findSpanin (v3.1) Apollo

StepAnnotation
Step 1: Unknown Tool with id 'edu.tamu.cpt2.webapollo.export'
Step 2: Get open reading frames (ORFs) or coding sequences (CDSs)
Output dataset 'fasta_out' from step 1
11. Bacterial
Look for ORFs (check for stop codons only, ignore start codons)
30
Search both the forward and reverse strand
Step 3: Unknown Tool with id 'edu.tamu.cpt2.webapollo.fetch_jbrowse'
Step 4: GFF3 Add Gene to CDS
Output dataset 'out_gff3_file' from step 2
Step 5: GFF3 Filter: Require Phage Start
From History
Output dataset 'fasta_out' from step 1
Output dataset 'output' from step 4
Step 6: Gff3 Filter: Require SD
From History
Output dataset 'fasta_out' from step 1
Output dataset 'stdout' from step 5
Step 7: GFF3 Feature Sequence Export
From History
Output dataset 'fasta_out' from step 1
Output dataset 'stdout' from step 6
CDS
True
Step 8: Identify Lipoboxes
Output dataset 'stdout' from step 6
Output dataset 'fasta_out' from step 1
10
60
Step 9: Fasta Translate
Output dataset 'default' from step 7
Protein
[11] The Bacterial, Archaeal and Plant Plastid Code
True
False
Step 10: NCBI BLAST+ blastp
Output dataset 'default' from step 9
Locally installed BLAST database
nr_2019.6
Empty.
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
BLAST XML
Hide Advanced Options
Step 11: TMHMM (GFF3)
Output dataset 'default' from step 9
Step 12: Rebase GFF3 features
Output dataset 'stdout' from step 6
Output dataset 'output' from step 11
False
True
ID
Step 13: Intersect
Output dataset 'default' from step 12
Output dataset 'default' from step 8
Step 14: Remove Annotation Feature
Output dataset 'oa' from step 13
True
True

No value found for 'Remove 'region' features'. Using default: 'True'.
Step 15: Remove Annotation Feature
Output dataset 'ob' from step 13
True
True

No value found for 'Remove 'region' features'. Using default: 'True'.
Step 16: Unknown Tool with id 'jbrowse-cpt'
Step 17: Unknown Tool with id 'edu.tamu.cpt2.webapollo.create_or_update'