importing-manifest-file/18058 "2021-01-14T17:59:22Z")
Hi there! I am very new to bioinformatics and am analyzing a dietary dataset. I'm running QIIME 2 version 2020.11 through WSL and Ubuntu. I have run into some trouble while attempting to import my data. I ran into an er… --- ## [can we convert paired-end-demux.qza to fastq files](https://forum.qiime2.org/t/can-we-convert-paired-end-demux-qza-to-fastq-files/17590)
**Author:** [@drmusk](https://forum.qiime2.org/u/drmusk)\ **Replies:** 3\ **Last updated:** [November 26, 2020, 8:21pm UTC](https://forum.qiime2.org/t/can-we-convert-paired-end-demux-qza-to-fastq-files/17590 "2020-11-26T20:21:00Z")
Hello Colleagues I made paired-end-demux.qza using a manifest file and paired-end reads. I lost or deleted fastq files. Now I need them for some good reason. Is it possible to convert paired-end-demux.qza to fastq files… --- ## [An error was encountered while running DADA2 in R (return code 1), please inspect stout and stderr to learn more (Single end data)](https://forum.qiime2.org/t/an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stout-and-stderr-to-learn-more-single-end-data/15292)
**Author:** [@jd.lozano](https://forum.qiime2.org/u/jd.lozano)\ **Replies:** 1\ **Last updated:** [June 8, 2020, 8:14pm UTC](https://forum.qiime2.org/t/an-error-was-encountered-while-running-dada2-in-r-return-code-1-please-inspect-stout-and-stderr-to-learn-more-single-end-data/15292 "2020-06-08T20:14:58Z")
Please read the following before posting! Hello I received a fasta file with single end demultiplexed sequences and no quality file. Since I was interested in performing diversity analysis with qiime2, i converted it to… --- ## [I got an error importing my fastq files](https://forum.qiime2.org/t/i-got-an-error-importing-my-fastq-files/14690)
**Author:** [@ptalebic](https://forum.qiime2.org/u/ptalebic)\ **Replies:** 5\ **Last updated:** [May 23, 2020, 2:11am UTC](https://forum.qiime2.org/t/i-got-an-error-importing-my-fastq-files/14690 "2020-05-23T02:11:35Z")
Dear Experts I am trying to import my fastq files generated using Miseq Illumina. My samples are demultiplexed and they are single end reads. I used this command: qiime tools import --type 'SampleData\[SequencesWithQu… --- ## [Manifest Errors Issues](https://forum.qiime2.org/t/manifest-errors-issues/13490)
**Author:** [@DanielAgVal](https://forum.qiime2.org/u/DanielAgVal)\ **Replies:** 8\ **Last updated:** [February 6, 2020, 5:52am UTC](https://forum.qiime2.org/t/manifest-errors-issues/13490 "2020-02-06T05:52:24Z")
Hello Guys, I am having the same problem here, as the tool keep continuing saying that I have an error in the manifest: pe-33-manifest is not a(n) PairedEndFastqManifestPhred33V2 file: Filepath on line 10 and column "… --- ## [How to create a proper manifest file and how to import it?](https://forum.qiime2.org/t/how-to-create-a-proper-manifest-file-and-how-to-import-it/7342)
**Author:** [@Aditya\_Ragil\_Suharto](https://forum.qiime2.org/u/Aditya_Ragil_Suharto)\ **Replies:** 2\ **Last updated:** [December 9, 2018, 1:35am UTC](https://forum.qiime2.org/t/how-to-create-a-proper-manifest-file-and-how-to-import-it/7342 "2018-12-09T01:35:12Z")
Hello guys... I have 2 paired end file that are already demultiplexed, and i tried to import it using fastq manifest format, but i am always failed to do that, is my manifest format are wrong? iam already following the … --- ## [Manifest importing issue](https://forum.qiime2.org/t/manifest-importing-issue/7051)
**Author:** [@Xio\_Lee](https://forum.qiime2.org/u/Xio_Lee)\ **Replies:** 1\ **Last updated:** [November 17, 2018, 8:04pm UTC](https://forum.qiime2.org/t/manifest-importing-issue/7051 "2018-11-17T20:04:48Z")
Hi, I encountered this issue when importing the manifest file in jupyter notebook: code: !qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path 16SF@16SR\_manifest.csv --output-path qii… --- ## [BOM in Manifest](https://forum.qiime2.org/t/bom-in-manifest/6061)
