# Problem: Use of .fq file while importing
**URL:** https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942
**Category:** Technical Support
**Tags:** import
**Created:** [January 18, 2024, 7:29am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942 "2024-01-18T07:29:20Z")
**Posts on this page:** 15
**Page:** 1
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [January 18, 2024, 7:29am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/1 "2024-01-18T07:29:20Z")
Hi,
I am working with 16S amplicon data obtained via outsourcing our 1 sample, and they provided us with two files **A01\_R1.fq** and **A01\_R2.fq,** where my sample id is A01.
**Can I use these files in QIIME2???
Can somebody tell me, how to import such kind of data/file?**
I am very new to this kind of analysis. Any kind of help will be appreciated.
Best Regards,
Rashmi
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [January 18, 2024, 8:49am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/2 "2024-01-18T08:49:52Z")
Hello!
So, for your sample AO1 you have forward (R1) and reverse (R2) reads. To import it to qiime2, you can rename the extension of the files to .fastq instead of .fq and then use "gzip" to zip the files (you will get .fastq.gz). Then search for qiime2 importing tutorial and import it as paired reads with manifest.
Best,
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [January 18, 2024, 9:24am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/3 "2024-01-18T09:24:57Z")
Hi @timanix,
Thanks for your response. I already tried that way to import, but it's not working.
In fact I tried another command by using manifest
> qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path manifest.csv --input-format PairedEndFastqManifestPhred33 --output-path paired-end-demux.qza
But getting error: screenshot attached
and
This how manifest file looks like:
Please suggest, what I can do further???
Best Regards
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [January 18, 2024, 9:40am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/4 "2024-01-18T09:40:08Z")
Did you check the importing tutorial?
Here is an example of manifest file.
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [January 18, 2024, 12:43pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/5 "2024-01-18T12:43:37Z")
Yes, I tried with this format too, but it is not working.
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [January 18, 2024, 8:02pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/6 "2024-01-18T20:02:40Z")
Is the error changed, or it was the same?
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [January 23, 2024, 5:41am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/7 "2024-01-23T05:41:48Z")
no, it's changed.
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [January 23, 2024, 2:49pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/9 "2024-01-23T14:49:50Z")
Hi @Rashmi_Ira,
It looks like QIIME is having a hard time finding your data. Can you confirm your data is in this file path?
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [January 23, 2024, 6:09pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/10 "2024-01-23T18:09:52Z")
Hi @cherman2,
Yes, my .fastq data (AJ01\_R1.fq and AJ01\_R2.fq) is present in the above-mentioned path.
---
### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [January 23, 2024, 6:37pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/11 "2024-01-23T18:37:54Z")
Hi @Rashmi_Ira,
Can you please provide a screenshot that includes the full filepath confirming the location of `AJ01_R1.fastq`? Additionally, it may be helpful for us to take a look at the manifest file you've created to make sure there are no formatting issues. Thanks! 🦎
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [January 23, 2024, 8:48pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/12 "2024-01-23T20:48:57Z")
Hi @Rashmi_Ira,
I noticed you might have a capitalization error in your file path. This screenshot shows that you have a directory named Metagenoics\_OOty\_AJ
But your manifest error says that its looking in a directory called Metagenoics\_Ooty\_AJ. The difference in capitalization here would cause qiime2 not to find your files. Can you confirm that the files are in the file path that contains "Metagenoics\_OOty\_AJ". If that's the case you will have to edit your manifest to contain the correct file path!
Hope that helps!
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [February 12, 2024, 6:06am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/13 "2024-02-12T06:06:54Z")
HI @lizgehret
Sorry for the late response.
Here is the path for AJ01\_R1.fq and AJ01\_R2.fq files:
>
/home/rashmi/Rashmi\_IMPRINT\_PhD\_data/Metagenoics\_OOty\_AJ
Please find the manifest file:
[manifest.csv](https://forum.qiime2.org/uploads/short-url/h7KdTfvf1SZ9OQnXVdmxi2LnT2n.csv) (226 Bytes)
sample-id,absolute-filepath,direction
AJ01\_R1.fq,/home/rashmi/Rashmi\_IMPRINT\_PhD\_data/Metagenoics\_Ooty\_AJ/MBL\_AJ/AJ01\_R1.fq,forward
AJ01\_R2.fq,/home/rashmi/Rashmi\_IMPRINT\_PhD\_data/Metagenoics\_Ooty\_AJ/MBL\_AJ/AJ01\_R2.fq,reverse
Thanks and Regards,
Rashmi
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [February 12, 2024, 6:28am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/14 "2024-02-12T06:28:37Z")
Hi @cherman2
Thank you so much for your response.
Yes I checked that, there's some problem with the manifest file. I am trying to Capitalize both OO but unable to do that.. so I have generated another file, after changing the folder name from "Metagenoics\_OOty\_AJ" to "Metagenoics\_Ooty\_AJ"
sample-id,absolute-filepath,direction
AJ01\_R1.fq,/home/rashmi/Rashmi\_IMPRINT\_PhD\_data/Metagenoics\_Ooty\_AJ/MBL\_AJ/AJ01\_R1.fq,forward
AJ01\_R2.fq,/home/rashmi/Rashmi\_IMPRINT\_PhD\_data/Metagenoics\_Ooty\_AJ/MBL\_AJ/AJ01\_R2.fq,reverse
---
### Author:  [@Rashmi\_Ira](https://forum.qiime2.org/u/Rashmi_Ira)
#### Post date: [February 12, 2024, 8:46am UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/15 "2024-02-12T08:46:36Z")
@lizgehret @cherman2 @timanix
Thank you all, it's working now. I have changed the folder name as well as the style of manifest file
[manifest-manifest.tsv](https://forum.qiime2.org/uploads/short-url/5B5NWbko4nNS6d8bm4N4FXPo0na.tsv) (217 Bytes)
and imported the data under
**qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest-manifest.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2**
Thanks and Regards,
Rashmi Ira
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 14, 2024, 2:47pm UTC](https://forum.qiime2.org/t/problem-use-of-fq-file-while-importing/28942/16 "2024-03-14T14:47:34Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.