Cannot run Topairy on my dataset.

[Akado2009]

Greetings. Looks like I have faced an issue that wasn't mentioned before. Having downloaded your tool, I began with running an example with my vcf as an input (it can be downloaded below). ./topiary --vcf input_1.vcf --mhc-predictor netmhcpan-iedb --mhc-alleles H-2-Kk --output-csv epitopes.csv Gives as an output the following message: ValueError: Unable to infer reference genome for input_1.vcf In one of the issues I found --reference-name, but now it is unrecognized arguments: --reference-name grch37. I have several version of reference genome in my cache, downloaded with pyensembl. Looking forward for any help. I might be doing something wrong. input_1.vcf.zip

[serge2016]

https://github.com/hammerlab/topiary/issues/11#issuecomment-273455885

[serge2016]

# topiary --vcf pat98.all.hc.fp-filtered.SV-filtered.Somatic.vcf --output-csv t1.csv --mhc-predictor netmhciipan-iedb --mhc-alleles "HLA-A02:01,HLA-B07:02" --mhc-epitope-lengths 8 --genome grch37
Topiary commandline arguments:
Namespace(genome='grch37', ic50_cutoff=None, json_variants=[], maf=[], mhc_alleles='HLA-A02:01,HLA-B07:02', mhc_alleles_file=None, mhc_epitope_lengths=[8], mhc_predictor='netmhciipan-iedb', only_novel_epitopes=False, output_csv='t1.csv', output_csv_sep=',', output_html=None, padding_around_mutation=None, percentile_cutoff=None, print_columns=False, rename_output_column=None, rna_gene_fpkm_tracking_file=None, rna_min_gene_expression=0.0, rna_min_transcript_expression=0.0, rna_transcript_fpkm_gtf_file=None, rna_transcript_fpkm_tracking_file=None, skip_variant_errors=False, subset_output_columns=None, variant=[], vcf=['pat98.all.hc.fp-filtered.SV-filtered.Somatic.vcf'], wildtype_ligandome_directory=None)
Traceback (most recent call last):
  File "/usr/local/bin/topiary", line 58, in <module>
    main(args)
  File "/usr/local/bin/topiary", line 43, in main
    epitopes = predict_epitopes_from_args(args)
  File "/usr/local/lib/python2.7/dist-packages/topiary/predict_epitopes.py", line 296, in predict_epitopes_from_args
    raise_on_variant_effect_error=not args.skip_variant_errors)
  File "/usr/local/lib/python2.7/dist-packages/topiary/predict_epitopes.py", line 263, in predict_epitopes_from_variants
    wildtype_ligandome_dict=wildtype_ligandome_dict)
  File "/usr/local/lib/python2.7/dist-packages/topiary/predict_epitopes.py", line 159, in predict_epitopes_from_mutation_effects
    binding_predictions = mhc_model.predict(protein_subsequences)
  File "/usr/local/lib/python2.7/dist-packages/mhctools/iedb.py", line 191, in predict
    response_df = _query_iedb(request, self.url)
  File "/usr/local/lib/python2.7/dist-packages/mhctools/iedb.py", line 127, in _query_iedb
    response = urlopen(req).read()
  File "/usr/lib/python2.7/urllib2.py", line 127, in urlopen
    return _opener.open(url, data, timeout)
  File "/usr/lib/python2.7/urllib2.py", line 410, in open
    response = meth(req, response)
  File "/usr/lib/python2.7/urllib2.py", line 523, in http_response
    'http', request, response, code, msg, hdrs)
  File "/usr/lib/python2.7/urllib2.py", line 448, in error
    return self._call_chain(*args)
  File "/usr/lib/python2.7/urllib2.py", line 382, in _call_chain
    result = func(*args)
  File "/usr/lib/python2.7/urllib2.py", line 531, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 500: INTERNAL SERVER ERROR
root@56febe96c255:/out#

pat98.all.hc.fp-filtered.SV-filtered.Somatic.zip.txt (remove .txt and unpack)

[iskandr]

Huh, I wonder if IEDB changed their service. Alternatively it just might be down.

@Akado2009 -- does this work if you instead use a local predictor?

[Akado2009]

@iskandr, thank you for you replie. Now I get another error, which I cant resolve. It occurs when using local predictor with the following command: ./topiary --vcf input_1.vcf --mhc-predictor netmhcpan-iedb --mhc-alleles H-2-Kk --output-csv epitopes.csv

So, I get: Topiary commandline arguments: Namespace(genome=None, ic50_cutoff=None, json_variants=[], maf=[], mhc_alleles='H-2-Kk', mhc_alleles_file=None, mhc_epitope_lengths=[8, 9, 10, 11], mhc_predictor='netmhcpan', only_novel_epitopes=False, output_csv='epitopes.csv', output_csv_sep=',', output_html=None, padding_around_mutation=None, percentile_cutoff=None, print_columns=False, rename_output_column=None, rna_gene_fpkm_tracking_file=None, rna_min_gene_expression=0.0, rna_min_transcript_expression=0.0, rna_transcript_fpkm_gtf_file=None, rna_transcript_fpkm_tracking_file=None, skip_variant_errors=False, subset_output_columns=None, variant=[], vcf=['input_1.vcf'], wildtype_ligandome_directory=None) Traceback (most recent call last): File "./topiary", line 58, in <module> main(args) File "./topiary", line 43, in main epitopes = predict_epitopes_from_args(args) File "/home/akado2009/.local/lib/python2.7/site-packages/topiary/predict_epitopes.py", line 275, in predict_epitopes_from_args mhc_model = mhc_binding_predictor_from_args(args) File "/home/akado2009/.local/lib/python2.7/site-packages/mhctools/cli/args.py", line 141, in mhc_binding_predictor_from_args epitope_lengths=epitope_lengths) File "/home/akado2009/.local/lib/python2.7/site-packages/mhctools/netmhc_pan.py", line 41, in NetMHCpan program_name, "--version", "3", File "/usr/lib/python2.7/subprocess.py", line 567, in check_output process = Popen(stdout=PIPE, *popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory