Pipeline job

demo_phage

DemoPhage synthetic mini sequence for Phase 0 harness testing

succeeded

Length228 bp

GC56.58%

Targetphage

Baseline ORFs2

Exports

JSON report ORF CSV Review CSV Proteins FASTA

Draft review queue

2 gene calls

Draft OK0

Check start0

Check boundary0

Needs evidence2

Phase 2 derives this queue from ORF length, start codons, and neighbor gaps/overlaps. BLAST/Pfam/tRNA evidence is still pending, so these are review prompts rather than final annotation calls.

tRNA evidence

Aragorn

No tRNAs were detected in this genome.

Predicted proteins

2 translated

Baseline ORFs translated to amino-acid sequences (download as FASTA above). These feed Pfam/BLAST evidence and are drafts, not final calls.

Pfam domain hits

unavailable

Pfam/HMMER is not configured on this worker yet. Install hmmscan and set PFAM_DB to a pressed Pfam-A.hmm for domain-based function hints. (Pfam/HMMER not configured: missing Pfam HMM DB (set PFAM_DB to a pressed Pfam-A.hmm).)

BLASTp function hints

unavailable

BLASTp is not configured on this worker. Set BLASTP_DB to a local curated phage protein DB, or PHAGEFLOW_REMOTE_BLAST=1 to use NCBI remote BLAST (slow, rate-limited; fine for class-scale volume). (BLASTp not configured: set BLASTP_DB to a local protein DB, or PHAGEFLOW_REMOTE_BLAST=1 to use NCBI remote BLAST.)

Review warnings

Sequence is 228 bp, which is much shorter than a typical complete phage genome.
Baseline ORFs are not final gene calls.
Compare against Glimmer/GeneMark/PHEONA and instructor review before accepting annotations.

Tool availability

blastninstalled

blastpinstalled

aragorninstalled

hmmscaninstalled

genemarkmissing

glimmer3missing

makeblastdbinstalled

trnascan_semissing

Baseline ORFs

six-frame start/stop ORF scan

ID	Strand	Frame	Start	End	Codons	Length
+1.1	+	1	10	114	ATG → TAA	34 aa
+1.2	+	1	124	228	ATG → TAG	34 aa

Review details

Phase 2 draft curation

Gene	ORF	Status	Coordinates	Flags	Decision	Note	Save
gene-001	+1.1ATG → TAA, 34 aa	needs evidence	10..114 (+1)adjacent/first	Short ORF (34 aa)
gene-002	+1.2ATG → TAG, 34 aa	needs evidence	124..228 (+1)9 nt gap	Short ORF (34 aa)