These are chat archives for dereneaton/ipyrad

18th
Nov 2016
LinaValencia85
@LinaValencia85
Nov 18 2016 01:44
@isaacovercast I actually just specified l, s, p, u, k. I will run it again sometime tomorrow with vcf. I will let you know if it runs ok.
Isaac Overcast
@isaacovercast
Nov 18 2016 02:28
Great, thx.
Amely Martins
@amelymartins
Nov 18 2016 16:21

@isaacovercast step 7 worked with the new version, but without the option for vcf file.
I've tried it using the -c 1 flag, in a computer node with 512GB and still got the error when writing the vcf file. The ipyrad_log.txt is:
2016-11-18 10:05:31,053 pid=71774 [write_outfiles.py] ERROR error in vcf build chunk 0: MemoryError()

It looks like the assembly.py worked now, but it failed when writing the output.

Sara Lipshutz
@slipshut
Nov 18 2016 20:54
Hey y'all, I opened my GBS-generated fastq files in FastQC and saw that they still contained adapter sequences even after Step 2 filtering. I had used 0 for #16 filter_adapters in my params file, so I'm thinking I'll need something more strict - what's the difference between 1 and 2 here?
Edgardo M. Ortiz
@edgardomortiz
Nov 18 2016 22:01
@slipshut: 1 does quality trimming, 2 does quality trimming + adapter removal (works better if you specify the cutsite sequences in parameter [8])