These are chat archives for dereneaton/ipyrad

27th
Sep 2016
James Clugston
@Cycadales_twitter
Sep 27 2016 18:23
@dereneaton @isaacovercast I guys I have a problems that keeps cropping up. I don't think it ipyrad but something to do with the online servers I am using (iPlant). I have had two analyses that have gone kind of strange. The first one was running for 9 days (about 100 samples 150 PE) in step 3 and I know there was a big update to ipyrad (0.42) so I stopped the analysis after step four had finished updated ipyrad and then tried to continue at step 4 using -f. However, it did not recognise any of the steps past step two although ipyrad created the stats files. I gave up with that one after as I ran out of resources. So I have been running another analysis for the past week (or less) and it seemed to hold at the indexing cluster during step 6 so I stopped it to rerun it from step six (without updating ipyrad) and it did the same! did not recognise anything past step 2. If there anything I can do? it has complexly stressed me out...
Edgardo M. Ortiz
@edgardomortiz
Sep 27 2016 18:30
I ran into the same problem, it seems something related whit the .json files not being updated if something breaks along the way (or you interrupt execution), so now I am running step by step and saving a copy of the .json file after a step has been successfully completed in case I have to repeat a step
James Clugston
@Cycadales_twitter
Sep 27 2016 18:46
@edgardomortiz ahh ok well I have not had to do that before...but it kind of throws a spanner in the works with what I have done now.
Edgardo M. Ortiz
@edgardomortiz
Sep 27 2016 21:16
clustS_gz.png
Just wanted to share a linux alias I made to see ipyrad files in color in the terminal:
alias grep_dna="GREP_COLOR='1;31' grep --color=always [A/_] | GREP_COLOR='1;32' grep --color=always [C/_] | GREP_COLOR='1;33' grep --color=always [G/_] | GREP_COLOR='1;36' grep --color=always [T/_] | less -R"
To use it just cat or zcat the file and pipe to grep_dna, to quit it just press q, I use it with the .loci and .clustS files:
zcat sample.clustS.gz | grep_dna
And this is a screen capture from that command:
Deren Eaton
@dereneaton
Sep 27 2016 21:33
dang, that's cool as hell
Edgardo M. Ortiz
@edgardomortiz
Sep 27 2016 23:21
thanks! I am curious about how slow it is in other systems... it takes a couple of seconds per page on mine