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Parsnp: Error creating Gingr input file

3

I'm getting an error with Parsnp at the last step creating the Gingr input file: chaconas@chaconas-X10DRi:~/Programs/Parsnp-Linux64-v1.2$ ./parsnp -d /home/chaconas/Desktop/Projects/RDVParsnpTrial/References/GenomesAndContigs/ -g /home/chaconas/Desktop/Projects/RDVParsnpTrial/Queries/11-282_06052015.gbk -P 30000000 |--Parsnp v1.2--| For detailed documentation please see...

verheytb

Using parsnp with a draft reference

4

Hi, I'd like to use parsnp with the genbank option on, but my reference is a draft genome. Is this a problem for parsnp or can it handle the situation?...

mgroussi

parsnp ignores file called "1.fasta"

1

Interesting 'bug'. I had a sequence file called '1.fasta' and parsnp persistently ignored it from the alignment until I renamed it 1_seq.fasta. parsnp -c -p 30 -d seqs/ -o26 -r...

tallnuttcsiro

parsnp consider - in contig names as gaps

1

When the name of a contig contains dashes, parsnp identifies them as gaps and produce the following error: "ERROR: ref genome sequence %s seems to aligned! remove and restart" Even...

jgugliel

ignoring sequences ending with the same numbers as the reference genome

1

I noticed this odd little bug in parsnp v1.2. When running parsnp using the -c -d options and a reference ending with numbers, genomes that have names that are contained...

aldertzomer

I try to run parsnp (downloaded binay) on my Manjaro (a flavour of Archlinux) laptop but the program fails with the following error: ``` $ parsnp -r ./0.0_ref/Scedosporium_apiospermum.ScApio1_0.31.dna.toplevel.fna -p 6...

lduvaux

The default font sizes are too small when using gingr to visualize alignments on hidpi displays. Is it possible to specify a custom font or font size when starting gingr?

hvbakel

Dear Dr. Treangen, Here's a simple bug. If parsnp is run with both -c and -M, it crashes. The output is below. Once I realized that -c could be incompatible...

adam-lab

Generating a whole genome POA

10

Hi Guys I'd like to be able to take a Harvest core genome MSA + the non-core bits that were cut out, and make a partial order alignment. i.e. I'd...

iqbal-lab

Question

1

Hi- Is there a way to create an alignment with parsnp/harvesttools that includes the unaligned sequences in addition to the core sequences? I have 99% coverage in my genome alignments...

gotero