Mercurial > repos > mbernt > maxbin2

annotate test-data/1/out.log @ 0:614d53aa795f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
author mbernt
date Tue, 29 Oct 2019 06:44:19 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
1 MaxBin 2.2.7
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
2 Input contig: /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
3 out header: out
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
4 Thread: 1
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
5 Located reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
6 Running Bowtie2 on reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]...this may take a while...
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
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]...
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
8 Try harder to dig out marker genes from contigs.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
9 Done data collection. Running MaxBin...
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
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
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
11 Minimum contig length set to 1000.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
12 Reading seed list...
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
13 Looking for seeds in sequences.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
14 contig-201_2 [2.848706]
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
15 contig-201_100 [2.993483]
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
16 Get 2 seeds.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
17
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
18 Start EM process.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
19 Iteration 1
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
20 Iteration 2
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
21 Iteration 3
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
22 Iteration 4
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
23 Iteration 5
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
24 Iteration 6
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
25 Iteration 7
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
26 Iteration 8
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
27 Iteration 9
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
28 Iteration 10
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
29 Iteration 11
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
30 Iteration 12
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
31 Iteration 13
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
32 Iteration 14
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
33
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
34 EM finishes successfully.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
35
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
36 Classifying sequences based on the EM result.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
37 Minimum probability for binning: 0.50
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
38 Ignoring 0 bins without any sequences.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
39 Number of unclassified sequences: 0 (0.00%)
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
40 Elapsed time: 0 days 00:00:01
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
41
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
42 Deleting intermediate files.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
43
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
44
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
45 ========== Job finished ==========
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
46 Yielded 2 bins for contig (scaffold) file /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
47
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
48 Here are the output files for this run.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
49 Please refer to the README file for further details.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
50
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
51 Summary file: out.summary
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
52 Marker counts: out.marker
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
53 Marker genes for each bin: out.marker_of_each_gene.tar.gz
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
54 Bin files: out.001.fasta - out.002.fasta
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
55 Unbinned sequences: out.noclass
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
56 Marker plot: out.marker.pdf
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
57
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
58 Store abundance information of reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] in [out.abund1].
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
59
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
60
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
61 ========== Elapsed Time ==========
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
62 0 hours 0 minutes and 6 seconds.
614d53aa795f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit f67400e30b69d2bb47bffed380ac547041b767ac"
mbernt
parents:
diff changeset
63