-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_1713227-1862144

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.104076_t
Valid prediction for GeneMark_model.104090_t
Valid prediction for GeneMark_model.104057_t
Valid prediction for GeneMark_model.104079_t
Valid prediction for Augustus_model.g39678.t1
Valid prediction for Augustus_model.g39680.t1
Valid prediction for GlimmerHMM_glimmerT_59599-T1
Valid prediction for GeneMark_model.104052_t
Valid prediction for Augustus_model.g39669.t1
Valid prediction for GeneMark_model.104080_t
Valid prediction for GlimmerHMM_glimmerT_59624-T1
Valid prediction for snap_scaffold_28-snap.419-T1
Valid prediction for snap_scaffold_28-snap.403-T1
Valid prediction for snap_scaffold_28-snap.409-T1
Valid prediction for snap_scaffold_28-snap.411-T1
Valid prediction for Augustus_model.g39663.t1
Valid prediction for snap_scaffold_28-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_59610-T1
Valid prediction for GeneMark_model.104074_t
Valid prediction for Augustus_model.g39666.t1
Valid prediction for snap_scaffold_28-snap.432-T1
Valid prediction for snap_scaffold_28-snap.427-T1
Valid prediction for GeneMark_model.104072_t
Valid prediction for GlimmerHMM_glimmerT_59620-T1
Valid prediction for GlimmerHMM_glimmerT_59614-T1
Valid prediction for GlimmerHMM_glimmerT_59619-T1
Valid prediction for snap_scaffold_28-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_59609-T1
Valid prediction for Augustus_model.g39667.t1
Valid prediction for GeneMark_model.104092_t
Valid prediction for GeneMark_model.104101_t
Valid prediction for snap_scaffold_28-snap.412-T1
Valid prediction for Augustus_model.g39665.t1
Valid prediction for Augustus_model.g39675.t1
Valid prediction for GlimmerHMM_glimmerT_59608-T1
Valid prediction for snap_scaffold_28-snap.441-T1
Valid prediction for GeneMark_model.104085_t
Valid prediction for GeneMark_model.104059_t
Valid prediction for Augustus_model.g39672.t1
Valid prediction for GeneMark_model.104088_t
Valid prediction for GeneMark_model.104089_t
Valid prediction for GeneMark_model.104068_t
Valid prediction for snap_scaffold_28-snap.430-T1
Valid prediction for GeneMark_model.104082_t
Valid prediction for GeneMark_model.104050_t
Valid prediction for snap_scaffold_28-snap.437-T1
Valid prediction for snap_scaffold_28-snap.398-T1
Valid prediction for GeneMark_model.104097_t
Valid prediction for snap_scaffold_28-snap.404-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.400-T1
Valid prediction for GeneMark_model.104061_t
Valid prediction for GlimmerHMM_glimmerT_59615-T1
Valid prediction for GeneMark_model.104055_t
Valid prediction for Augustus_model.g39677.t1
Valid prediction for GeneMark_model.104094_t
Valid prediction for snap_scaffold_28-snap.402-T1
Valid prediction for GeneMark_model.104063_t
Valid prediction for GlimmerHMM_glimmerT_59605-T1
Valid prediction for snap_scaffold_28-snap.429-T1
Valid prediction for Augustus_model.g39664.t1
Valid prediction for GlimmerHMM_glimmerT_59601-T1
Valid prediction for Augustus_model.g39670.t1
Valid prediction for GeneMark_model.104099_t
Valid prediction for GlimmerHMM_glimmerT_59598-T1
Valid prediction for GlimmerHMM_glimmerT_59622-T1
Valid prediction for GlimmerHMM_glimmerT_59602-T1
Valid prediction for GlimmerHMM_glimmerT_59617-T1
Valid prediction for GlimmerHMM_glimmerT_59606-T1
