VAPiD

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VAPID run error

2

Hi, I have downloaded VAPiD-master folder and running VAPID with the following command, it shows following error. Please help me to figure out the error. run command: python /VAPiD-master/vapid.py --db...

sekhwal

nboundLocalError: local variable 'name_of_virus' referenced before assignment for Insect virus

3

Hi sir, I am using Vapid3 to annotate the insect virus following the command "python vapid3.py /media/shanmu/shanmu_data/Sanjay_Viral_whole_genome/denovo_with_reference_alignment_27th_Nov_2021/Final_for_paper/NNG1/NNG1_Picard_VirgenA/out_NNg1/ragtag_scaffold.fasta IIPR05_template.sbt --online --r AP010907.1" I have checked the availability of the reference virus...

shanmugavadivelps

running VAPiD throws IndexError: list index out of range

3

Hi Ryan, **I ran the command below** `python3 vapid3.py WUSTL_000226.consensus.fa template.sbt --spell_check --all` **But it throws this Error:** ``` Searching local blast database at all_virus.fasta Warning: [blastn] Examining 5 or...

anajung

Please help, I have problems

4

Hi everyone, Hope you'll help me. I uploaded VAPiD and all necessary modules. Unfortunately, I couldn't start. Here, the result with my own files. PS C:\Users\shank\PycharmProjects\BioPython_Tree\VAPiD> python vapid.py C:\Users\shank\PycharmProjects\BioPython_Tree\BioPython_Tree\data\Measles_FORT_L16.fasta ###...

ShankoAndrei

Is VAPiD suitble for metatranscriptome virus?

1

Is VAPiD suitble for metatranscriptome virus? Or only some special Virus?

zhaoxvwahaha

Spliced genes + ncRNAs

1

Hi Ryan, Great tool! I've been using it for a couple of side projects and seems to work great (python3 version). However, now I want to submit some human cytomegalovirus...

joanmarticarreras

How similar do inputs need to be?

3

Do you have a sense of how similar an input should be to the nearest available reference in NT? Is it more like 99% ANI or 90% ANI? I couldn't...

mtisza1

UnboundLocalError: local variable 'ref_seq_gb' referenced before assignment

1

Greetings, I keep running into an issue with ref_seq_gb. I'm working with potential viral regions, and using the All_virus blast db as is (No additional sequences added), have you ran...

Cerebro409

Hi, I would like to recommend you include a yaml file in the github directory to allow for easy installation of VAPiD. There's a number of dependencies, which I think...

ammaraziz

Hi, Thanks for creating vapid. I'm having a similar problem to issue #14 . However it's on a different line of code: ``` Searching local blast database at ref_seq_vir Traceback...

ammaraziz