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core gene alignment looks like it aligns paralogs by accident

4

Hi, We are analyzing Mycobacteria isolated from cystic fibrosis patients and two patients are known to have infected each other (twins). For these two genomes isolated from these two patients...

pallevillesen

Hi, I got an error message saying: > 2020/08/26 23:40:29 Running command: protein_alignment_from_nucleotides -v pan_genome_sequences/proS.fa > 2020/08/29 12:26:05 Running command: prank -d=pan_genome_sequences/proS.fa -o=pan_genome_sequences/proS.fa.aln -codon -F -quiet -once > /dev/null 2>&1...

weishwu

Hi, I've used scoary to find gene present/absent in bacteria genomes. I found many genes recorded as "absent" in the gene_presence_absence.csv were actually present when I blastn the gene sequence...

meiym-012

Unique genes on query_pan_genome

1

Hi, I'm trying to separate my genomes into shared and unique genes between two groups, and while running query_pan_genome with the different parameters it seems to work. I get three...

reedus-123

Hi all, While I was installing Roary via: "cpanm Bio::Roary --force" I had an alert about a potential ransomware due to some systemic encryption activities. Is this normal? Thank you,...

casaburi

Illegal division by zero error

2

I am running roary on using following command roary -f ./demo -e -t 4 -p 10 -n *.gff and I got following errors 1-Use of uninitialized value in require at...

hafizmtalha

Could not open .proteome.faa

3

Hello, I had run Roary successfully once on some test data, but when I ran it using my main data, after running Roary for several hours I got this message:...

kashrest

query_pan_genome Multifasta

1

I'm querying my .gff files to pull out sequences for certain genes but it is giving me output in amino acids. I saw in a supplementary document that you can...

jhaendiges

Hi All, I have been running Roary to construct some pangenomes. I've git cloned and installed from source and have no idea why this might be. I have tried to...

RobLeighBioinformatics

dear Roary staff, I got this error, and I do not know how to fix it? 2020/05/21 11:31:15 Input files have identical MD5 hashes, only using the first file: /pbs/data/bis/test_massi/RfSara2/GFFS/17-71857-51644604.gff...

massiizsve