arangrhie
commented
11 months ago Hi @JennyCNS,
Sorry, somehow I missed this. Is Merqury the latest version on github? There is no v1.4 release yet :)
Besides, I'd advice not to use homopolymer compressed kmers for evaluating non-compressed genome assemblies.
I made the -c option available only for experimental purposes - to check the spectra-cn plots in compressed space.
QV will be generated, however is not reliable.
Best, Arang
Hello,
I am using v1.4 of both merqury and meryl and I get an error after merging the output files.
the command I run is:
$MERQURY/eval/spectra-cn.sh -c merged.hamour.meryl fEpiCoi_cnag1_curated_primary.no_mt.fa test1
the error I get is:
Can't interpret 'fEpiCoi_cnag1_curated_primary.no_mt.0.meryl': not a meryl command, option, or recognized input file. /home/jnascime/merqury/eval/spectra-cn.sh: line 118: -: syntax error: operand expected (error token is "-") No asm2_fa given. Done. Found test1.spectra-asm.hist
Plot test1.spectra-asm.hist
Rscript /home/jnascime/merqury/plot/plot_spectra_cn.R -f test1.spectra-asm.hist -o test1.spectra-asm -z test1.dist_only.hist Loading required package: argparse Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘argparse’ Loading required package: ggplot2 Loading required package: scales Error in ArgumentParser(description = "Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be generated.") : could not find function "ArgumentParser" Execution halted
Clean up
rm: cannot remove ‘read.k.fEpiCoi_cnag1_curated_primary.no_mt.0.meryl’: No such file or directory rm: cannot remove ‘read.k.fEpiCoi_cnag1_curated_primary.no_mt.meryl’: No such file or directory Done! (merqury) [jnascime@login02(eddie) meryl-output]$ mv fEpiCoi_cnag1_curated_primary.no_mt.0.meryl/ fEpiCoi_cnag1_curated_primary.no_mt.meryl mv: cannot stat ‘fEpiCoi_cnag1_curated_primary.no_mt.0.meryl/’: No such file or directory
I tried the statistics option
(merqury) [jnascime@login02(eddie) meryl-output]$ meryl statistics merged.hamour.meryl/ | head
Found 1 command tree. Number of 20-mers that are: unique 5887771867 (exactly one instance of the kmer is in the input) distinct 7677571429 (non-redundant kmer sequences in the input) present 53880823950 (...) missing 1091834056347 (non-redundant kmer sequences not in the input)
frequency kmers distinct total (1e-6)
I do not really know how to solve the issue!
Many thanks, Jenny