Mercurial > repos > iuc > merqury
comparison test-data/output_05_log.txt @ 2:589078edd230 draft
"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 |
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| 1:39edec572bae | 2:589078edd230 |
|---|---|
| 1 read: read-db.meryl | |
| 2 | |
| 3 Haplotype dbs provided. | |
| 4 Running Merqury in trio mode... | |
| 5 | |
| 6 hap1: pat.meryl | |
| 7 hap2: mat.meryl | |
| 8 asm1: assembly_01.fasta | |
| 9 asm2: assembly_02.fasta | |
| 10 out : output_05 | |
| 11 | |
| 12 | |
| 13 Get spectra-cn plots and QV stats | |
| 14 | |
| 15 Get blob plots | |
| 16 | |
| 17 Get haplotype specfic spectra-cn plots | |
| 18 | |
| 19 Get phase blocks | |
| 20 | |
| 21 | |
| 22 Get block N plots | |
| 23 No modules available.. | |
| 24 # Generate assembly_01.fasta.fai | |
| 25 | |
| 26 *** # Found assembly_01.gaps.bed *** | |
| 27 | |
| 28 # No gaps found. This is a contig set. | |
| 29 | |
| 30 # Generate assembly_02.fasta.fai | |
| 31 | |
| 32 *** # Found assembly_02.gaps.bed *** | |
| 33 | |
| 34 # No gaps found. This is a contig set. | |
| 35 | |
| 36 # Convert output_05.assembly_01.100_20000.phased_block.bed to sizes | |
| 37 Result saved as output_05.assembly_01.100_20000.phased_block.sizes | |
| 38 | |
| 39 # Plot output_05.assembly_01.100_20000.phased_block.bed | |
| 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 | |
| 41 Loading required package: argparse | |
| 42 Loading required package: ggplot2 | |
| 43 Loading required package: scales | |
| 44 Error in read.table(dat, header = F) : no lines available in input | |
| 45 Calls: block_n -> attach_n -> read.table | |
| 46 Execution halted | |
| 47 | |
| 48 # Convert output_05.assembly_02.100_20000.phased_block.bed to sizes | |
| 49 Result saved as output_05.assembly_02.100_20000.phased_block.sizes | |
| 50 | |
| 51 # Plot output_05.assembly_02.100_20000.phased_block.bed | |
| 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 | |
| 53 Loading required package: argparse | |
| 54 Loading required package: ggplot2 | |
| 55 Loading required package: scales | |
| 56 Error in read.table(dat, header = F) : no lines available in input | |
| 57 Calls: block_n -> attach_n -> read.table | |
| 58 Execution halted | |
| 59 |