Open mutantjoo0 opened 4 years ago
Hello Joo-Young,
This is indeed a memory error from BinSanity wich happens frequently above 100,000 contigs (For example when I have recently run datasets with 400,000 contigs >2kbp I used ~600GB RAM). I think your best bet would actually be to run 'Binsanity-lc' which I believe you'll have to do outside anvi'o and then import the results into anvio manually. You can install BinSanity via conda. When you run it through 'Binsanity-lc' this should help reduce the memory intensity although depending on your system it may or may not be enough to completely alleviate the issue. If that is the case there are some other work arounds we can try, but they may sacrifice some amount of the methods accuracy.
-Elaina
Thank you for the answer Elaina,
I will try and keep it posted here how it works.
Stay safe and healthy, Joo-Young
Hi
I am having the same error as above. However, I don't want to run Binsanity-lc because I would like to work with the results of just binning by coverage. Could you suggest possible workarounds? Thanks!
Hello,
As soon as I get some time I will add a flag to Binsanity-lc to make this possible. In the meantime the quickest workaround that you can do now (unless you want to do a little coding) is to run 'Binsanity-lc' (You can cancel it after it finishes the K-MEAN clustering step or the Stage 1 clustering). This will produce a directory in the output folder named '[Prefix]-KMEAN-BINS'. You'll want to take these subsetted clusters and use the solo 'Binsanity' script on each individual '.fna' file in the directory '[Prefix]-KMEAN-BINS'. Then collate the results.
Let me know if you have further questions, and I'll work on getting the additional flag added to Binsanity-lc as soon as possible.
-Elaina
Thanks for the rapid response Elaina. I'll give it a go but it's a little hard to cancel it at the right moment. I don't think my python is good enough to code but would be lovely if you could add a flag (and let me know when you do!). Thanks!
Hello BinSanity developers and community,
I am trying to bin contigs with BinSanity using anvi'o v6.2 and got error which seems like I have a memory issue as shown below. I ran a command
anvi-cluster-contigs -p PROFILE.db -c ../../GR_contigs.db -C binsanity --driver binsanity --just-do-it
. I wonder if there is a solution to avoid this issue. Thank you for your time and consideration.Stay healthy and safe, Joo-Young