Problem with file importing

Hi,

I am having forward, reverse and manifest file in a folder named as "empsingle". I tried several times but I still facing the same problem.

(qiime2-2021.8) [email protected] empsingle % qiime tools import --type EMPPairedEndSequences --input-path /Users/sandels401/empsingle --output-path fastqgz.qza

There was a problem importing /Users/sandels401/empsingle:

Missing one or more files for EMPPairedEndDirFmt: 'forward.fastq.gz'

Thank you
Aditya

Hi @Aditya,

Welcome to the :qiime2: forum!

The error is telling you that you do not have a file named forward.fastq.gz in your directory. You can check the contents of the directory using the ls command:

ls  /Users/sandels401/empsingle

My suggestion would be to start looking there.

Best,
Justine

2 Likes

My files are demultiplexed, I have 4 files 2 forward read and 2 reverse read, 1 manifest file and 1 metadata file.

(qiime2-2021.8) [email protected] ~ % ls /Users/sandels401/empsingle

0131xBV1_S181_L001_R1_001.fastq.gz 0131xFV2_S191_L001_R2_001.fastq.gz

0131xBV1_S181_L001_R2_001.fastq.gz manifest.txt

0131xFV2_S191_L001_R1_001.fastq.gz veggie-n16-tsv.tsv

This is the error I am getting,

(qiime2-2021.8) [email protected] ~ % qiime tools import --type EMPPairedEndSequences --input-path /Users/sandels401/empsingle --output-path fastqgz.qza

There was a problem importing /Users/sandels401/empsingle:

Missing one or more files for EMPPairedEndDirFmt: 'forward.fastq.gz'

Can you please help?

Thank you
Aditya

Hi @Aditya. Justine explained the proximal error above. I suspect you have a bigger issue, though. The type argument in your command tells QIIME 2 what type of data you have so that it can be imported correctly. You are telling the framework that you have EMP data, which does not appear to be the case. Please read the importing tutorial, figure out what kind of data you have, and run the command with the appropriate type.