AssertionError: Different number of R1 and R2 files

[laaryjc]

Did a new install of conda and iPyrad, and now I'm getting this error at step 1.
checked the files and there are no extra fastq.gz files inthe folder, ls | wc -l shows 96 samples, F and R files, totalling 192 Any thoughts? Thanks!

(base) laary@:~/iPyradWork/070121$ ipyrad -p params_070121_micpet.txt -s 1 -f

---

ipyrad [v.0.9.81] Interactive assembly and analysis of RAD-seq data

Parallel connection | hillary: 64 cores

Step 1: Demultiplexing fastq data to Samples [############ ] 61% 0:08:09 | chunking large files Encountered an Error. Message: AssertionError: Different number of R1 and R2 files Parallel connection closed.

(base) laary@:~/iPyradWork/data$ ls R1 | wc -l 96 (base) laary@:~/iPyradWork/data$ ls R2 | wc -l 96 (base) laary@:~/iPyradWork/data$ ls | wc -l 192

[isaacovercast]

Question: Do you have 96 pairs of raw data files that are not already demultiplexed? Or do you have 96 pairs of fastq.gz files with one pair (R1/R2) per sample? I think what you want you want is to use the sorted_fastq_path parameter in the params file, instead of the raw_fastq_path. If your data have already been demultiplexed to samples this is 100% what you want. With pre-demux'd data you still need to run step1, but all it does is read in the numbers of raw reads per sample. Good luck.

[laaryjc]

Absolutely correct and such an overlooked mistake. I read tha tparameter file so many times and didn't see my error in placing the path to the demultiplexed data in the raw reads parameter. Thanks for the help!