**Author:** [@Cybele\_C](https://forum.qiime2.org/u/Cybele_C)\ **Replies:** 2\ **Last updated:** [September 18, 2018, 2:04am UTC](https://forum.qiime2.org/t/bom-in-manifest/6061 "2018-09-18T02:04:21Z")
Hello! There does seem to be a problem with my manifest file. I tried the absolute file path, though it did seem to be in the correct directory (at bottom). I altered the names of the raw files so that they don't have th… --- ## [Importing data-unfamiliar format](https://forum.qiime2.org/t/importing-data-unfamiliar-format/4417)
**Author:** [@troytao](https://forum.qiime2.org/u/troytao)\ **Replies:** 1\ **Last updated:** [June 4, 2018, 11:08pm UTC](https://forum.qiime2.org/t/importing-data-unfamiliar-format/4417 "2018-06-04T23:08:01Z")
Hi there, I am new to QIIME2. I'm trying to import my data, which were generated by a sequencing institute. However, I have no idea for which stage they have processed the data, and what command should I use (it seems t… --- ## [QIIME2 virtual box help](https://forum.qiime2.org/t/qiime2-virtual-box-help/4268)
**Author:** [@Ankita](https://forum.qiime2.org/u/Ankita)\ **Replies:** 5\ **Last updated:** [May 25, 2018, 5:14pm UTC](https://forum.qiime2.org/t/qiime2-virtual-box-help/4268 "2018-05-25T17:14:37Z")
Hi, I assume this might have been answered but considering my ignorance to QIIME and general bioinformatics skills, I would really appreciate if someone could proceed to still help me. I have installed QIIME2 in a virt… --- ## [Importing data using Qiime studio](https://forum.qiime2.org/t/importing-data-using-qiime-studio/3892)
**Author:** [@Walid](https://forum.qiime2.org/u/Walid)\ **Replies:** 1\ **Last updated:** [April 23, 2018, 9:04pm UTC](https://forum.qiime2.org/t/importing-data-using-qiime-studio/3892 "2018-04-23T21:04:56Z")
Hello, I am trying to import data using the studio application in Qiime2, I have also tried using command line from the tutorials, import help and suggestions from the forum. Thus far I have been stuck on this for 2 wee… --- ## [Importing fastq, demultiplexed paired end data](https://forum.qiime2.org/t/importing-fastq-demultiplexed-paired-end-data/3753)
**Author:** [@venkar](https://forum.qiime2.org/u/venkar)\ **Replies:** 3\ **Last updated:** [April 20, 2018, 7:24pm UTC](https://forum.qiime2.org/t/importing-fastq-demultiplexed-paired-end-data/3753 "2018-04-20T19:24:54Z")
Hi, This is my first time using qiime2 and I am having questions about the import. I have my Fastq files in a directory and I am trying to execute the following command in a directory where I have the manifest file. I b… --- ## [White space parsing issue in manifest](https://forum.qiime2.org/t/white-space-parsing-issue-in-manifest/3847)
**Author:** [@tengfey](https://forum.qiime2.org/u/tengfey)\ **Replies:** 2\ **Last updated:** [April 19, 2018, 12:47am UTC](https://forum.qiime2.org/t/white-space-parsing-issue-in-manifest/3847 "2018-04-19T00:47:10Z")
I noticed that if there is whitespace at the end of a manifest file, it will raise errors like this qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path cancer10-manifest --output-pat… --- ## [Help formatting FASTQ manifest file](https://forum.qiime2.org/t/help-formatting-fastq-manifest-file/3337)
**Author:** [@PLD](https://forum.qiime2.org/u/PLD)\ **Replies:** 2\ **Last updated:** [March 13, 2018, 1:32pm UTC](https://forum.qiime2.org/t/help-formatting-fastq-manifest-file/3337 "2018-03-13T13:32:43Z")
Hi, Similar to the problems above, I am also having issues importing ion torrent fastq files. Again I have one fastq file per sample which has been demultiplexed. I have created the se-33-manifest.csv file and have mod… --- ## [Error : not a phred 33 file](https://forum.qiime2.org/t/error-not-a-phred-33-file/3356)
