Stephanie Getto created ticket #7

Abundances of each bin are 0.00

liaochen posted a comment on ticket #2

Hello, I have the same problem on Mac system. When I run fraggenescan against the test example, the output file .out is empty. So I started to run the command FragGeneScan directly without running the wrapper run_FrageGeneScan.pl, it generates the error code "bus error: 10". Could you elaborate a bit more about how to "reset the permission"?

Lance Parsons created ticket #6

"official MaxBin website" is unavailable http://downloads.jbei.org/data/MaxBin.html

Yu-Wei Wu committed [36ba17]

Change auxiliary download server

MaxBin updated /MaxBin-2.2.7.tar.gz

Igor Molchanov posted a comment on ticket #5

I have checked it and it all works now, thank you. Can you update the software now to make it possible to use this script in MaxBin ?

Yu-Wei Wu posted a comment on ticket #5

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...

Igor Molchanov created ticket #5

MaxBin 2.2.7 failed on CentOS7

Yu-Wei Wu posted a comment on ticket #4

Resolved. Thanks for the letting me know the problem.

MaxBin released /MaxBin-2.2.7.tar.gz

Yu-Wei Wu committed [073ee5]

fix download auxiliary

Igor Molchanov created ticket #4

IDBA is not available

ZOU posted a comment on ticket #2

Hi,Many thanks for your email!It works fine on Linux machine. Kind regards,Yuting发自我的华为手机 -------- 原始邮件 --------主题：[maxbin:tickets] #2 Error running FragGeneScan发件人：Yu-Wei Wu <yuwwu@users.sourceforge.net>收件人："[maxbin:tickets] " <2@tickets.maxbin.p.re.sourceforge.net>抄送：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...

Yu-Wei Wu posted a comment on ticket #2

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.

Bikeparty posted a comment on ticket #2

Thanks for your reply. The problem came from the access permission which needed to be re-set. Thanks again. On Mon, May 27, 2019 at 3:30 AM ZOU yutingzou@users.sourceforge.net wrote: Hi, Sorry for the late reply. Are you running a Mac？I emailed the author and she told me that FragGeneScan could not be used on mac os system. And she recommended me to find a linux machine to run this software. I hope this would make sense. Kind regards, Yuting 发自我的华为手机 -------- 原始邮件 -------- 主题：[maxbin:tickets] #2...

ZOU posted a comment on ticket #2

Hi,Sorry for the late reply. Are you running a Mac？I emailed the author and she told me that FragGeneScan could not be used on mac os system. And she recommended me to find a linux machine to run this software. I hope this would make sense. Kind regards,Yuting发自我的华为手机 -------- 原始邮件 --------主题：[maxbin:tickets] #2 Error running FragGeneScan发件人：Maude David <bikeparty2@users.sourceforge.net>收件人："[maxbin:tickets] " <2@tickets.maxbin.p.re.sourceforge.net>抄送：Hi, Did anyone got this back and running? I'm...

Bikeparty posted a comment on ticket #2

Hi, Did anyone got this back and running? I'm using FragGeneScan1.31 with Maxbin and also got the "Output recorded" - Thanks

ZOU posted a comment on ticket #2

I have the same problem as well. Would you mind telling me how do you solve this problem? Thanks in advance.

MaxBin released /MaxBin-2.2.6.tar.gz

Yu-Wei Wu committed [ab5015]

Realtime log flushing

Yu-Wei Wu posted a comment on ticket #3

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

Mayeul Marcadella created ticket #3

v2.2.5 will show version "2.2.4" when running -v

s4251484 created ticket #2

Error running FragGeneScan

Yu-Wei Wu posted a comment on ticket #1

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...

Vinh Phan posted a comment on ticket #1

Yu-Wei, I seems there are more executables that are creating files directly in the same directory . . marker.hmm and bacar_marker.hmm. . these both create files called "d" "i" and "m". Do you have a suggestion how we can specify and output directory for these files?

Binnerman modified a comment on discussion General Discussion

Dear all, I have a question regarding the command line when handling pe reads: run_MaxBin.pl -contig mycontig -reads myreads -reads2 my2ndreads -reads3 my3rdreads ... -out myout For this command line, should I feed MaxBin with "interleaved paired-end" reads? instead of two files forward and reverse. Or should I put the forward reads in -reads and the reverse reads in -reads2 and so on? I have 4 samples (same material but from different time points) for the binning, and therefore 8 files (forward...

Binnerman posted a comment on discussion General Discussion

Dear all, I have a question regarding the command line when handling pe reads: run_MaxBin.pl -contig mycontig -reads myreads -reads2 my2ndreads -reads3 my3rdreads ... -out myout For this command line, should I feed MaxBin with "interleaved paired-end" reads? instead of two files forward and reverse. Or should I put the forward reads in -reads and the reverse reads in -reads2 and so on? I have 4 read samples for the binning, and therefore 8 files (forward and reverse). Best and thanks, binnerman

Yu-Wei Wu posted a comment on ticket #1

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.

