Encountered an Error. Message: Can't recognize paired fastq files.

[ClaudiaPaetzold]

I'm running Ipyrad v 0.9.104 installed via conda on an HPC using already demultiplexed paired gbs reads.

On step 1 the Loading of the fastq files failes with the following output:

---

ipyrad [v.0.9.104]
Interactive assembly and analysis of RAD-seq data

Parallel connection | paul03.sc.uni-leipzig.de: 8 cores

Step 1: Loading sorted fastq data to Samples

Encountered an Error.
Message: Can't recognize paired fastq files. Check the format of fastq path names

I have tried various ways to name my paired files, inlcuding: _1.fastq.gz/_2.fastq.gz, _R1.fastq.gz/_R2.fastq.gz and R1.fastq.gz/R2.fastq.de. A list of filenames is here: fileslist.txt

I have also checked the path to the files in the [parameter] (https://github.com/user-attachments/files/20410924/params-Trog_asm.txt) file.
I can not figure out what the issue with the fileames is. Could somebody help me? Thank you.

[isaacovercast]

@ClaudiaPaetzold Looking at the fileslist.txt you sent I can see that there is variation in the R1/R2 file names among samples. The R1/R2 signifiers in sample names are pretty flexible, but they have to be identical across all samples. So all R1 files must use _R1_.fastq.gz and all R2 files must use _R2_.fastq.gz, for example. Please make sure all your files use the same convention for indicating R1/R2 and try again and let me know if it doesn't work.