Error in f(...) : Graphics API version mismatch

[ksc289]

Hi!! :) I'm trying to run merqury but I can't obtain all the results. Could you help me please? I'm following the steps:

Step 1. Create meryl db:

/opt/merqury-1.3/meryl count k=21 output /path/to/read-db.meryl /path/to/reads.fastq

Step 2. Run merqury:

/opt/merqury/merqury.sh ./read-db.meryl final_assembly.fa ./merqury_analysis

I get these results: ls -lsa total 16528 4 drwxrwxrwx 6 karen_bioinfo karen_bioinfo 4096 jun 5 13:02 . 4 drwxrwxr-x 8 karen_bioinfo karen_bioinfo 4096 may 30 10:58 .. 4 drwxrwxr-x 2 karen_bioinfo karen_bioinfo 4096 jun 5 12:43 logs 0 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 0 jun 5 13:01 merqury_analysis.completeness.stats 4 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 34 jun 5 13:02 merqury_analysis.dist_only.hist 4 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 63 jun 5 13:00 merqury_analysis.qv 2168 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 2217598 jun 5 13:02 merqury_analysis.spectra-asm.hist 4 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 19 jun 5 13:00 merqury_analysis.yahs.out_scaffolds_final.only.hist 32 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 31196 jun 5 13:01 merqury_analysis.yahs.out_scaffolds_final.qv 884 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 897773 jun 5 13:00 merqury_analysis.yahs.out_scaffolds_final.spectra-cn.hist 12 drwxrwxr-x 2 karen_bioinfo karen_bioinfo 12288 may 30 15:44 meryl_db 4 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 2 jun 5 12:43 meryl_db.filt 4 drwxrwxr-x 2 karen_bioinfo karen_bioinfo 4096 jun 5 12:43 meryl_db.gt0.meryl 0 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 0 jun 5 12:43 meryl_db.hist 4 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 28 jun 5 12:43 meryl_db.hist.ploidy 0 lrwxrwxrwx 1 karen_bioinfo karen_bioinfo 30 jun 5 12:43 yahs.out_scaffolds_final.fa -> ../yahs.out_scaffolds_final.fa 12 drwxrwxr-x 2 karen_bioinfo karen_bioinfo 12288 jun 5 12:57 yahs.out_scaffolds_final.meryl 6900 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 7061688 jun 5 13:01 yahs.out_scaffolds_final_only.bed 6480 -rw-rw-r-- 1 karen_bioinfo karen_bioinfo 6631630 jun 5 13:01 yahs.out_scaffolds_final_only.wig

I'm not getting all the results. Part of the log that the program provides me indicates the following: PROCESSING TREE #1 using 128 threads. opIntersect meryl_db yahs.out_scaffolds_final.meryl output to read.k21.yahs.out_scaffolds_final.meryl

Cleaning up.

Bye.

Found 1 command tree.

Found 1 command tree.

Found 1 command tree. Loading required package: argparse Loading required package: ggplot2 Loading required package: scales Error in f(...) : Graphics API version mismatch Calls: spectra_cn_plot -> save_plot -> ggsave -> dev -> png_dev -> f In addition: Warning message: Using ragg device as default. Ignoring type and antialias arguments Execution halted rm: cannot remove 'meryl_db.gt.meryl': No such file or directory

Thanks!!

[arangrhie]

Hello,

If you installed merqury via conda, that version does not understand .fa. You could try the latest version in the main branch here (download, set $MERQURY) and re run it in your conda environment, or simply rename your fa to fasta and try again. I'd recommend to use the latest meryl release + latest version of Merqury on this github repo. Meryl DBs are compatible, no need to re-generate those.

Thanks, Arang

[ksc289]

Thank you very much for the help. I have reinstalled merqury with conda and meryl (latest versions) and it worked! Greetings, Karen