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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Loading data #6

Open jiffen opened 6 years ago

jiffen commented 6 years ago

Hi Brian I did following command and it give me following error. All the databases and --gene_trans_map are there in the working directory. How to resolve it?

-bash-4.2$ /usr/local/bin/Trinotate-v3.1.1/Trinotate Trinotate.sqlite --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep usage: /usr/local/bin/Trinotate-v3.1.1/Trinotate [...]

: * Initial import of transcriptome and protein data: init --gene_trans_map --transcript_fasta --transdecoder_pep * Transdecoder protein search results: LOAD_swissprot_blastp LOAD_pfam LOAD_tmhmm LOAD_signalp * Trinity transcript search results: LOAD_swissprot_blastx LOAD_rnammer * Load custom blast results using any searchable database LOAD_custom_blast --outfmt6 --prog --dbtype * report generation: report [ -E (default: 1e-5) ] [--pfam_cutoff DNC|DGC|DTC|SNC|SGC|STC (default: DNC=domain noise cutoff)] Error, do not recognize command: --gene_trans_map
brianjohnhaas commented 6 years ago

Hi,

You need to put 'init' before the --gene_trans_map

best,

~b

On Sun, Sep 9, 2018 at 8:23 PM jiffen notifications@github.com wrote:

Hi Brian I did following command and it give me following error. All the databases and --gene_trans_map are there in the working directory. How to resolve it?

-bash-4.2$ /usr/local/bin/Trinotate-v3.1.1/Trinotate Trinotate.sqlite --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep usage: /usr/local/bin/Trinotate-v3.1.1/Trinotate [...] :

-

Initial import of transcriptome and protein data: init --gene_trans_map --transcript_fasta --transdecoder_pep

Transdecoder protein search results:

      LOAD_swissprot_blastp <file>
      LOAD_pfam <file>
      LOAD_tmhmm <file>
      LOAD_signalp <file>

-

  Trinity transcript search results:

      LOAD_swissprot_blastx <file>
      LOAD_rnammer <file>

  -

  Load custom blast results using any searchable database
  LOAD_custom_blast --outfmt6 --prog <blastp|blastx> --dbtype
  <database_name>
  -

  report generation:

      report [ -E (default: 1e-5) ] [--pfam_cutoff DNC|DGC|DTC|SNC|SGC|STC (default: DNC=domain noise cutoff)]

Error, do not recognize command: --gene_trans_map

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--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas