Mercurial > repos > mbernt > maxbin2
comparison 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 |
| parents | |
| children |
comparison
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| 5:8a0473eb465e | 6:2bc40bfbcfb4 |
|---|---|
| 1 MaxBin 2.2.7 | |
| 2 Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat | |
| 3 out header: out | |
| 4 Min contig length: 1000 | |
| 5 Max iteration: 50 | |
| 6 Probability threshold: 0.5 | |
| 7 Thread: 1 | |
| 8 Located reads file [test4_reads.fastqsanger_0] | |
| 9 Located reads file [test4_reads.fastqsanger_1] | |
| 10 Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while... | |
| 11 Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while... | |
| 12 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]... | |
| 13 Try harder to dig out marker genes from contigs. | |
| 14 Done data collection. Running MaxBin... | |
| 15 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 | |
| 16 Minimum contig length set to 1000. | |
| 17 Reading seed list... | |
| 18 Looking for seeds in sequences. | |
| 19 k141_99 [0.017288] [0.017288] | |
| 20 k141_239 [0.015466] [0.015466] | |
| 21 Get 2 seeds. | |
| 22 | |
| 23 Start EM process. | |
| 24 Iteration 1 | |
| 25 Iteration 2 | |
| 26 Iteration 3 | |
| 27 Iteration 4 | |
| 28 Iteration 5 | |
| 29 Iteration 6 | |
| 30 Iteration 7 | |
| 31 Iteration 8 | |
| 32 | |
| 33 EM finishes successfully. | |
| 34 | |
| 35 Classifying sequences based on the EM result. | |
| 36 Minimum probability for binning: 0.50 | |
| 37 Ignoring 0 bins without any sequences. | |
| 38 Number of unclassified sequences: 0 (0.00%) | |
| 39 Elapsed time: 0 days 00:00:01 | |
| 40 | |
| 41 Deleting intermediate files. | |
| 42 | |
| 43 | |
| 44 ========== Job finished ========== | |
| 45 Yielded 2 bins for contig (scaffold) file /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat | |
| 46 | |
| 47 Here are the output files for this run. | |
| 48 Please refer to the README file for further details. | |
| 49 | |
| 50 Summary file: out.summary | |
| 51 Genome abundance info file: out.abundance | |
| 52 Marker counts: out.marker | |
| 53 Marker genes for each bin: out.marker_of_each_gene.tar.gz | |
| 54 Bin files: out.001.fasta - out.002.fasta | |
| 55 Unbinned sequences: out.noclass | |
| 56 Marker plot: out.marker.pdf | |
| 57 | |
| 58 Store abundance information of reads file [test4_reads.fastqsanger_0] in [out.abund1]. | |
| 59 Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2]. | |
| 60 | |
| 61 | |
| 62 ========== Elapsed Time ========== | |
| 63 0 hours 0 minutes and 3 seconds. | |
| 64 |