missing make_plot output

[gdanetzk]

I'm wondering where is make_plot written to by default? I did not specify arguments for --output or --tax since I was fine with the default directory names. I expected the plot to be located in output, but alas it is not. It also does not appear in my working directory, and does not appear in taxonomy_assignments.

[liberjul]

Hi Kristi, when --make_plot is specified, it should output a file called TaxonomicAssignmentComparison_plot.pdf to the folder specified with -o/--output. I just tested it with the lastest version and seems to work as expected on my end. Can you upload the job script which you have tried using?

Thanks,
Julian

[gdanetzk]

Here are the arguments I used:

constax
--num_threads $SLURM_CPUS_PER_TASK
--mem $SLURM_MEM_PER_NODE
--db /mnt/home/gdanetzk/unite_db_10.05.2021/sh_general_release_dynamic_euk_10.05.2021.fasta
--train
--trainfile /mnt/home/gdanetzk/constax2
--input /mnt/home/gdanetzk/SundinLab/Wilson_ITS/rep_set_lib1_fungi_otus.fasta
--pathfile /mnt/home/gdanetzk/constax2/pathfile.txt
--blast
--sintax_path /mnt/research/rdp/public/thirdParty/usearch10.0.240_i86linux64
--rdp_path /mnt/home/gdanetzk/anaconda3/pkgs/rdptools-2.0.3-hdfd78af_1/bin/classifier
--constax_path /mnt/home/gdanetzk/anaconda3/envs/CONSTAX2/opt/constax-2.0.16-0
--high_level_db /mnt/home/gdanetzk/unite_db_10.05.2021/sh_general_release_dynamic_euk_10.05.2021.fasta
--high_level_query_coverage=60
--high_level_percent_identity=40
--conf 0.7
--output /mnt/home/gdanetzk/SundinLab/Wilson_ITS/high_level_out2
--tax /mnt/home/gdanetzk/SundinLab/Wilson_ITS/high_level_tax2
--make_plot