Open shanmugavadivelps opened 2 years ago
Hey there,
I originally built this only for human viruses so that is why AP010907 is not in the local database. I would try using the -f command to specify a local .gbf file to annotate your submission.
I recommend downloading the AP010907.gbf file from genbank (It will download with the name sequence.gb so I like to rename them right away).
Then try running the command:
python vapid3.py your_file.fasta template.sbt -f AP010907.gbf
Let me know if you have difficulties with this step or if this does not fix the problem!
Ryan
Thanks sir for reply and help
I have done as you said but it failed. the command and output is given below for your reference
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 --f /home/shanmu/VAPiD-master/all_virus/AP010907.gbf
Output:
Warning: [blastn] Examining 5 or more matches is recommended
Error: NCBI C++ Exception:
T0 "/opt/conda/conda-bld/blast_1595737360567/work/blast/c++/src/corelib/ncbiobj.cpp", line 981: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
Stack trace:
/home/shanmu/anaconda3/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x5D addr=0x7f1274fff29d
/home/shanmu/anaconda3/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CStackTrace::CStackTrace(std::cxx11::basic_string<char, std::char_traits
Traceback (most recent call last):
File "vapid3.py", line 968, in
should i make blast database with makeblastdb?
Shoot, well I haven't seen the error you pasted ever before. I haven't really tested VAPiD on non-human viruses so I'm not surprised weird stuff is happening.
Yeah, adding your reference to the blast database with the makeblastdb command is a good thing to try next.
If you upload the file you're trying to annotate I can take a look at it. If you don't want to publicly upload it to github you can email it to ryanshean1@gmail.com. I think if I can see your input I might get a better idea of why this happening.
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 (AP010907.1) in .nhr and .nin files/databases but it was not available.
when I run the command, it throws an error like below.
AP010907.1 was the selected reference Traceback (most recent call last): File "vapid3.py", line 968, in
strain2species[virus_strain_list[x]] = annotate_a_virus(virus_strain_list[x], virus_genome_list[x],
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 210, in blast_n_stuff
print(name_of_virus + ' was the parsed name of the virus')
UnboundLocalError: local variable 'name_of_virus' referenced before assignment
what to do if the selected reference are not available in .nin and .nhr?
pls help me to solve the issue