Thanks for the major update of the Freebayes wrapper, excellent! I've run into two issues, however. 1) When using "set allelic scope" I get the following error: Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ? 2) When using a vcf file as input I get the following error: Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests? -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
Lance: Here is github URL: https://github.com/nekrut/freebayes On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons <lparsons@princeton.edu> wrote:
Thanks for the major update of the Freebayes wrapper, excellent!
I've run into two issues, however.
1) When using "set allelic scope" I get the following error:
Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ?
2) When using a vcf file as input I get the following error:
Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz
I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests?
-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Anton Nekrutenko Associate Professor Dept. of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>* (814) 826-3051
Il 2014-06-30 18:40 Anton Nekrutenko ha scritto:
Lance:
Here is github URL:
https://github.com/nekrut/freebayes [3]
On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons <lparsons@princeton.edu [4]> wrote:
Thanks for the major update of the Freebayes wrapper, excellent!
I've run into two issues, however.
1) When using "set allelic scope" I get the following error:
Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ?
This bug (and other 2) would be fixed by this pull request: https://github.com/nekrut/freebayes/pull/1 Best, Nicola
2) When using a vcf file as input I get the following error:
Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz
I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests?
-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ [1]
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ [2]
--
Anton Nekrutenko Associate Professor Dept. of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu [5] (814) 826-3051
Links: ------ [1] http://lists.bx.psu.edu/ [2] http://galaxyproject.org/search/mailinglists/ [3] https://github.com/nekrut/freebayes [4] mailto:lparsons@princeton.edu [5] http://nekrut.bx.psu.edu
participants (3)
-
Anton Nekrutenko -
Lance Parsons -
Nicola Soranzo