running VAPiD throws IndexError: list index out of range

[anajung]

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 more matches is recommended
KJ473815.1 was the selected reference
BtRs-BetaCoV/GX2013, was the parsed name of the virus
Aligning reference and query...
Traceback (most recent call last):
  File "vapid3.py", line 969, in <module>
    meta_list[x], coverage_list[x], sbt_file_loc, full_name_list[x],nuc_acid_type)
  File "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 "vapid3.py", line 253, in blast_n_stuff
    if '_R_' in ali_list[1]:
IndexError: list index out of range

It would be great to receive assistance on this, thanks!
-Ana

[rcs333]

Hi Ana,

I think I've seen this one before but it has been a while. If it's not too much trouble can you upload the sequence you are trying to annotate and the version of vapid you are using?

Ryan

[anajung]

Hi Ryan,

Thank you for the prompt reply.
I am using vapid3.py v1.6.7.
Github does not seem to accept fasta format files so I am attaching it as a text file.

WUSTL_000226_A131.consensus.fa.txt

Ana

[rcs333]

Okay I took a look at your sequence on my computer.

The command

python3 vapid3.py WUSTL_000226_A131.fasta example.sbt --r MW938189.1

Produces the error free and correctly annotated result I've attached.
WUSTL_000226_A131.gbf.txt

The problem is almost certainly a missing dependency, and I'm pretty sure for you it's maafft. Please verify you are you able to run the example test files.

python3 vapid3.py example.fasta example.sbt

If you're sure you've got mafft correctly installed zip the entire output folder and send it to me.