Hello,
I would like to use KSNP4 but all the files I enter are rejected. I made fasta files with Shovill (contigs), than built a data file…
Thanks in advance
Hi @VROUX
It is hard to guess without seeing the data. You are welcome to share your work for community feedback. How to is in the banner, also here:
Let’s start there, thanks! 
Hello,
Thank you to answer.
I uploaded the illumina files ant assembled them with shovill or A5 pipeline to obtained contigs. I renamed the files SAUR01.fasta, SAUR06.fasta and SAUR11.fasta. I built a dataset list, I named ST398. I tried to used MakeFasta.
But: Une erreur est survenue avec ce jeu de données: can’t open scaffold_0 for reading. No such file or directory at makeFasta.pl line 181.
MakeKSNPinfile: I entered my dataset list. It was OK.
KSNP: I entered the file obtained from MakeKSNPinfile, k-mer size 20, ref SAUR01.fasta. I obtained only result in SNPs_all
If : do full annotations, calculate core SNPs and core parsimony tree, estimate maximum likelihood tree, generate VCF, yes selected
Une erreur est survenue avec ce jeu de données:
fasta_list: /afs/galaxy/database/files/001/302/dataset_1302984.dat Output directory: /afs/galaxy/database/jobs_directory/000/729/729503/working/outdir Error: Unrecognized argument (no valid argument: /afs/galaxy/database/files/001/303/dataset_1303000.dat
display with IGV local
Thank you for your help,
VROUX
Hi @VROUX
As a guess, errors like this
can indicate one of these problems:
-
A mismatch between the input files. Meaning, data in one file is not labeled the same was as in another file. For this case, this could be how the fasta
>title lines are formatted. Or if the data is in a collection folder, how the element identifiers are formatted. You could modify and simplify these formats across all inputs. If a sequence is labeled a certain way in one file, then all files need to have the same sequence labeled that same way. -
A problem with the tool as installed on the server where you are working. This is something the administrators would address. Sending in a bug report is one way to directly report it.
We can try to help to determine which is going on with your runs. The link you shared is to a local IGV display. Instead, try sharing the Galaxy history itself. The FAQ I linked above explains how to generate the link. You can post it back here, then unshare once we are done.
Thanks!