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

When running a normalization function from the Vt tools ( 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
Traceback (most recent call last):
  File "/home/mat29/Desktop/FinalReadyPythonSoftwareFeb13-2017/", line 128, in normvcf
    execute('bash ./')
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/", line 166, in execute
    return execute_prepared(ExternalCommand(*command, **options))
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/", line 195, in execute_prepared
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/", line 1113, in start
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/", line 1156, in wait
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/", line 1274, in check_errors
    raise self.error_type(self)
executor.ExternalCommandFailed: External command failed with exit code 1! (command: bash -c 'bash ./')

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

sequencing vttools ngs wgs vcf • 1.5k views
ADD COMMENTlink modified 3.8 years ago by WouterDeCoster44k • written 3.8 years ago by genome2110

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

ADD REPLYlink written 3.8 years ago by Pierre Lindenbaum131k

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

ADD REPLYlink written 3.8 years ago by Devon Ryan97k

Hello genome21!

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


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.


ADD REPLYlink written 3.8 years ago by Michael Dondrup48k
Please log in to add an answer.
The thread is closed. No new answers may be added.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1213 users visited in the last hour