Vinh Phan created ticket #1

run_MaxBin.pl permission denied errors

Yu-Wei Wu posted a comment on discussion General Discussion

Dear Maisie, I did not notice that there is a comment in the discussion until today. Sorry for my late reply. The reads coverage of each bin were calculated as follows. Assuming that there are n contigs c1 to cn, each with coverages a1 to an. So the coverage for c1 is a1, c2 is a2, etc. The bin abundance was estimated by Bin_abund = sum(a_i * len(c_i)) / sum(len(c_i)) where i ranges from 1 to n, and len() indicates the contig length. Hope that helps.

Maisie Nash posted a comment on discussion General Discussion

Hi, I was wondering specifically how the read coverage is caululated for each bin created by MaxBin2? I could not find this in the ReadMe! Any information would be greatly apreciated. Thanks!

Yu-Wei Wu committed [e6da76]

add ThreadPool class

MaxBin released /MaxBin-2.2.5.tar.gz

Joy Buongiorno posted a comment on discussion General Discussion

I am having the same problem. Did you ever figure out the answer to the issue?

Mabel Wong posted a comment on discussion General Discussion

According to the readme file: (out).summary -- a summary file describing which contigs are being classified into which bin. However, I was only able to view the statistics of the bins: Bin name Abundance Completeness Genome size GC content Dan_AbySS_Maxbin.001.fasta 699.97 24.3% 925012 35.2 Dan_AbySS_Maxbin.002.fasta 673.01 18.7% 954665 51.7 Dan_AbySS_Maxbin.003.fasta 489.28 95.3% 6248111 52.9 Please let me know where I could see which contigs are being classified into which bin. Thanks a lot!

Yu-Wei Wu committed [df62ae]

change from c++0x to c++11

MaxBin released /MaxBin-2.2.4.tar.gz

Yu-Wei Wu committed [234da9]

Add support to gzipped contigs/scaffolds

Yu-Wei Wu committed [b39930]

add more error message into abundance checking

MaxBin released /MaxBin-2.2.3.tar.gz

Yu-Wei Wu committed [34decb]

change version from 2.2.2 to 2.2.3

Yu-Wei Wu committed [ac7a95]

fix abundance file reading error

Ilnam Kang posted a comment on discussion General Discussion

Hello, I'd like to share my experience during the installation of MaxBin-2.2.2. 'autobuild_auxiliary'...

MaxBin released /MaxBin-2.2.2.tar.gz

Yu-Wei Wu committed [5497a6]

bug fixes

Yu-Wei Wu committed [35c120]

Fix buildapp and other bugs

MaxBin released /MaxBin-2.2.1.tar.gz

Yu-Wei Wu committed [2740ca]

Restart from middle and updated FragGeneScan ve...

Yu-Wei Wu committed [bfe0ed]

Add changelog context

Yu-Wei Wu committed [6ff12f]

Added marker gene extraction for the bins

MaxBin released /MaxBin-2.2.tar.gz

MaxBin released /MaxBin-2.1.1.tar.gz

MaxBin released /MaxBin-2.1.tar.gz

MaxBin released /README.txt

Yu-Wei Wu committed [0fb6a6]

MaxBin can now "make" on mac os X

Yu-Wei Wu committed [da6b29]

Make autobuild_auxiliary more user-friendly

Yu-Wei Wu committed [ef6ace]

Fix IDBA-UD setting path

Yu-Wei Wu committed [86e08f]

Upgrade to MaxBin 2.1

Yu-Wei Wu committed [03f473]

ugprade to v1.4.5. Reassembly will now put in a...

MaxBin released /MaxBin-1.4.5.tar.gz

MaxBin released /MaxBin-1.4.4.tar.gz

Yu-Wei Wu committed [2727bd]

Reassembly support interleaved fastq file

MaxBin released /MaxBin-1.4.3.tar.gz

Yu-Wei Wu committed [32f36e]

Add support for yielding one bin if only one ge...

Yu-Wei Wu committed [52c618]

Fixed a bug that cannot recruit reads for reass...

MaxBin released /MaxBin-1.4.2.tar.gz

MaxBin released /MaxBin-1.4.1.tar.gz

Yu-Wei Wu committed [f6283d]

Fix all N bug

Yu-Wei Wu committed [3cf9f6]

Fixed a bug that crashs MaxBin when sequences w...

MaxBin released /README

Yu-Wei Wu committed [febdfa]

Initial commit

MaxBin released /MaxBin-1.4.tar.gz

MaxBin released /MaxBin-1.3.tar.gz

MaxBin released /MaxBin-1.3.tar.gz

MaxBin released /MaxBin-1.3.tar.gz

MaxBin released /MaxBin-1.3.tar.gz