odp

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In this case, it only makes sense to shuffle the genome of the organism being tested as the sister clade to the other two. This is testing specifically that the...

conchoecia

Give the option to provide a gff or gtf file instead of a .chrom.

conchoecia

Unexpected keyword retries in rule definition (odp, line 294)

2

Hi conchoecia, Thank you for developing this nice pipeline. I have a problem after I installed the software and run the test example. snakemake --cores 10 -p --snakefile ../../scripts/odp SyntaxError...

LittleFrogHill

MissingInputException in line 289 of .../scripts/odp: Missing input files for rule n_ways_reciprocal_best:

1

Hiya! I've been trying to run ODP, and am successfully generating the ALG plots, however whenever I try to run the #plot_sp_sp: True to generate synteny plots, I get this...

piamer

hmmsearch --incE 1E-5 --tblout odp/step0-blastp_results/BCnSSimakov2022_against_Csch.hmmsearch --cpu 8 --noali --notextw /Share/user/dzw/software/odp/LG_db/BCnSSimakov2022/BCnSSimakov2022.hmm odp/db/Csch_prots.pep > /dev/null

1

I used my own data to test it before and found that this error was reported. Later, I downloaded the data from NCBI and processed it with a script to...

dzwzs

Hi, I had a few problems getting this to run on my M1 mac with python 3.11.5, but with a few changes, I think it's all worked okay now. 1)...

madeleineaaseremedios

Hi, great work on this pipeline, I'm really enjoying playing around with it. I came across a strange error when running the odp_nway_rbh script, where some chromosomes in the assembly...

tbrown91

I have successfully run odp_nway_rbh and obtained the results. However, I want to customize the color and chromosome order of the image. How can I customize the drawing directly through...

hhzhao713

Error running test again

2

Hi: I ran the test_odp_basic, and I got an error in job 16 (unfortunately I didn't save it). I tried to run it again but I get the following error...

aebaci