Panseq

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Hi, I am trying to use Panseq for 7 fungal genomes of 30 Mb on HPC. The allocated memory was 80GB and analysis failed due to memory limit. I can't...

Zuanira

Hi Chad, I've coded Panseq so to output locus name and snp position (per the reference) to the end of each row of the snp_table.txt output. With many genomes core_snps.txt...

moorembioinfo

I ran the following perl script perl /apps/eb/Panseq/3.2.1-foss-2019b-Perl-5.30.0/lib/treeNumberToName.pl out/snp.phylip out/phylip_name_conversion.txt > out_tree Gives the following error Could not match 1 Could not match 2 Could not match 3 Could not...

ga23981

Hi there, I am having trouble getting Panseq to work. I reinstalled and tried to run perl Build.PL but get the following error. ``` WARNING: the following files are missing...

kenscripts

Hi, managed to execute the tool to detect unique regions. however the output files i obtained are incomplete compared to the descriptions in the readme. seems like it is incomplete...

azam17

unexpected char in string error

4

Hi Chad, I'm trying to run panseq on some publically available genomes, and was successful when running the genomes from a subspecies. As soon as I included two other subspecies,...

ChristyPeterson

loci_selector.pl

1

Hello while runnig loci_selector.pl I have a bunch of warnings it was runn with pan_genome_2.3.0.txt from test data ``` Use of uninitialized value in concatenation (.) or string at /local/gensoft2/exe/Panseq/3.2.1/lib/perl5/Modules/LociSelector/LociSelector.pm...

EricDeveaud

"UPDATE: Readme now includes optional instructions on how to install panseq with Conda"

jamez-eh

jamez-eh

Minimum length of scaffolds?

4

Hello, I was wondering if there is a minimum length requirement for scaffolds somewhere hard-coded in the program? I performed a test where I compared the length of genomes before...

MrOlm