**Author:** [@lttnguye](https://forum.qiime2.org/u/lttnguye)\ **Replies:** 5\ **Last updated:** [March 9, 2018, 7:26pm UTC](https://forum.qiime2.org/t/error-not-a-phred-33-file/3356 "2018-03-09T19:26:03Z")
Hello, I've kept on having the same error saying that my manifest file is not a phred 33 file and am really out of ideas how to fix it and I felt like I've read all the posts related to this issue :frowning: My command … --- ## [Importing paired end demultiplexed MiSeq data](https://forum.qiime2.org/t/importing-paired-end-demultiplexed-miseq-data/3014)
**Author:** [@David\_Bradshaw](https://forum.qiime2.org/u/David_Bradshaw)\ **Replies:** 20\ **Last updated:** [February 28, 2018, 2:35pm UTC](https://forum.qiime2.org/t/importing-paired-end-demultiplexed-miseq-data/3014 "2018-02-28T14:35:11Z")
Dear Whom It May Concern, I need to import paired end demultiplexed sequences into QIIME2 and I have been having trouble. My sequences do not have barcodes or primers the names look like the following for one sequence w… --- ## [Problems of importing data](https://forum.qiime2.org/t/problems-of-importing-data/2940)
**Author:** [@Mengyuan](https://forum.qiime2.org/u/Mengyuan)\ **Replies:** 6\ **Last updated:** [February 17, 2018, 4:38pm UTC](https://forum.qiime2.org/t/problems-of-importing-data/2940 "2018-02-17T16:38:58Z")
Hi,I am new to qiime2 and I want to import my faetq data using a manifest like this, then I keep getting this error, but my fastq data is actually in that file, so I am so confused,and I really hope you can hel… --- ## [Incorporating metadata when using manifests](https://forum.qiime2.org/t/incorporating-metadata-when-using-manifests/2808)
**Author:** [@atgustin](https://forum.qiime2.org/u/atgustin)\ **Replies:** 3\ **Last updated:** [February 16, 2018, 5:14pm UTC](https://forum.qiime2.org/t/incorporating-metadata-when-using-manifests/2808 "2018-02-16T17:14:34Z")
Hello! I'm new to using Qiime2 and am working through my first project. My import step involved a manifest, as I already have demultiplexed fastqs: qiime tools import --type SampleData\[PairedEndSequencesWithQuality\] … --- ## [Qiime tools import missing one or more files](https://forum.qiime2.org/t/qiime-tools-import-missing-one-or-more-files/2604)
**Author:** [@kedi](https://forum.qiime2.org/u/kedi)\ **Replies:** 6\ **Last updated:** [February 5, 2018, 4:15pm UTC](https://forum.qiime2.org/t/qiime-tools-import-missing-one-or-more-files/2604 "2018-02-05T16:15:55Z")
Good day Please help, i ran qiime tools import --type SampleData\[PairedEndSequencesWithQuality\] --input-path /scratch/sysusers/kedibone/reanalysis --output-path emp-paired-end-sequences.qza and I got this error, missin… --- ## [Creating manifest file for fastq files that contain both forward and reverse reads](https://forum.qiime2.org/t/creating-manifest-file-for-fastq-files-that-contain-both-forward-and-reverse-reads/2803)
**Author:** [@kristiny](https://forum.qiime2.org/u/kristiny)\ **Replies:** 2\ **Last updated:** [January 31, 2018, 2:57pm UTC](https://forum.qiime2.org/t/creating-manifest-file-for-fastq-files-that-contain-both-forward-and-reverse-reads/2803 "2018-01-31T14:57:56Z")
My .fastq files contain both forward and reverse reads in the same file. The manifest requires specification of forward or reverse reads: sample-1,$PWD/some/filepath/sample1\_R1.fastq.gz,forward sample-2,$PWD/some/filep… --- ## [How to demultiplex fastq file that still includes Barcodes and LinkerPrimer?](https://forum.qiime2.org/t/how-to-demultiplex-fastq-file-that-still-includes-barcodes-and-linkerprimer/1828)
**Author:** [@Martin](https://forum.qiime2.org/u/Martin)\ **Replies:** 3\ **Last updated:** [December 22, 2017, 5:57pm UTC](https://forum.qiime2.org/t/how-to-demultiplex-fastq-file-that-still-includes-barcodes-and-linkerprimer/1828 "2017-12-22T17:57:37Z")
Hi, I have a single fastq file. This file includes the sequences of 19 samples from a single Illumina MiSeq run. Each sample has a different barcode (8 bp). After the barcode an additional LinkerPrimer is attached (17 b… [Next page](https://forum.qiime2.org/tag/fastq-manifest/47.md?match_all_tags=true&page=1&tags%5B%5D=fastq-manifest)