"1" ("2") instead of "_R1_" ("_R2_) in .fq data files

[jesus-mavarez]

Hi. I tried to run the first step in a ipyrad analysis with paired-end data, but I got this message.

Step 1: Demultiplexing fastq data to Samples Encountered an Error. Message: First read files names must contain 'R1'.

I checked the data and there no R1 (neither R2) in sequence names. Is there a way to solve issue this directly in ipyrad?

Thanks in advance

[isaacovercast]

For paired-end data the raw files will normally be named like this: xxxxxxxxxxxxxxxxxxxxR1.fastq.gz and xxxxxxxxxxxxxxxxxxxxR2.fastq.gz, to distinguish the forward and reverse reads. Sometimes the files will have different naming schemes like xxxx_1_fastq.gz (which is the most common alternate, but still is rare). This message from ipyrad is saying that your raw data files do not contain _R1_ in the filename, so ipyrad doesn't know how to identify the forward reads. You need to rename your raw data files so the file names include _R1_ in the forward reads and _R2_ in the reverse. Let me know how it goes.

[isaacovercast]

Closing this as stale. If you're still having problems reopen it.