call-short-variants 'does not exist'

[S-ES]

Hi ! I would like to report this issue : gkno_launcher apple$ ./gkno pipe call-short-variants

Usage: gkno pipe [options]

 <pipeline name>:
      align-pe:                      Align paired-end fastq files using Mosaik.
      align-pe-special:              Align fastq files using Mosaik. In this version additional 'special'
                                     reference sequences are included (usually mobile element insertions)
                                     in the reference.
      align-se:                      Align single-end fastq files using Mosaik (additional processing
                                     steps included).
      align-se-special:              Align single-end fastq files using Mosaik. In this version
                                     additional 'special' reference sequences are included (usually
                                     mobile element insertions) in the reference.
      bam-tangram:                   Build Mosaik reference files and align fastq files using Mosaik
                                     (additional processing steps included).
      build-moblist-reference:       Concatenate reference fasta files and generate Mosaik reference and
                                     jump database.
      fastq-short-variants:          Starting from fasta and fastq files, prepare MOSAIK reference files,
                                     align reads and call short variants.
      fastq-tangram:                 Starting from fasta and fastq files, prepare MOSAIK reference files,
                                     align reads and search for mobile element insertions (MEIs).
      jellyfish-get-fasta-hashes:    Generate hashes for a reference fasta.
      mei-confirm:                   Check MEI calls using local graph alignment.
      merge-bam:                     Merge together all bam files for a sample and mark duplicate reads.
      run-test:                      Test pipeline to ensure proper operation.
      simulation:                    Simulate reads from one reference, then align reads to a different
                                     reference.
      simulation-call:               Simulate reads from one reference, then align reads to a different
                                     reference and search for short variants.

 The following pipelines have been identified as experimental, so should be used with caution:

      rufus:                         Compare parent and mutant strains..

 The following pipelines have malformed configuration files, so are currently unusable:

      detect-mei:                    Starting from fasta and fastq files, prepare MOSAIK reference files,
                                     align reads and search for mobile element insertions (MEIs).

Additional messages

ERROR: Requested pipeline 'call-short-variants' does not exist. Check available pipelines in usage above.

[pezmaster31]

You're right - no pipeline with that name exists. Maybe you're looking for fastq-short-variants?

[S-ES]

Not really, because I am starting with bam files, instead of fastq/fasta files.. If I am not wrong, this pipe existed and was previously functioning..

[pezmaster31]

Ah, I see. @AlistairNWard will be able to help with more specific pipe/tool info when he sees this. Sorry I'm not much help in the meantime.

• Derek

[AlistairNWard]

You're right that the pipeline doesn't exist. This is might fault for not pulling down old tutorials from the website. We no longer use some of the tools that appear in older pipelines, due to improvements in the calling software themselves. As such, some of these older pipelines are no longer what we would consider suitable for modern analysis. I am putting together a newer version of the pipeline that omits some of the tools we no longer consider necessary. I'll have it up in an hour or two.

On Thu, Jun 5, 2014 at 4:09 PM, Derek Barnett notifications@github.com wrote:

Ah, I see. @AlistairNWard https://github.com/AlistairNWard will be able to help with more specific pipe/tool info when he sees this. Sorry I'm not much help in the meantime.

• Derek

— Reply to this email directly or view it on GitHub https://github.com/gkno/gkno_launcher/issues/14#issuecomment-45267825.

[AlistairNWard]

Ok, I have put a new version of call-short-variants up. Please update to version 1.24.0. This pipeline takes one or more BAM files and a region or list of regions. See the tutorial http://blog.gkno.me/post/87905883290/using-lists-for-command-line-arguments for instructions on parallelizing freebayes across multiple regions. If multiple BAM files are given, the specified regions from each file are merged then streamed to a tool that tries to improve placement of gaps in low entropy regions of the genome. This is then streamed to Freebayes for calling. The final regions are merged together to provide a single VCF file which is then compressed using gzip.

If you wish to modify any of the arguments for Freebayes, please use the syntax:

gkno pipe call-short-variants [options] --freebayes [--argument ...]

I will add freebayes arguments as pipeline arguments soon and I'll also get the tutorial updated to reflect the modified pipeline and how best to use it.

[AlistairNWard]

Apologies, I meant Version 1.25.0.

[S-ES]

Many thanks !!

I will try them according to your comments.

Thanks again