These are chat archives for dereneaton/ipyrad

Sep 2016
Sep 02 2016 09:27
Hi Deren/Isaac, in my outfiles, the .loci file is normal, but others ar almost empty. such as .snp.phy, I can see the head of the file including number of samples and number of snps, but the following SNP sequences is gone. Any suggestion? Thanks
Deren Eaton
Sep 02 2016 14:33
@jianlizhao do you see any errors reported in the ipyrad_log.txt file?
Shea Lambert
Sep 02 2016 19:07
Hi Deren et al., I've got some data encoded in phred64, and although I've specified this one line 10 of the params file, all samples are failing the derep_concat_split portion of Step 3 as vsearch returns: "Fatal error: FASTQ quality value above qmax."
Deren Eaton
Sep 02 2016 19:09
I see, I think we should be able to fix that easily. We only filter by phred scores in our own code in step 2, so we should be able to set the limit in vsearch to be arbitrarily high.
Emily Warschefsky
Sep 02 2016 21:21
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