Yu-Wei Wu

I tried to test MaxBin on a clean centOS system (simulated using docker centos:latest) and identified that MaxBin can run on centOS. Here are the things that I do to make MaxBin running on the very clean system. sudo yum groupinstall 'Development Tools' sudo yum install perl-CPAN sudo yum install which In the above steps, step 1 installs most necessary packages for compiling programs; step 2 installs CPAN for PERL, and step 3 installs which packages. The three steps may not be neede in every centOS...

Resolved. Thanks for the letting me know the problem.

Hi. I just noticed that there are tickets on Souceforge. Sorry for being late. Yes as Zou thankfully pointed out that the auxiliary software FragGeneScan cannot make it to Mac so that I recommend using a Linux system--I have tested it on a variety of Linux systems so that it should work well on most Linux machine. Thank you.

Thank you for notifying me. I will fix it along in the next release in a few days.

The abundance file is for reporting the abundances for the "bins." There are also some other files named "abund1," "abund2," "abund3," etc. for recording the abundances calculated for the contigs of each metagenomic read set. I did not include reads number but you can easily derive this value using "cat (contig file) | grep '>' | wc -l" command. Hope that helps.

This is a bit weird. May I ask if you have tried the simulated dataset like 20X, as posted on https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html ? Thanks. Yu-Wei

Hi. I tried to trace the cause of the problem but found that I cannot replicate your problem since I am not working on a cluster. The perl script will try to locate the Bin directory and the current directory; however I do not know what these directories are on the cluster run. For example, if I install MaxBin in "/usr/bin/MaxBin", and I tried to run it from "/home/yuwwu/maxbin_test", then the Bin directory is /usr/bin/MaxBin and the current directory would be /home/yuwwu/maxbin_test. I guess it...

Dear Vinh Phan, Thank you for your suggestions in the code. I certainly did not thought about this possibility but will be very happy to test your suggestion in various conditions and incorporate that into the new version. The no-cleanup is also possibly related to this condition. Thanks for letting me know that.