pan-genome-analysis
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neherlab
Processing pipeline for pan-genome visulization and exploration
Hi I encounter an error while running the next command line ./panX.py -fn ./data/Vibrio_complete -sl Vibrio_complete -dmdc -t 1 > Vibrio_complete.log The error follows as Traceback (most recent call last):...
Hi! I saw from the introduction that this software is designed for use by prokaryotes. We now want to do a simple mammalian diploid for pan-genomics research. I don’t know...
Hello, I can't get to visualize my Roary results with panX. Using the link-to-server.py scrpit, i tried giving it my roary results directory (as -s) and the absolute path to...
Hello, I got the recommendation to use this programs. But, when i use my file, I used this command `./panX.py -fn data/burk_sample -sl burkholderia -t 32` the error came. Running...
Hello I am teaching myself how to run panX using TestSet. Here is the command I run exactly following the instructions. ./panX.py -fn data/TestSet/ -sl TestSet -t 32 > TestSet.log...
Hi, Since yesterday panX visualization wont show the gene tree (individual gene) for data I've already analyzed and looked at with the visualization panel and that used to work fine....
I found an issue in the step 9 and I am not able to sort it out. The screenshots attached are of the .err and .log file. It will be...
hello, I am running panX with branch associations. I have a metadata.tsv file and a descriptive metainfo.tsv file. I keep getting this error on step 11: /beegfs/work/workspace/ws/fr_na50-panx-0/pan-genome-analysis/scripts/sf_association.py:188: RuntimeWarning: divide by...
The docs state to install miniconda2 instead of miniconda3. Python2 is depreciated and should be discouraged. If py2 is still needed for panx, then the user can create a py2...
Do you have guidance on how to run your workflow on new genomes not available on RefSeq. I am interested in producing the all_genes_alignment file shown on the PanX website....
