bpucker / myb_annotator Goto Github PK

Hi Pucker,
Thanks for this tool,
I was wondering, how log does it take it to complete a tetraploid plant genome with 120,000 genes?
My job with 32 cores has been running for almost 24 days and is yet to be completed.

It seems RAxML_tree.raxml construction takes longer, do you have any suggestions to get this sooner?

I'm currently at the - RAxML_tree.raxml.ckp and RESULTS/01_initial_candidates.pep.fasta completed sofar.

#---------cmd used------------------ python3 ${myb_path}/MYB_annotator.py \ --baits ${myb_path}/MYB_baits.fasta \ --info ${myb_path}/MYB_baits.txt \ --subject Bnapus_1N99.pep_20220722.fasta \ --cpu $NSLOTS \ --mode raxml \ --refmybs ${myb_path}/AthRefMYBs.txt \ --raxml /home/sap223/anaconda3/envs/myb/bin/raxml-ng \ --out ${out_dir}

Thanks for your help,
sam

When i used MYB_annotator to detect MYBs in Arabidopsis_thaliana.
I got a few number of 1R-MYBs. Does it normal?

Number of 1R-MYBs: 2
Number of R2R3-MYBs: 121
Number of 3R-MYBs: 5
Number of pseudo MYBs and unclassified ones: 5

The running code is:

python /data/chaofan/software/MYB_annotator-main/MYB_annotator.py  --baits /data/chaofan/software/MYB_annotator-main/MYB_baits.fasta --info /data/chaofan/software/MYB_annotator-main/MYB_baits.txt --out Arabidopsis_thaliana --subject Arabidopsis_thaliana.pep --refmybs /data/chaofan/software/MYB_annotator-main/AthRefMYBs.txt --raxml /data/chaofan/miniconda/bin/raxmlHPC --cpu 20

Hi! @bpucker

How could i get 1R-MYBs and MYB-like sequences using this pipeline? Do you have some advises? The 1R-MYBs and MYB-like sequences are very important to me.

Thank you for your reply!

--zcf