Mercurial > repos > mbernt > maxbin2

comparison test-data/1/out.log @ 2:6a638de7915c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
author iuc
date Tue, 29 Oct 2019 08:45:20 -0400
parents 35aa0df55a62
children
comparison
equal deleted inserted replaced
1:864279a0d64b 2:6a638de7915c
1 MaxBin 2.2.4 1 MaxBin 2.2.7
2 Input contig: Bin_Sample3_contigs.fasta 2 Input contig: /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat
3 out header: out 3 out header: out
4 Located reads file [interleavedPE_unmapped_Sample3_total.fasta] 4 Thread: 1
5 Running Bowtie2 on reads file [interleavedPE_unmapped_Sample3_total.fasta]...this may take a while... 5 Located reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]
6 Searching against 107 marker genes to find starting seed contigs for [Bin_Sample3_contigs.fasta]... 6 Running Bowtie2 on reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]...this may take a while...
7 Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat]...
7 Try harder to dig out marker genes from contigs. 8 Try harder to dig out marker genes from contigs.
8 Done data collection. Running MaxBin... 9 Done data collection. Running MaxBin...
9 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 10 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
10 Minimum contig length set to 1000. 11 Minimum contig length set to 1000.
11 Reading seed list... 12 Reading seed list...
12 Looking for seeds in sequences. 13 Looking for seeds in sequences.
13 contig-201_2 [11.293216] 14 contig-201_2 [2.848706]
14 contig-201_100 [10.048304] 15 contig-201_100 [2.993483]
15 Get 2 seeds. 16 Get 2 seeds.
16 17
17 Start EM process. 18 Start EM process.
18 Iteration 1 19 Iteration 1
19 Iteration 2 20 Iteration 2
34 35
35 Classifying sequences based on the EM result. 36 Classifying sequences based on the EM result.
36 Minimum probability for binning: 0.50 37 Minimum probability for binning: 0.50
37 Ignoring 0 bins without any sequences. 38 Ignoring 0 bins without any sequences.
38 Number of unclassified sequences: 0 (0.00%) 39 Number of unclassified sequences: 0 (0.00%)
39 Elapsed time: 0 days 00:00:00 40 Elapsed time: 0 days 00:00:01
40 41
41 Deleting intermediate files. 42 Deleting intermediate files.
42 43
43 44
44 ========== Job finished ========== 45 ========== Job finished ==========
45 Yielded 2 bins for contig (scaffold) file Bin_Sample3_contigs.fasta 46 Yielded 2 bins for contig (scaffold) file /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat
46 47
47 Here are the output files for this run. 48 Here are the output files for this run.
48 Please refer to the README file for further details. 49 Please refer to the README file for further details.
49 50
50 Summary file: out.summary 51 Summary file: out.summary
51 Marker counts: out.marker 52 Marker counts: out.marker
52 Marker genes for each bin: out.marker_of_each_gene.tar.gz 53 Marker genes for each bin: out.marker_of_each_gene.tar.gz
53 Bin files: out.001.fasta - out.002.fasta 54 Bin files: out.001.fasta - out.002.fasta
54 Unbinned sequences: out.noclass 55 Unbinned sequences: out.noclass
56 Marker plot: out.marker.pdf
55 57
56 Store abundance information of reads file [interleavedPE_unmapped_Sample3_total.fasta] in [out.abund1]. 58 Store abundance information of reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] in [out.abund1].
57 59
58 60
59 ========== Elapsed Time ========== 61 ========== Elapsed Time ==========
60 0 hours 0 minutes and 14 seconds. 62 0 hours 0 minutes and 6 seconds.
61 63