Hi,
Hope you're doing well.
Thank you for your previous response. The previous issue has been successfully resolved, and I have obtained my phylogenetic tree. However, my leaf nodes cannot fully display my MAGs (some are missing). When I checked the log file, I found this kind of error: "Not enough markers (93/100) found in "/ifs1/User/leiyu/metagenome/Binning_dir/10GTDBtk/Phylophlan/tmp/map_aa/DG23_bin.18.b6o.bz2". After searching online and modifying my script, the problem still persists. Below is my modified script:
phylophlan
-i /ifs1/User/leiyu/metagenome/Binning_dir/112_AA_seq
-t a
-d phylophlan
--diversity medium
-f /ifs1/User/leiyu/biosoft/phylophlan/supermatrix_aa.cfg
--nproc 20
-o /ifs1/User/leiyu/metagenome/Binning_dir/10_GTDBtk/Phylophlan1/
--min_num_markers 45
--proteome_extension .pep
echo "Job End at date"
I originally thought that "--min_num_markers 45" could solve my problem, but the issue still persists, and the number of missing MAGs remains the same before and after adding "--min_num_markers 45". I used Prodigal to predict the protein sequences of the MAGs and built a phylogenetic tree based on the protein sequences. Could you please help me address the above issues?
Hi, Hope you're doing well. Thank you for your previous response. The previous issue has been successfully resolved, and I have obtained my phylogenetic tree. However, my leaf nodes cannot fully display my MAGs (some are missing). When I checked the log file, I found this kind of error: "Not enough markers (93/100) found in "/ifs1/User/leiyu/metagenome/Binning_dir/10GTDBtk/Phylophlan/tmp/map_aa/DG23_bin.18.b6o.bz2". After searching online and modifying my script, the problem still persists. Below is my modified script:
!/bin/bash
echo "Job Start at date"
source ~/mambaforge/bin/activate /ifs1/User/leiyu/mambaforge/envs/phylophlan
phylophlan -i /ifs1/User/leiyu/metagenome/Binning_dir/112_AA_seq -t a -d phylophlan --diversity medium -f /ifs1/User/leiyu/biosoft/phylophlan/supermatrix_aa.cfg --nproc 20 -o /ifs1/User/leiyu/metagenome/Binning_dir/10_GTDBtk/Phylophlan1/ --min_num_markers 45 --proteome_extension .pep
echo "Job End at date"
I originally thought that "--min_num_markers 45" could solve my problem, but the issue still persists, and the number of missing MAGs remains the same before and after adding "--min_num_markers 45". I used Prodigal to predict the protein sequences of the MAGs and built a phylogenetic tree based on the protein sequences. Could you please help me address the above issues?
Looking forward to your reply. cheers