Mercurial > repos > mbernt > maxbin2
view test-data/1/out.log @ 7:28a0b1446d2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit be3f3d0eb7e565cea414babb410e6ae32875c5f2
| author | iuc |
|---|---|
| date | Wed, 20 Dec 2023 20:27:57 +0000 |
| parents | 6a638de7915c |
| children |
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MaxBin 2.2.7 Input contig: /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat out header: out Thread: 1 Located reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] Running Bowtie2 on reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]...this may take a while... Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat]... Try harder to dig out marker genes from contigs. Done data collection. Running MaxBin... Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 Minimum contig length set to 1000. Reading seed list... Looking for seeds in sequences. contig-201_2 [2.848706] contig-201_100 [2.993483] Get 2 seeds. Start EM process. Iteration 1 Iteration 2 Iteration 3 Iteration 4 Iteration 5 Iteration 6 Iteration 7 Iteration 8 Iteration 9 Iteration 10 Iteration 11 Iteration 12 Iteration 13 Iteration 14 EM finishes successfully. Classifying sequences based on the EM result. Minimum probability for binning: 0.50 Ignoring 0 bins without any sequences. Number of unclassified sequences: 0 (0.00%) Elapsed time: 0 days 00:00:01 Deleting intermediate files. ========== Job finished ========== Yielded 2 bins for contig (scaffold) file /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat Here are the output files for this run. Please refer to the README file for further details. Summary file: out.summary Marker counts: out.marker Marker genes for each bin: out.marker_of_each_gene.tar.gz Bin files: out.001.fasta - out.002.fasta Unbinned sequences: out.noclass Marker plot: out.marker.pdf Store abundance information of reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] in [out.abund1]. ========== Elapsed Time ========== 0 hours 0 minutes and 6 seconds.