Comments (3)
Hi,
The tool looks for them in the working directory, so if the files are not in 'FASTA/' where you execute PPanGGOLiN, it will not find them. Looking at where you are executing PPanGGOLiN, they are in testingDataset/FASTA/.
If you put yourself in 'testingDataset/' and then run 'ppanggolin workflow --fasta organisms.fasta.list' it should work nicely.
For your personnal usage, using absolute paths in the 'organisms.fasta.list' file is probably better, this is what I usually do with my own data.
Adelme
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Thank you @axbazin for your prompt response, now it works well. I have another query, Is it possible to work on viral pangenome analysis with this ppanggolin tool?
from ppanggolin.
Great !
Originally it was designed for Archaea and Bacteria only, but another group managed to reconstruct pangenomes of phages / plasmids with PPanGGOLiN (see https://www.biorxiv.org/content/10.1101/2020.11.09.375378v1 ), so it is possible.
Beware however that the annotation tool used by ppanggolin is prodigal, so it may not be adapted to viruses and you might want to use your own annotations (--anno option rather than --fasta option for the input files, and using gff or gbff files instead of fasta files)
And parameters were chosen for bacterial species pangenomes so you might want to adapt the parameters as well, however I lack knowledge in viral genomics to know what would or would not be good there.
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Related Issues (20)
- Non-deterministic clustering (possibly due to defragmentation) HOT 11
- Attribute error drawing plots HOT 1
- Discrepancy between # of genes in RGPs? HOT 1
- Rarefaction curves_No Heaps calculation HOT 5
- RGP drawn in spot figure is incorrect HOT 3
- Locus tag missing from projection file HOT 2
- Gbk files HOT 4
- ppanggolin draw --spots all don't create plots for all spots HOT 6
- Projection file returns spots for genes not in RGPs HOT 3
- Ignore genes during clustering HOT 2
- Comparing core genomes HOT 7
- Exception: The gene family has not beed associated to a partition HOT 2
- Install bug HOT 2
- TypeError: invalid type (<class 'str'>) for column ``organism`` HOT 4
- RGP fasta HOT 6
- Missing genes in the projection.tsv files HOT 2
- Error since update to 2.0 HOT 7
- Cannot Import GeneFinder from Pyrodigal since update HOT 4
- invalid type <class 'str'> for column product HOT 5
- Written error core families sequences HOT 1
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