gubbins

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mask_gubbins_aln.py issue

2

Hi, I have problems running mask_gubbins_aln.py and get an error saying: Traceback (most recent call last): File "mask_gubbins_aln.py", line 71, in taxon.seq = MutableSeq(taxon.seq) File "/opt/rh/rh-python36/root/usr/lib64/python3.6/site-packages/Bio/Seq.py", line 1663, in __init__...

Dangoh

generate_ska_alignment.py problem

2

Hi，I prepared fastq-list files as follows JSAHVC01R1 /home/work/APECSRA/JSAHVC01R1.fastq JSAHVC01R2 /home/work/APECSRA/JSAHVC01R2.fastq JSAHVC02R1 /home/work/APECSRA/JSAHVC02R1.fastq JSAHVC02R2 /home/work/APECSRA/JSAHVC02R2.fastq JSAHVC03R1 /home/work/APECSRA/JSAHVC03R1.fastq JSAHVC03R2 /home/work/APECSRA/JSAHVC03R2.fastq JSAHVC04R1 /home/work/APECSRA/JSAHVC04R1.fastq JSAHVC04R2 /home/work/APECSRA/JSAHVC04R2.fastq JSAHVC05R1 /home/work/APECSRA/JSAHVC05R1.fastq JSAHVC05R2 /home/work/APECSRA/JSAHVC05R2.fastq JSAHVC06R1 /home/work/APECSRA/JSAHVC06R1.fastq JSAHVC06R2 /home/work/APECSRA/JSAHVC06R2.fastq,...

aslangabriel

Hi, Thank you for the amazing tool to filter recombination regions. May I kindly check, if the reference base in the vcf file is created based on the consensus from...

ramadatta

Run has already reached the number of specified iterations

3

My runs were interrupted on the final iteration, but when I try to resume the run I get "Run has already reached the number of specified iterations." The intermediate files...

nicolettacommins

Description of extensive-search mode?

1

I'm not able to find in the manual a description of what is happening in the extensive-search mode? Could the developers provide a quick explanation about what exactly is different...

nicolettacommins

Running raxML without -AVX2 options

8

Hi, I keep getting the error below when running gubbins Illegal instruction (core dumped) Command 'raxmlHPC-PTHREADS-AVX2 -T 4 -safe -m GTRGAMMA -s core.full.aln.snp_sites.aln -n core.full.iteration_1_reconstruction -t /home/ubuntu/slm/gubbins/tmp382_i35u/core.full.iteration_1.tre.rooted -f e -w...

slmiles

mask_gubbins_aln.py

3

Hi， When I used mask_gubbins_aln.py to mask recombination regions: `python ~/.conda/envs/gubbins-env/bin/mask_gubbins_aln.py --aln clean.full.aln --gff gubbins.recombination_predictions.gff --out clean.full.masked.aln` It called an error: `~/.conda/envs/gubbins-env/lib/python3.9/site-packages/Bio/Seq.py:1754: BiopythonDeprecationWarning: myseq.tomutable() is deprecated; please use MutableSeq(myseq) instead....

xuechunxu

RaxML fails -- Empirical base frequency for state number 2 is equal to zero in DNA data partition No Name Provided

3

Hi, I have some identical sequences in my input fasta but still would like to keep them in my analysis and run gubbins. I have the following error in regards...

ramadatta

Gubbins tree scale?

10

Hello, I'm having some trouble understanding the tree scale that is output in the newick formatted tree by Gubbins. Specifically, branch lengths in this tree are on the order of...

cizydorczyk

Gubbinsv3.1.4 hash symbol # to dash symbol _

2

Gubbins v3.1.4 is omitting hash symbol `#` to dash symbol `_` when trimming alignment files from SKA etc., which should be fine as long as other upstream inputs, for instance,...

drxilu