VAPID run error

[sekhwal]

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 all_virus.fasta rndm_assembly.fasta template.sbt error:

metadata not found in provided .csv or .csv not created - time for minimal manual entry for sequence - 1 Traceback (most recent call last): File "/VAPiD-master/vapid.py", line 958, in metadata, coverage, full_name_list[x] = do_meta_data(virus_strain_list[x], True, full_name_list[x]) File "/home/mmk6053/Bcov_new/rndm-reads/vapid_run/VAPiD-master/vapid.py", line 863, in do_meta_data col = ' [collection-date=' + raw_input('Enter collection date in the format (23-Mar-2005, Mar-2005, or 2005): ').strip() + ']' NameError: name 'raw_input' is not defined

[rcs333]

Hi!

This is a problem running the python 2 version on python 3. Instead try python vapid3.py ...

Hopefully this works for you and happy annotating!

Ryan

[sekhwal]

I am trying python vapid3.py. Also, I generated the index files of my genome fasta file using makeblastdb. However, it still showing following error.

running command:

python /VAPiD-master/vapid3.py --db all_virus.fasta rndm_assembly.fasta template.sbt --metadata_loc metadata.csv

---

BLAST Database error: No alias or index file found for nucleotide database [all_virus.fasta] in search path [/Bcov_new/rndm-reads/vapid_run::] Traceback (most recent call last): File "/VAPiD-master/vapid3.py", line 968, in strain2species[virus_strain_list[x]] = annotate_a_virus(virus_strain_list[x], virus_genome_list[x], File "/VAPiD-master/vapid3.py", line 634, in annotate_a_virus name_of_virus, our_seq, ref_seq, ref_accession, need_to_rc = blast_n_stuff(strain, strain + SLASH + strain + '.fasta') File "/VAPiD-master/vapid3.py", line 186, in blast_n_stuff record = Entrez.read(Entrez.esearch(db='nucleotide', term=ref_seq_gb)) UnboundLocalError: local variable 'ref_seq_gb' referenced before assignment