kuangzhuoran
commented
2 years ago I found that the sequence names are the same between my different samples(bins)， So I rename them,maybe that worked
Open kuangzhuoran opened 2 years ago
kuangzhuoran
commented
2 years ago I found that the sequence names are the same between my different samples(bins)， So I rename them,maybe that worked
Hi ! Co assembly is running, So I used the results of assembly and binning of each sample(I have done it before) to REFINEMENT.
And I see this, Does this mean that the results of A(MaxBin) and B(MetaBin) do not intersect？ O
log file is :
metawrap bin_refinement -o BIN_REFINEMENT_50_10 -t 8 -A /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin -B /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin -c 50 -x 10
----- There is 40 RAM and 8 threads available, and each pplacer thread uses >40GB, so I will ----- ----- use 1 threads for pplacer -----
########################################################################################################################
BEGIN PIPELINE!
########################################################################################################################
----- setting up output folder and copying over bins... -----
Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/1.sh because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/abundance.list because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/maxbin.sh because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/maxbin.sh.job202191194801 because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.0024.out.0001.out.0001.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.0063.out.0001.out.0001.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B2A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B3A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B3A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B3A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B3A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B3A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B4A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B4A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B4A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B4A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B4A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.0027.out.0002.out.0001.out.0002.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.0035.out.0002.out.0001.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B6A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.0044.out.0001.out.0003.out.0004.out.0001.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.0045.out.0002.out.0001.out.0002.out.0001.out.0001.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.0045.out.0002.out.0001.out.0002.out.0001.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.0048.out.0001.out.0001.out.0001.out.0002.out.0001.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B7A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.0073.out.0002.out.0002.out.0002.out.0001.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_B9A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.0008.out.0001.out.0002.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.0067.out.0001.out.0002.out.0002.out.0002.out.0001.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.0067.out.0001.out.0002.out.0002.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C1A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.0043.out.0002.out.0002.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C2A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.0052.out.0002.out.0001.out.0001.out.0001.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.0071.out.0001.out.0001.out.0002.out.0001.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C3mbin_B.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.0035.out.0002.out.0001.out.0002.out.0002.out.0001.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.0035.out.0002.out.0001.out.0002.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C4mbin_B.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.0062.out.0002.out.0002.out.0001.out.0002.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C5A.tooshort because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.0070.out.0001.out.0001.out.0002.out.0002.out.0001.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.0070.out.0001.out.0002.out.0002.out.0003.out.0002.out.seed because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.log because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.marker because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.noclass because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.summary because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MaxBin/mbin_C6A.tooshort because the bin size is not between 50kb and 20Mb
----- there are 1318 bins in binsA -----
Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B2A.37.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B3A.47.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B3A.88.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B4A.63.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B4A.6.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B6A.23.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B7A.91.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/B9A.7.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C2A.42.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C3B.35.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C3B.80.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C4B.2.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C4B.74.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C5A.52.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C5A.7.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/C6A.6.fa because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/metabat2 because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/metabin.sh because the bin size is not between 50kb and 20Mb Skipping /data/01/user164/workspace_for_whole_object/metagenome_gut/05.binning/MetaBin/metabin.sh.job202198102610 because the bin size is not between 50kb and 20Mb
----- there are 1115 bins in binsB -----
----- There are 2 bin sets! -----
----- Fix contig naming by removing special characters... -----
########################################################################################################################
BEGIN BIN REFINEMENT
########################################################################################################################
----- There are two bin folders, so we can consolidate them into a third, more refined bin set. -----
Specified 2 input bin sets: -1 binsA -2 binsB Add folder/bin name to contig name for binsA bins Add folder/bin name to contig name for binsB bins Combine all bins together
----- there are 0 refined bins in binsAB -----
Bin_refiner did not finish correctly. Exiting...