Mercurial > repos > iuc > merqury

annotate test-data/output_05_log.txt @ 2:589078edd230 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/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
author iuc
date Mon, 25 Apr 2022 11:20:41 +0000
parents
children f8113c25bc6b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
1 read: read-db.meryl
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
3 Haplotype dbs provided.
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
4 Running Merqury in trio mode...
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
5
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
6 hap1: pat.meryl
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
7 hap2: mat.meryl
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
8 asm1: assembly_01.fasta
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
9 asm2: assembly_02.fasta
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
10 out : output_05
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
11
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
12
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
13 Get spectra-cn plots and QV stats
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
14
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
15 Get blob plots
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
16
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
17 Get haplotype specfic spectra-cn plots
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
18
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
19 Get phase blocks
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
20
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
21
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
22 Get block N plots
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
23 No modules available..
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
24 # Generate assembly_01.fasta.fai
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
25
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
26 *** # Found assembly_01.gaps.bed ***
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
27
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
28 # No gaps found. This is a contig set.
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
29
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
30 # Generate assembly_02.fasta.fai
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
31
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
32 *** # Found assembly_02.gaps.bed ***
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
33
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
34 # No gaps found. This is a contig set.
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
35
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
36 # Convert output_05.assembly_01.100_20000.phased_block.bed to sizes
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
37 Result saved as output_05.assembly_01.100_20000.phased_block.sizes
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
38
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
39 # Plot output_05.assembly_01.100_20000.phased_block.bed
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
40 Rscript /home/laptop/miniconda3/envs/mulled-v1-df114ce4641e6c1c408ddc8230d91a93fc95c8ba1dfeff221f556e667abb43c0/share/merqury/plot/plot_block_N.R -b output_05.assembly_01.100_20000.phased_block.sizes -c output_05.assembly_01.contig.sizes -o output_05.assembly_01
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
41 Loading required package: argparse
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
42 Loading required package: ggplot2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
43 Loading required package: scales
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
44 Error in read.table(dat, header = F) : no lines available in input
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
45 Calls: block_n -> attach_n -> read.table
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
46 Execution halted
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
47
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
48 # Convert output_05.assembly_02.100_20000.phased_block.bed to sizes
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
49 Result saved as output_05.assembly_02.100_20000.phased_block.sizes
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
50
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
51 # Plot output_05.assembly_02.100_20000.phased_block.bed
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
52 Rscript /home/laptop/miniconda3/envs/mulled-v1-df114ce4641e6c1c408ddc8230d91a93fc95c8ba1dfeff221f556e667abb43c0/share/merqury/plot/plot_block_N.R -b output_05.assembly_02.100_20000.phased_block.sizes -c output_05.assembly_02.contig.sizes -o output_05.assembly_02
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
53 Loading required package: argparse
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
54 Loading required package: ggplot2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
55 Loading required package: scales
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
56 Error in read.table(dat, header = F) : no lines available in input
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
57 Calls: block_n -> attach_n -> read.table
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
58 Execution halted
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents:
diff changeset
59