spectra-cn plots and QV stats not generating

[LaurenHuet]

Hello,

I'm having some issues getting any output from Merqury.

I'm working with Illumina data.
I built the meryl database with the following code (in a nextflow workflow)

meryl k=21 count output '${reads[0].baseName}.meryl' ${reads[0]}
meryl k=21 count output '${reads[1].baseName}.meryl' ${reads[1]}
meryl union-sum output '${sample_id}.meryl' '${reads[0].baseName}.meryl' '${reads[1].baseName}.meryl'
meryl histogram '${sample_id}.meryl' > '${sample_id}.meryl.hist'

I'm now using this database with a bash script to try and generate the QV results

sample=$1
rundir=$2
meryl_db="$rundir/$sample/kmers"
assembly="$rundir/$sample/assemblies/genome/$sample.v129mh.fna"
merq_dir="$rundir/$sample/assemblies/genome/merqury"

mkdir -p "$merq_dir"

Run merqury

singularity run $SING/merqury:1.3.sif merqury.sh "$meryl_db/*.meryl" $assembly $merq_dir/$sample.merqury 2>&1 | tee $merq_dir/$sample.merqury.log

and am getting the following error

read: AbuSept_212878_F15-955.ilmn.10X.meryl

No haplotype dbs provided.
Running Merqury in non-trio mode...

asm1: AbuSept_212878_F15-955.ilmn.10X.v129mh.fna
out : /scratch/pawsey0812/lhuet/subsample_project/subsample10X/AbuSept_212878_F15-955.ilmn.10X/assemblies/genome/merqury/AbuSept_212878_F15-955.ilmn.10X.merqury

Get spectra-cn plots and QV stats
/usr/local/bin/merqury.sh: line 71: logs//scratch/pawsey0812/lhuet/subsample_project/subsample10X/AbuSept_212878_F15-955.ilmn.10X/assemblies/genome/merqury/AbuSept_212878_F15-955.ilmn.10X.merqury.spectra-cn.log: read: AbuSept_212878_F15-955.ilmn.10X.meryl

No haplotype dbs provided.
Running Merqury in non-trio mode...

asm1: AbuSept_212878_F15-955.ilmn.10X.v129mh.fna
out : /scratch/pawsey0812/lhuet/subsample_project/subsample10X/AbuSept_212878_F15-955.ilmn.10X/assemblies/genome/merqury/AbuSept_212878_F15-955.ilmn.10X.merqury

Get spectra-cn plots and QV stats
/usr/local/bin/merqury.sh: line 71: logs//scratch/pawsey0812/lhuet/subsample_project/subsample10X/AbuSept_212878_F15-955.ilmn.10X/assemblies/genome/merqury/AbuSept_212878_F15-955.ilmn.10X.merqury.spectra-cn.log: No such file or directory

There is no output generated into the folder i provide either.

Both meryl and merqury are being run from the same singularity container using Version 1.3

I can't seem to figure out why its looking for the .spectra-cn.log prior to generating it?

[arangrhie]

Hello @LaurenHuet ,

Can you link your assembly with a .fasta suffix, and run Merqury in your output directory?
The "No such file or directory" message is shown because the path does not exist.
Merqury assumes you are running it inside the 'output' directory, and creates the log file as a sub dir.

Perhaps something like this might work:

cd $merq_dir
ln -s $assembly AbuSept_212878_F15-955.ilmn.10X.v129mh.fasta
asm=AbuSept_212878_F15-955.ilmn.10X.v129mh.fasta
singularity run $SING/merqury:1.3.sif merqury.sh "$meryl_db/*.meryl" $asm $sample.merqury 2>&1 | tee logs/$sample.merqury.log

Best,
Arang