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liberjul / CONSTAXv2

MIT License
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missing make_plot output #6

Open gdanetzk opened 2 years ago

gdanetzk commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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