Mercurial > repos > mbernt > maxbin2
view test-data/4/out.log @ 6:2bc40bfbcfb4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
| author | iuc |
|---|---|
| date | Mon, 16 Oct 2023 07:46:13 +0000 |
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| children |
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MaxBin 2.2.7 Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat out header: out Min contig length: 1000 Max iteration: 50 Probability threshold: 0.5 Thread: 1 Located reads file [test4_reads.fastqsanger_0] Located reads file [test4_reads.fastqsanger_1] Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while... Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while... Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat]... Try harder to dig out marker genes from contigs. Done data collection. Running MaxBin... Command: /home/gitpod/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -abund2 out.contig.tmp.reads.abund2 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 Minimum contig length set to 1000. Reading seed list... Looking for seeds in sequences. k141_99 [0.017288] [0.017288] k141_239 [0.015466] [0.015466] Get 2 seeds. Start EM process. Iteration 1 Iteration 2 Iteration 3 Iteration 4 Iteration 5 Iteration 6 Iteration 7 Iteration 8 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/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat Here are the output files for this run. Please refer to the README file for further details. Summary file: out.summary Genome abundance info file: out.abundance 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 [test4_reads.fastqsanger_0] in [out.abund1]. Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2]. ========== Elapsed Time ========== 0 hours 0 minutes and 3 seconds.