search

bergmanlab / mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data
93 stars 30 forks source link

Miss --make_annotations and --mem arguments #69

Closed yanhaidong1 closed 4 years ago

yanhaidong1 commented 4 years ago

Dear Bergman,

I am Haidong, a user of the mcclintock. I found this tool is more convenient to use than before. Thanks for the updating! But I found there is no --make_annotations and --mem arguments in the current version. Or I go a wrong way to use it. Thanks!

Best wishes, Haidong

pbasting commented 4 years ago

Hi Haidong,

You are right that the --mem argument has been removed, I'll update the readme to remove this from the usage. It was removed because, in previous versions, only a few steps had memory usage limited by the --mem option, while most of the pipeline would use memory unconstrained, so the --mem option gave the false impression that the entire pipeline was limited by the value provided to --mem.

The --make_annotations option is new to the most recent commit to master: https://github.com/bergmanlab/mcclintock/commit/3b6efab5f6eb10a432ba0818f561308a4cb3d22c . You may be using an older version of mcclintock if this option is not available. You can check the commit hash with:

$ cd /path/to/mcclintock/
$ git rev-parse HEAD
3b6efab5f6eb10a432ba0818f561308a4cb3d22c

If your hash doesn't match the newest commit you will need to install the newest version of mcclintock to use the --make_annotations flag. If you are using the most recent version of mcclintock and the --make_annotations is still not working, please post an example of the command you are using so I can try and figure out what is going on.

Thanks, Preston

yanhaidong1 commented 4 years ago

Hi Preston, Thanks! I will try the new version. Best wishes, Haidong