I’m using Stacks de novo map for population usage with my data but the work has been runing for one week and it dosn’t load. My data consist in 10 samples wih and average of 231.06MB before using Trimmomatic tool. I would like to run different combinations but it’s not possible due to the time run for the jobs is extremely long.
I can’t find where the issue is, could anybody help me?
Thanks in advance.
@berta_mateos I see all your jobs still running. I will provide those tools more cores so this might help.
Please also try the brand new Stacks2 tools, e.g. https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/stacks2_denovomap/stacks2_denovomap/2.4+galaxy0
Thank you very much for the reply.
Now I’m trying Stacks2 de novo map tool to process my data but it seems I can’t change the -m value (Minimum number of identical raw reads required to create a stack) in assembly options. There is any way I can give a new value or it means it will always take the default vaule (m=3)?
Hi stacks2 denovo map has no option -m http://catchenlab.life.illinois.edu/stacks/comp/denovo_map.php. If you like to change parameters of the programs used in the pipleline you need to run them separately.