Mercurial > repos > mbernt > maxbin2
comparison test-data/3/out.log @ 0:35aa0df55a62 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
| author | mbernt |
|---|---|
| date | Thu, 28 Jun 2018 08:49:29 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:35aa0df55a62 |
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| 1 MaxBin 2.2.4 | |
| 2 Input contig: /tmp/tmpES_iZn/files/000/dataset_1.dat | |
| 3 out header: out | |
| 4 Reassembly: 1 | |
| 5 Located reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat] | |
| 6 Running Bowtie2 on reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat]...this may take a while... | |
| 7 Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpES_iZn/files/000/dataset_1.dat]... | |
| 8 Try harder to dig out marker genes from contigs. | |
| 9 Done data collection. Running MaxBin... | |
| 10 Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.4/opt/MaxBin-2.2.4/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 | |
| 11 Minimum contig length set to 1000. | |
| 12 Reading seed list... | |
| 13 Looking for seeds in sequences. | |
| 14 contig-201_2 [11.293216] | |
| 15 contig-201_100 [10.048304] | |
| 16 Get 2 seeds. | |
| 17 | |
| 18 Start EM process. | |
| 19 Iteration 1 | |
| 20 Iteration 2 | |
| 21 Iteration 3 | |
| 22 Iteration 4 | |
| 23 Iteration 5 | |
| 24 Iteration 6 | |
| 25 Iteration 7 | |
| 26 Iteration 8 | |
| 27 Iteration 9 | |
| 28 Iteration 10 | |
| 29 Iteration 11 | |
| 30 Iteration 12 | |
| 31 Iteration 13 | |
| 32 Iteration 14 | |
| 33 | |
| 34 EM finishes successfully. | |
| 35 | |
| 36 Classifying sequences based on the EM result. | |
| 37 Minimum probability for binning: 0.50 | |
| 38 Ignoring 0 bins without any sequences. | |
| 39 Number of unclassified sequences: 0 (0.00%) | |
| 40 Elapsed time: 0 days 00:00:00 | |
| 41 | |
| 42 Performing reassembly. Reads file found. | |
| 43 Separating reads according to the bins... | |
| 44 Reassembling bin 001 | |
| 45 Command: idba_ud -r out.reads.001 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err | |
| 46 Placing reassembled contigs into out.reassem | |
| 47 cp out.tmp/scaffold.fa out.reassem/out.001.fasta | |
| 48 Reassembling bin 002 | |
| 49 Command: idba_ud -r out.reads.002 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err | |
| 50 Placing reassembled contigs into out.reassem | |
| 51 cp out.tmp/scaffold.fa out.reassem/out.002.fasta | |
| 52 Deleting intermediate files. | |
| 53 | |
| 54 | |
| 55 ========== Job finished ========== | |
| 56 Yielded 2 bins for contig (scaffold) file /tmp/tmpES_iZn/files/000/dataset_1.dat | |
| 57 | |
| 58 Here are the output files for this run. | |
| 59 Please refer to the README file for further details. | |
| 60 | |
| 61 Summary file: out.summary | |
| 62 Marker counts: out.marker | |
| 63 Marker genes for each bin: out.marker_of_each_gene.tar.gz | |
| 64 Bin files: out.001.fasta - out.002.fasta | |
| 65 Unbinned sequences: out.noclass | |
| 66 | |
| 67 Store abundance information of reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat] in [out.abund1]. | |
| 68 | |
| 69 | |
| 70 ========== Elapsed Time ========== | |
| 71 0 hours 2 minutes and 34 seconds. | |
| 72 |