Activity for MaxBin2
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Shankha Nath modified a comment on ticket #12
I also have encountered exactly same error for Maxbin2.. Only in my case the line number is 5739.. please help .. nohup: ignoring input MaxBin 2.2.7 Input contig: /data/sata_data/home/souvik_p1/sewage_analysis/analysis/trimmomatic_out/CLEAN_READS/COASSEMBLY_OUTPUT/assembly.fa Located abundance file [/data/sata_data/home/souvik_p1/sewage_analysis/analysis/trimmomatic_out/CLEAN_READS/Metawrap_megahit/maxbin2_ready_depth.txt] out header: /data/sata_data/home/souvik_p1/sewage_analysis/analysis/trimmomatic_out/CLEAN_READS/Metawrap_megahit/INITIAL_BINNING/maxbin2_bins/...
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I also have encountered exactly same error for Maxbin2.. Only in my case the line number is 5739.. please help ..
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Maos Yang posted a comment on discussion General Discussion
For some reasons, I interrupted the MaxBin2 run. Is the bin.contig.tmp.abund1 file generated during this run a complete abundance file? Can I directly use this file in the next MaxBin2 run, for example, by specifying -abund /path/maxbin2/work_files/maxbin2_out/bin.contig.tmp.abund1, to skip the abundance calculation step?
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Petr Dvorak posted a comment on discussion General Discussion
Dear authors, I am struggling with this issue for a while. Maxbin shuts down with error: MaxBin 2.2.4 Input contig: final.contigs.fa out header: .bin Located reads file [read.list] Thread: 24 Running Bowtie2 on reads file [read.list]...this may take a while... Error header found in reads file. ====== /mnt/78ccaa56-0fc3-44e1-b0cc-844a6eb6cfab/SRA/SRR11829738/SRR11829738.output_forward_paired.fq.gz It seems that the index is formed good but it stops afterwards. Megahit and trimmomatic reads the files...
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Rodrigo Taketani created ticket #13
MAxbin not utilizing multiple threads
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George Kitundu posted a comment on ticket #8
Hi, I am looking at the log file and I can not see any error lmessage in there
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Hi, I am getting the same problem even after setting contig legnth to 200
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Scott Klasek created ticket #12
Error: failed to get abundance information
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Josh L. Espinoza created ticket #11
Feature requests to generalize the approach
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Viola A Manning created ticket #10
Same contigs in multiple bins
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Nick Youngblut posted a comment on ticket #5
It appears that the error was due to the output directory not existing. Adding mkdir to the code (https://perldoc.perl.org/functions/mkdir) should fix the issue
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I get the same error. If I run the command stated in the log Command: ..., then that runs successfully. Given that it's been a year since this ticket was originally created, I'm guessing the developers are not going to deal with this issue. Generally, it would be very helpful to have better error messages.
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Silas Kieser posted a comment on ticket #9
I put an unofficial download resource here: https://zenodo.org/record/4247277/files/MaxBin-2.2.7.tar.gz
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Martin Z posted a comment on ticket #4
Same with me. A documentation to clarify how 'Abundance' is calculated would be great.
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Can you make maxbin2 available
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MaxBin2 updated /MaxBin-2.2.7.tar.gz
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Shi Ming posted a comment on ticket #8
Attached is the log file.
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Error encountered while running core MaxBin program.
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Matthias Bernt created ticket #7
default prob_threshold
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dgg32 posted a comment on ticket #6
After a new examination, it is now clear to me that maxbin has a default min_contig_length of 1000. For my case, I have set it to 200 and now I get my genome for 99% complete. @Javier, have a trial with run_MaxBin.pl -min_contig_length 200 please.
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Same problem. I have a 4.2 Mb contig fasta. I have digged a little bit: Maxbin uses a set 106 marker genes and none of them could be identified according to Maxbin in my contigs. However, if I run checkm directly on the contig fasta, out of this, 568 single copy genes were identified. These two sets share 16 genes. That means, these 16 genes are positive in checkm but negative in Maxbin. So perhaps Maxbin occassionally has a problem to identify marker genes? Because I have only encountered this problem...
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Same problem. I have a 4.2 Mb contig fasta. I have digged a little bit: Maxbin uses a set 106 marker genes and none of them could be identified according to Maxbin in my contigs. However, if I run checkm directly on the contig fasta, out of the 568 single copy genes were identified. These two sets share 16 genes. That means, these 16 genes are positive in checkm but negative in Maxbin. So perhaps Maxbin occassionally has a problem to identify marker genes? Because I have only encountered this problem...
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Javier created ticket #6
Maxbin don't find enough marker genes
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error but log is empty
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Emilie Spasov created ticket #4
interpreting .summary file
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Yu-Wei Wu posted a comment on ticket #3
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.
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claire campbell created ticket #3
interpreting ".abundance" files
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i had a similar question - did you ever get an answer? I ran maxbin2 with -reads option specified. The resulting ".abundance" file has values for the forward and reverse reads for each bin. Is this a coverage value or # of reads mapped to that bin?
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Kevin Chan posted a comment on ticket #2
Hi Yu-Wei, I was actually able to run MaxBin2 successfully on a Linux cluster (I was previously trying to run it locally on Mac OSX), so I will consider this issue closed. Thanks!
