diff 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"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_05_log.txt	Mon Apr 25 11:20:41 2022 +0000
@@ -0,0 +1,59 @@
+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 /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 
+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 /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 
+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
+