pan-genome-analysis
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neherlab
Processing pipeline for pan-genome visulization and exploration
I have a question. Most genome assemblies from ncbi are now available as gbff files. I am running into an issue where 2,124 genomes of a bacteria (Strep pyogenes) fail...
Hi, I runned the command-line ./panX.py -fn /.data/MyData -sl T_species Everything seemed good till step 6 I think... Now this step is running for 10 minutes. I only have 5...
Hello, I am attempting to run panX on a dataset of 82 genomes from a single family of Alphaproteobacteria. Using the divide and conquer strategy, my command reads as follows:...
Hi, I have used PanX successfully a few month ago. Now that i have migrated on ubuntu 18.04, i tried to reinstall it via git clone then conda install, but...
Hi, I would kindly ask for some assistance. I tried panX with 22 genomes of a marine bacteria downloaded from Patric server (files downloaded as gto and converted to gbk...
Hi, What I am reporting is still ongoing issue since I noticed a few months ago. I attached system log below. Traceback (most recent call last): File "/home/Program/pan-genome-analysis/panX.py", line 256,...
Traceback (most recent call last): File "./panX.py", line 287, in myPangenome.process_clusters() File "/home/Project2/pan-genome-analysis/scripts/pangenome_computation.py", line 163, in process_clusters strain_list=self.strain_list, AttributeError: pangenome instance has no attribute 'strain_list' I want to use strain's...
(panX) anna@Anna-PC:~/work/pan-genome-analysis$ sudo sh run-TestSet.sh Traceback (most recent call last): File "./panX.py", line 6, in from pangenome_computation import pangenome File "/home/anna/work/pan-genome-analysis/scripts/pangenome_computation.py", line 16, in from sf_gain_loss import process_gain_loss File "/home/anna/work/pan-genome-analysis/scripts/sf_gain_loss.py",...
Hello guys, how r u? I'm having a problem with step08. I get the following error message: ``` ====== starting step08: run fasttree and raxml for tree construction fasttree time-cost:...
Hello, I wanted to look at protein presence-absence of a broader group of genomes (several different orders from alpha-proteobacteria). Would you say it's possible with panX, or should I just...
