Question: (Closed) VT tools can`t input reference when attempting to normalize a VCF file
0
gravatar for genome21
2.2 years ago by
genome2110
genome2110 wrote:

When running a normalization function from the Vt tools (http://genome.sph.umich.edu/wiki/Vt) I have:

normalize v0.5

options:     input VCF file                                  DecomposedPilonReducedresult.vcf
         [o] output VCF file                                 VTPilonVCF.vcf
         [w] sorting window size                             10000
         [m] no fail on masked reference inconsistency       false
         [n] no fail on reference inconsistency              false
         [q] quiet                                           false
         [d] debug                                           false
         [r] reference FASTA file                            H37Rv_reference.fasta

[variant_manip.cpp:72 is_not_ref_consistent] failure to extract base from fasta file: AL123456:24697-24715
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
Traceback (most recent call last):
  File "/home/mat29/Desktop/FinalReadyPythonSoftwareFeb13-2017/Execute.py", line 128, in normvcf
    execute('bash ./norm.sh')
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 166, in execute
    return execute_prepared(ExternalCommand(*command, **options))
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 195, in execute_prepared
    command.start()
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1113, in start
    self.wait()
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1156, in wait
    self.check_errors(check=check)
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1274, in check_errors
    raise self.error_type(self)
executor.ExternalCommandFailed: External command failed with exit code 1! (command: bash -c 'bash ./norm.sh')

Does anybody know how to eliminate this errors and what are the reasons?

sequencing vttools ngs wgs vcf • 964 views
ADD COMMENTlink modified 2.2 years ago by WouterDeCoster38k • written 2.2 years ago by genome2110
4

Hi user 'gotohelldevon' ! .. sorry... user 'human_genomeXXX' ! :-)

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum118k
1

The link in the error message is surprisingly informative (hint, you're probably using the wrong fasta file).

ADD REPLYlink written 2.2 years ago by Devon Ryan89k

Hello genome21!

We believe that this post does not fit the main topic of this site.

WHYT?

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.2 years ago by Michael Dondrup46k
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