step3: vsearch 2.20 deprecated --derep_fulllength

[Uniltiranyu]

ipyrad -p params-test2.txt -s 123

---

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

Parallel connection | master: 64 cores

Step 1: Loading sorted fastq data to Samples
[####################] 100% 0:00:54 | loading reads
50 fastq files loaded to 50 Samples.

Step 2: Filtering and trimming reads
[####################] 100% 0:08:23 | processing reads

Step 3: Clustering/Mapping reads within samples
[####################] 100% 0:00:01 | dereplicating

Encountered an Error.
Message: IPyradError:

Fatal error: FASTQ input is only allowed with the fastx_uniques command

Parallel connection closed.
Is there something wrong with my fastq file?
I'm using the default parameters, nothing has changed except the pathname, the same fastq files can be recognized by stacks.
ipyrad is downloaded by conda.
so sorry for my English.

[isaacovercast]

Well this looks like an issue with vsearch. They just implemented some change which causes this to break:

torognes/vsearch#348

Ok, so it looks like derep_fulllength was deprecated in vsearch 2.20. You can fix this by rolling back vsearch to 2.19:
conda install -c bioconda vsearch=2.19

I will think about a longer term solution.

[isaacovercast]

Pinned vsearch to 2.19 in ipyrad version 0.9.82

[isaacovercast]

Added a check to handle this in clustmap.py.