No resulting plots..

[kwiyounghan]

Hi,

I'm trying to use Merqury for assessing phased assembly produced by hifiasm using hifi reads and hic integrated data.
But I don't get any plots after Merqury run, and searching in google and this issue page doesn't seem to help. (I've looked at issue #51 No plots generated #51 , but it doesn't contain any answers that work for me)

What I did,
Step1. create meryl database
There are two files from two hifi runs from same library so

meryl k=19 count threads=32 output AL556_194_1_hifi_reads_19.meryl ../raw/AL556_194_1_hifi_reads.fastq  
meryl k=19 count threads=32 output AL556_194_2_hifi_reads_19.meryl ../raw/AL556_194_2_hifi_reads.fastq    

Step 2. Merge

 meryl union-sum threads=32 output AL556_194_12_19_combined.meryl AL556_194_1_hifi_reads_19.meryl AL556_194_2_hifi_reads_19.meryl

Step3. Merqury

asm_hap1=../00_assembly/hifiasm/AL556_194_12_hic_hifiasm.asm.hic.hap1.p_ctg.fa
asm_hap2=../00_assembly/hifiasm/AL556_194_12_hic_hifiasm.asm.hic.hap2.p_ctg.fa

$MERQURY/merqury.sh AL556_194_12_19_combined.meryl $asm_hap1 $asm_hap2 AL556_194_12_hic_hifiasm.asm.hic_hap12_19

But in the end there are no plots generated.
Information that I'm not sure relevant but from the other issue #51 might be:

• all my *.only.hist files contain two lines

 meryl statistics AL556_194_12_hic_hifiasm.asm.hic.hap1.p_ctg.meryl | head

Found 1 command tree.
Number of 19-mers that are:
  unique              364045140  (exactly one instance of the kmer is in the input)
  distinct            416942646  (non-redundant kmer sequences in the input)
  present             672465051  (...)
  missing          274460964298  (non-redundant kmer sequences not in the input)

             number of   cumulative   cumulative     presence
              distinct     fraction     fraction   in dataset
frequency        kmers     distinct        total       (1e-6)
--------- ------------ ------------ ------------ ------------

meryl statistics AL556_194_12_hic_hifiasm.asm.hic.hap2.p_ctg.meryl | head

Found 1 command tree.
Number of 19-mers that are:
  unique              330019187  (exactly one instance of the kmer is in the input)
  distinct            358808421  (non-redundant kmer sequences in the input)
  present             537132274  (...)
  missing          274519098523  (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'm using merqury from a conda environment, both merqury and meryl version 1.3
• I'm attaching the log file AL556_194_12_hic_hifiasm.asm.hic_hap12_19.spectra-cn.log

AL556_194_12_hic_hifiasm.asm.hic_hap12_19.spectra-cn.log

cheers,
kwi

[arangrhie]

Hello kwi,

It seems like the required packages aren't available on the conda version. :(
The required packages missing are argparse, ggplot2, and scale.
Ones the packages are installed, just executing the Rscript lines in the log should generate the plots.

I wonder if your cluster has an R module with no packages, which could cause this issue (relevant to #49).
Try replacing this line in your conda: /gxfs_home/geomar/smomw426/.conda/envs/mercury/share/merqury/util/util.sh (line 15) to

echo 1

Thanks,
Arang

[kwiyounghan]

HI Arang,

Thanks for your response!
Changing the line to "echo 1" solved the problem!!

best,
Kwi