Error when running

[JennyCNS]

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)

         number of   cumulative   cumulative     presence
          distinct     fraction     fraction   in dataset

frequency kmers distinct total (1e-6)

I do not really know how to solve the issue!

Many thanks, Jenny

[arangrhie]

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

[arangrhie]

Closing this for now as well. Please use meryl v1.4.1 release..!