These are chat archives for dereneaton/ipyrad
@bbarker505 I am not certain, but if you paste the param line for the path to your data, and also paste an example of the path to one of your data files - we may be able to spot a problem. Although it sounds like you may have already checked that?
For example, for one of my recent runs, param 4 is:
/panfs/pfs.local/work/bi/jkarch/cam/data/*.fq ##  [sorted_fastq_path]: Location of demultiplexed/sorted fastq files
and the actual path to one data file is:
*.fastqprompt is just a suggestion. You have to match the file type of your raw data files. So you may need to change this to
*.fqor whatever, depending on the format of your data.
Hi @fangbohao_twitter, this is a bug with the current installation which we're working quickly to try to fix. Right now it installs pysam v.0.6, whereas it should install pysam v.0.10 or higher. One way to work around this for now is to run the following conda commands in this order
conda remove ipyrad pysam samtools bcftools htslib conda install pysam=0.10.0 -c bioconda conda install ipyrad -c ipyrad -f
This workaround will be temporary until we get the versions updated correctly so that they can all be installed from the
ipyrad channel instead of requiring the