checkm merger

[chloelulu]

Hi, I have used checkm merger function produced the merger.tsv file. I have also looked at the paper published 'Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life'. Something confused for me. As in the paper you listed, 'The ‘merge’ method of CheckM v.1.0.6 was used to identify pairs of bins where the completeness increased by ≥10% and the contamination increased by ≤1% when merged into a single bin'. But based on my analysis, see attached. I have seen one bin can be suggested to be merged to three or four bins. May I have some suggestions from you how to choose the merger bins? Does that mean can one bin be merged with two or three separately? Thanks so much. merger.xlsx

[donovan-h-parks]

That results would indicate that such a merger is possible given the criteria you provided to the 'merge' method. I'm not sure it is advisable to merge so many bins together though. Merging bins in general needs to be done with considerable care since an incorrect merger will result in a chimeric bin.

[chloelulu]

Hi, Thanks for your answer. May I know if I merge the two bins, if there is a method that can be used to check the chimeric status of the merged bins?

[donovan-h-parks]

You could run the bin through RefineM to check if it looks like it might be chimeric.

https://github.com/dparks1134/RefineM

[chloelulu]

Thanks so much. Very informative! Is there another way to install RefineM? Since I do not have the sudo privilege. 'sudo pip install refinem' does not works for me. Can I have another way?

[donovan-h-parks]

You can install RefineM into your home directory, but it is probably best to request it be install globally on your system the same way CheckM is.

[chloelulu]

I used conda for installing checkm. I have tried pip install refinem. It gave the message as described in the file attached. Also I have also installed diamond, ncbi blast, krona, prodigal. But I type in refinem, it gave the error. refinem File "/home/luyang/anaconda3/bin/refinem", line 55 print '' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int '')? So I think refinem may only support python2. How can I deal with this? Thanks in advance.

refinem.txt

[donovan-h-parks]

RefineM, like CheckM, must be run with Python 2. The error message indicates you are using Python 3.

[chloelulu]

Hi, Always failed. I think it could be the problem of pip version. I am using python 2.7. I pip install refinem Traceback (most recent call last): File "/home/luyang/anaconda3/envs/python2/bin/pip", line 7, in from pip._internal import main ImportError: No module named _internal. Then I rerun 'pip2 install refinem' I got the error as the file attached. I do not have the sudo right. May I know how to deal with it? Thanks so much. refinem_error.txt

[donovan-h-parks]

Hello. I'm not that familiar with pip, but I believe you need to request that you want things installed in your home directory. Perhaps the following will be useful: https://stackoverflow.com/questions/2915471/install-a-python-package-into-a-different-directory-using-pip

[chloelulu]

I am gonna breakdown. I have tried 'pip2 install --target=/home/RefineM/ refinem ' for the whole afternoon. I still got the error. A lot if files were downloaded into the directory. Error file was in the attachment.I do not know how to do now. :( refinem_error2.txt

[donovan-h-parks]

Can your sys admin install RefineM?

[chloelulu]

I will try to communicate with the administrator of the server. Thanks so much for the help and quick reply always.