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 |
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date | Thu, 28 Jun 2018 08:49:29 -0400 |
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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 |