Roland Wilhelm

Thanks, I'll try with a higher cut-off for contig length. R On Tue, Jun 27, 2017 at 10:05 PM, OliverLin oliverlinnhri@users.sf.net wrote: Hi Roli, It should takes more than 1T RAM. Please check the file size of "Similarities.txt" in 4_CLR_transformation_SNE. AP (Affinity propagation) takes this file usin memory. So, if you did not have enough RAM, you would not run AP successfully. I tested MyCC with 1G assembly, it worked. However, it depends on how many contigs you have , not on how large the assembly...

Hi Oliver, To clarify it takes up > 1 Tb of hard drive space, not RAM. What is the largest assembly that myCC has handled (just for reference). Thanks, On Tue, Jun 27, 2017 at 9:25 PM, OliverLin oliverlinnhri@users.sf.net wrote: Thank you for this information. Yes, MyCC did require disk space and memory for "Affinity propogation". Usually MyCC fails in running this kind of big assembly, do you have a large momery? (over 1T RAM? cool!). Any way, thank you for sharing. [tickets:#4] https://sourceforge.net/p/sb2nhri/tickets/4/...

Unable to Manage a 1.8 Gb Assembly - Huge Intermediary Files

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,...

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_-...

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...

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...

Segmentation fault - Error