These are chat archives for dereneaton/ipyrad

22nd
May 2017
Isaac Overcast
@isaacovercast
May 22 2017 15:02
Hi @Israelornis can you verify this file is properly formatted, since this is the one it's erroring out on: /data/Piranga/Piranga_hepatica_KU_4970_RAD.fastq Can you run head on this file?
Isaac Overcast
@isaacovercast
May 22 2017 15:09
New Version: v.0.6.21: Fix for reference mapped CHROM/POS output to vcf file. Also significant fix for any denovo+reference assembly.
Lily Roberta Lewis
@LilyRobertLewis_twitter
May 22 2017 17:56
Hello, I just had an ipyrad run timeout just before step 3 completed (my institutions cluster has a 4 day time limit). Is there a way to have step 3 resume where it left off? or will I need to start over from the beginning of step 3? Thank you for your help!
Katherine Silliman
@ksil91
May 22 2017 17:57
@isaacovercast Thanks for the help with Step 1! Turns out it was a permissions error, my files were -rwx------. Once I changed them to -rwxrwxrwx it worked fine. Maybe some way to check for that and spit out an error if you think that's a common issue.
Isaac Overcast
@isaacovercast
May 22 2017 19:04
@LilyRobertLewis_twitter We are working on checkpointing step 3 better, but for now it has to run to completion or else it starts over. If you can allocate more cores or more RAM it'll probably speed up the assembly. Another way to do it (if you can't get more cores) would be to branch 1/2 of the samples each to 2 new assemblies and then merge them after step 3. This is a little tricky (advanced workflow) so the easiest would be to see if you can get more resources on your cluster first.
Isaac Overcast
@isaacovercast
May 22 2017 19:47
New Version: v.0.6.22: Actually fix bug in vcf output for refmap.