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/src/snp_searching.c: line 185 Code: if(child_sequence[i] != '-' || child_sequence[i] != 'N') probably && operator necessary

maddin200

Why is Gubbins 2.3.1 so slow?

10

Hi I have 116 Whole genomes that I initially ran through ParSNP and now I'm running through Gubbins to remove recombination. I am just curious why it is taking so...

slvrshot

Test failure on i386: ""No usable version of RAxML could be found."

1

Hi, the Debian packaged gubbins has trouble to use RaXML. As you can see in the [complete build log](https://buildd.debian.org/status/fetch.php?pkg=gubbins&arch=i386&ver=2.4.1-1&stamp=1579695492&raw=0) it runs into ====================================================================== ERROR: test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction) ---------------------------------------------------------------------- Traceback (most recent...

tillea

Python deprecation warnings with 3.8

1

Hello, shout out if you prefer patches. The dendropy one is not your immediate business - anyway. Regards, Steffen ``` gubbins/python/gubbins/common.py:537: DeprecationWarning: invalid escape sequence \d elif re.match('^\d', vcf_line) is...

smoe

Dear Colleagues, Happy new year to everyone. I successfully run gubbins on the alignment of a number of genomes. I obtained a gff file with the coordinates of the recombination...

aliabenkahla

Hi sir Sorry that bother you again, since I am very new bioinformatic user. I have attempt to construct the ML tree of two chromosome bacteria. I split chr1 and...

Rathanin-github

failed while running raxml internal sequence reconstruction gubbins

2

I get the following error, the sequences are all of decent quality, I'm running gubbins installed through conda. What is the issue?

samlipworth

snippy-clean_full_aln did not replace --- by N

3

Hi @tseemann I have re-run snippy of short read (R1 and R2) against reference genome. after running snippy core, I got a core.full.aln that contain "----". I use snippy-clean_full_aln to...

Rathanin-github

how gubbins consider "-" or "n" character of input alignment file

1

Hi, how gubbins manage "-" or "n" character of input alignment file, they will be ignored or considered as 5th different base like "ATCG"? Thank you in advance!

zhaoxvwahaha

gubbins and parsnp

1

Hello, I am aware of the incompatibility of using gubbins on SNP alignments or on the core-gene-alignment from roary. However I am wondering whether we can use gubbins on the...

rpatnav