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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
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Segmentation fault: 11 during FragGeneScan
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Dear Rodolfo, Thank you for trying MaxBin. Your problem should be caused by the abundance file format, which is described in the README file. Currently MaxBin does not support SAM file input. Please consider inputting reads directly into MaxBin so that it can automatically parse the abundance information. Let me know if you need more information. Thanks, Yu-Wei
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rodolfo brizola toscan posted a comment on ticket #1
Hello, I am also having problems with running MaxBin2. this is the error I get ... Loaded 100000 sequences Loaded 200000 sequences Error encountered while running core MaxBin program. Error recorded in /home/administrator/storage/pipelines_mcgr/das_tool/binning_outputs/maxbin/maxbin_HPmin_bins.log. Program Stop. this is my run command /home/administrator/storage/pipelines_mcgr/das_tool/maxbin2/MaxBin-2.2.4/run_MaxBin.pl -contig /home/administrator/storage/pipelines_mcgr/sra_mm/assembly/HPmin_scaffolds.fa...
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Roland Wilhelm posted a comment on ticket #1
No problems Yu-Wei! Thanks for persisting with your assistance. I will go with the option to let MaxBin identify abundances. Roli On Fri, May 19, 2017 at 10:53 PM, Yu-Wei Wu yuwwu@users.sf.net wrote: (I don't know what went wrong, but this is the 3rd time I send this message via the ticket system. Sorry for the delay that the system caused) I tried to find a universal solution for your problem but cannot make it. From your error message your problem arised from the format of the abundance files,...
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(I don't know what went wrong, but this is the 3rd time I send this message via the ticket system. Sorry for the delay that the system caused) I tried to find a universal solution for your problem but cannot make it. From your error message your problem arised from the format of the abundance files, in which at least one contig does not have the abundance information. MaxBin requires that all contigs should have an abundance (coverage) value, and that a zero should be set if no reads can be mapped...
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Hi Yu-Wei, I'm happy to help, but now that we've clarified the error, I'm still not sure how to solve it. The error reads: Failed to get Abundance information for contig [k141_3129010|uncontaminated.1001470] in file [/home/roli/MAGs/maxbin2.foo/.contig.tmp.abund1] The problem contig is found in the following MaxBin2 files: .contig.tmp:>k141_3129010|uncontaminated.1001470 .contig.tmp.frag.faa:>k141_3129010|uncontaminated.1001470_1_1199_- .contig.tmp.frag.faa:>k141_3129010|uncontaminated.1001470_1260_2321_-...
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I sincerely thank you for giving me valuable suggestions and describing your difficulties to me. I have revised the code so that it will print out where exactly the format goes wrong. I made some mock abundance files with wrong formats and successfully get the message. For your reference the message will look like this (for unknown reason some of the following lines are mis-formatted by sourceforge.com. Please ignore the formatting) (omitted) Failed to get abudance information from input file [low.out.contig.tmp.abund1]....
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Hi Yu-Wei, I have updated MaxBin2 and re-run the command. I received the following error: "Failed to get Abundance information for contig [k141_3129010|uncontaminated.1001470] in file [metabat/maxbin2/composite_Bin.contig.tmp.abund1] Error encountered while running core MaxBin program. Error recorded in metabat/maxbin2/composite_Bin.log. Program Stop." I will look into why there is no abundance information and correct the problem. Unfortunately there is nothing written to the log file (is that supposed...
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I must admit that I do not know what caused your problem. I looked into your files but did not see problems. Personally I still suspect that the problem might be in the abundance files. I have updated the program so that it will abort and print out more messages if something's wrong with the abundance file. Could you please try downloading the newest MaxBin package and run again? I apologize for all the trouble that you encountered. Thanks, Yu-Wei
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Hi Yu-Wei! Thanks for your quick response. I've include the head of the contig file (assembly.fa), the temporary output generated while run_MaxBin2 was operating and a list of all the output files generated during the run. I hope that helps get to the bottom of it! Don't hesitate to ask for any additional information. Roli On Mon, May 8, 2017 at 12:35 PM, Yu-Wei Wu yuwwu@users.sf.net wrote: My guess is that you probably used a delimiter other than tab (\t) in your abundance file, although I am not...
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My guess is that you probably used a delimiter other than tab (\t) in your abundance file, although I am not completely sure about that. But in your case the program should have aborted when it was dealing with the abundance files. Please let me know if this is not the case. I will be very happy to keep digging out the problem.
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Dear Roland, Thank you very much for trying MaxBin. I may need more information to resolve this issue. Do you mind to let me peek into the first 20 lines of your sequence file and one of your abundance file? Thank you. Yu-Wei
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Segmentation fault - Error
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shahrok posted a comment on discussion General Discussion
I was wondering to get more details on the bin.abundance output file. What are the...
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I was wondering to get more details on the bin.abundance output file. What are the...
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JohnForadKelley posted a comment on discussion General Discussion
Error using make in g++ versions 4.3 - 4.7 Error: g++ -c -Wall -g -std=c++11 AbundanceLoader.cpp...
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