view test-data/output_05_log.txt @ 6:eb7b00ec347d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 9aec17d26f63629419228ef07e76e789e5244891

read: read-db.meryl

Haplotype dbs provided.
Running Merqury in trio mode...

hap1: pat.meryl
hap2: mat.meryl
asm1: assembly_01.fasta
asm2: assembly_02.fasta
out : output_05


Get spectra-cn plots and QV stats

Get blob plots

Get haplotype specfic spectra-cn plots

Get phase blocks


Get block N plots
No modules available..
# Generate assembly_01.fasta.fai

*** # Found assembly_01.gaps.bed ***

# No gaps found. This is a contig set.

# Generate assembly_02.fasta.fai

*** # Found assembly_02.gaps.bed ***

# No gaps found. This is a contig set.

# Convert output_05.assembly_01.100_20000.phased_block.bed to sizes
 Result saved as output_05.assembly_01.100_20000.phased_block.sizes

# Plot output_05.assembly_01.100_20000.phased_block.bed
Rscript /usr/local/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 
Loading required package: argparse
Loading required package: ggplot2
Loading required package: scales
Error in read.table(dat, header = F) : no lines available in input
Calls: block_n -> attach_n -> read.table
Execution halted

# Convert output_05.assembly_02.100_20000.phased_block.bed to sizes
 Result saved as output_05.assembly_02.100_20000.phased_block.sizes

# Plot output_05.assembly_02.100_20000.phased_block.bed
Rscript /usr/local/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 
Loading required package: argparse
Loading required package: ggplot2
Loading required package: scales
Error in read.table(dat, header = F) : no lines available in input
Calls: block_n -> attach_n -> read.table
Execution halted