Error in import-Data pairedEnd qiime2026.1

Technical Support
1

Hi, I am using the trimmed illumina PairedEnd sequences to import using qiime tools import. got this error:

qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path rawData-trimmed/ --output-path st-all_fastq.qza
/home/gilbert/anaconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/unifrac/init.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
There was a problem importing rawData-trimmed/:

Missing one or more files for SingleLanePerSamplePairedEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

Earlier I was using qiime 2024 and imported same data to .qza with no error.

2

Hello @majorRam

Here is the important part of the error:

So it looks like --input-path folder rawData-trimmed/ does not have all the files you need, or maybe this folder has been moved?

Okay, we know the data works, we just need to find the files!

3

Hi Files are there. i checked here…

qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path rawData-trimmed/*.fastq.gz --output-path st-all_fastq.qza

There was a problem with the command:
(1/1) Got unexpected extra arguments (rawData-trimmed/St_2_r1_2.fastq.gz
rawData-trimmed/St_2_r2_1.fastq.gz rawData-trimmed/St_2_r2_2.fastq.gz
rawData-trimmed/St_2_r3_1.fastq.gz rawData-trimmed/St_2_r3_2.fastq.gz
rawData-trimmed/St_3_r1_1.fastq.gz rawData-trimmed/St_3_r1_2.fastq.gz
rawData-trimmed/St_3_r2_1.fastq.gz rawData-trimmed/St_3_r2_2.fastq.gz
rawData-trimmed/St_3_r3_1.fastq.gz rawData-trimmed/St_3_r3_2.fastq.gz
rawData-trimmed/St_4_r1_1.fastq.gz rawData-trimmed/St_4_r1_2.fastq.gz
rawData-trimmed/St_4_r2_1.fastq.gz rawData-trimmed/St_4_r2_2.fastq.gz
rawData-trimmed/St_5_r1_1.fastq.gz rawData-trimmed/St_5_r1_2.fastq.gz
rawData-trimmed/St_5_r2_1.fastq.gz rawData-trimmed/St_5_r2_2.fastq.gz
rawData-trimmed/St_5_r3_1.fastq.gz rawData-trimmed/St_5_r3_2.fastq.gz
rawData-trimmed/St_6_r1_1.fastq.gz rawData-trimmed/St_6_r1_2.fastq.gz
rawData-trimmed/St_6_r2_1.fastq.gz rawData-trimmed/St_6_r2_2.fastq.gz
rawData-trimmed/St_6_r3_1.fastq.gz rawData-trimmed/St_6_r3_2.fastq.gz
rawData-trimmed/St_7_r1_1.fastq.gz rawData-trimmed/St_7_r1_2.fastq.gz
rawData-trimmed/St_7_r2_1.fastq.gz rawData-trimmed/St_7_r2_2.fastq.gz
rawData-trimmed/St_7_r3_1.fastq.gz rawData-trimmed/St_7_r3_2.fastq.gz)

4

The * will work with other Linux cli programs, but not Qiime2.

Try this:

What command did you use to import the files in 2024? That should still work in 2026.1

5

in 2024 i used manifest.tsv to give path to the files

6

That's great! Try using that to import these files!

7

I already did. it said, not corrrect path, did not recognized manifest.tsv

8

Would you like to post that command so we can take a look?

9

Hi colin, it seems this time it worked.

what about this userwarnings.

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path manifest.tsv --input-format PairedEndFastqManifestPhred33V2 --output-path st-all_reads.qza
/home/gilbert/anaconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/unifrac/init.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
Imported manifest.tsv as PairedEndFastqManifestPhred33V2 to st-all_reads.qza

10

You can ignore that warning!

Generally, errors are problems that need to be fixed while warnings are about possible issues.