Mercurial > repos > mbernt > maxbin2

annotate test-data/4/out.log @ 6:2bc40bfbcfb4 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 e0e4e512a0858295ce3d445b9413de2b5bcfcd78
author iuc
date Mon, 16 Oct 2023 07:46:13 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
1 MaxBin 2.2.7
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
2 Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
3 out header: out
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
4 Min contig length: 1000
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
5 Max iteration: 50
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
6 Probability threshold: 0.5
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
7 Thread: 1
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
8 Located reads file [test4_reads.fastqsanger_0]
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
9 Located reads file [test4_reads.fastqsanger_1]
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
10 Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while...
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
11 Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while...
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
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]...
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
13 Try harder to dig out marker genes from contigs.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
14 Done data collection. Running MaxBin...
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
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
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
16 Minimum contig length set to 1000.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
17 Reading seed list...
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
18 Looking for seeds in sequences.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
19 k141_99 [0.017288] [0.017288]
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
20 k141_239 [0.015466] [0.015466]
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
21 Get 2 seeds.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
22
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
23 Start EM process.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
24 Iteration 1
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
25 Iteration 2
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
26 Iteration 3
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
27 Iteration 4
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
28 Iteration 5
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
29 Iteration 6
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
30 Iteration 7
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
31 Iteration 8
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
32
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
33 EM finishes successfully.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
34
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
35 Classifying sequences based on the EM result.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
36 Minimum probability for binning: 0.50
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
37 Ignoring 0 bins without any sequences.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
38 Number of unclassified sequences: 0 (0.00%)
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
39 Elapsed time: 0 days 00:00:01
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
40
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
41 Deleting intermediate files.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
42
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
43
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
44 ========== Job finished ==========
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
45 Yielded 2 bins for contig (scaffold) file /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
46
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
47 Here are the output files for this run.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
48 Please refer to the README file for further details.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
49
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
50 Summary file: out.summary
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
51 Genome abundance info file: out.abundance
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
52 Marker counts: out.marker
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
53 Marker genes for each bin: out.marker_of_each_gene.tar.gz
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
54 Bin files: out.001.fasta - out.002.fasta
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
55 Unbinned sequences: out.noclass
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
56 Marker plot: out.marker.pdf
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
57
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
58 Store abundance information of reads file [test4_reads.fastqsanger_0] in [out.abund1].
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
59 Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2].
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
60
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
61
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
62 ========== Elapsed Time ==========
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
63 0 hours 0 minutes and 3 seconds.
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents:
diff changeset
64