Valid prediction for Augustus_model.g39673.t1
Valid prediction for snap_scaffold_28-snap.435-T1
Valid prediction for GeneMark_model.104077_t
Valid prediction for GlimmerHMM_glimmerT_59603-T1
Valid prediction for snap_scaffold_28-snap.418-T1
Valid prediction for GeneMark_model.104044_t
Valid prediction for snap_scaffold_28-snap.408-T1
Valid prediction for GeneMark_model.104095_t
Valid prediction for GlimmerHMM_glimmerT_59613-T1
Valid prediction for snap_scaffold_28-snap.416-T1
Valid prediction for GeneMark_model.104070_t
Valid prediction for snap_scaffold_28-snap.401-T1
Valid prediction for GeneMark_model.104056_t
Valid prediction for GeneMark_model.104065_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for Augustus_model.g39681.t1
Valid prediction for GeneMark_model.104096_t
Valid prediction for GlimmerHMM_glimmerT_59623-T1
Valid prediction for snap_scaffold_28-snap.440-T1
Valid prediction for snap_scaffold_28-snap.424-T1
Valid prediction for Augustus_model.g39676.t1
Valid prediction for snap_scaffold_28-snap.434-T1
Valid prediction for snap_scaffold_28-snap.431-T1
Valid prediction for GeneMark_model.104045_t
Couldn't classify 147232, 147428
Couldn't classify 148591, 148750
Sorry, prediction pasa_asmbl_37336.p1 fails validation.
(CCT)	 CA	147232-147428	GT	AGG
(ATA)	 AG	148591-148750	GG	CAG
Valid prediction for Augustus_model.g39674.t1
Valid prediction for GeneMark_model.104098_t
Valid prediction for snap_scaffold_28-snap.433-T1
Valid prediction for GeneMark_model.104083_t
Valid prediction for GlimmerHMM_glimmerT_59625-T1
Valid prediction for GeneMark_model.104047_t
Valid prediction for GlimmerHMM_glimmerT_59597-T1
Valid prediction for GeneMark_model.104053_t
Valid prediction for GeneMark_model.104049_t
Valid prediction for snap_scaffold_28-snap.439-T1
Valid prediction for GeneMark_model.104081_t
Valid prediction for GlimmerHMM_glimmerT_59611-T1
Valid prediction for snap_scaffold_28-snap.423-T1
Valid prediction for GeneMark_model.104062_t
Valid prediction for GlimmerHMM_glimmerT_59618-T1
Valid prediction for GeneMark_model.104102_t
Valid prediction for GlimmerHMM_glimmerT_59596-T1
Valid prediction for Augustus_model.g39668.t1
Valid prediction for snap_scaffold_28-snap.399-T1
Valid prediction for GeneMark_model.104100_t
Valid prediction for GeneMark_model.104066_t
Valid prediction for GlimmerHMM_glimmerT_59621-T1
Valid prediction for GlimmerHMM_glimmerT_59600-T1
Valid prediction for Augustus_model.g39671.t1
Valid prediction for GlimmerHMM_glimmerT_59616-T1
Valid prediction for GeneMark_model.104093_t
Valid prediction for snap_scaffold_28-snap.438-T1
Valid prediction for GeneMark_model.104069_t
Valid prediction for snap_scaffold_28-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_59595-T1
Valid prediction for snap_scaffold_28-snap.417-T1
Valid prediction for GeneMark_model.104054_t
Valid prediction for GeneMark_model.104091_t
Valid prediction for GeneMark_model.104060_t
Valid prediction for snap_scaffold_28-snap.415-T1
Valid prediction for GeneMark_model.104071_t
Valid prediction for Augustus_model.g39662.t1
Valid prediction for GeneMark_model.104086_t
Valid prediction for snap_scaffold_28-snap.420-T1
Valid prediction for snap_scaffold_28-snap.414-T1
Valid prediction for snap_scaffold_28-snap.405-T1
Valid prediction for snap_scaffold_28-snap.406-T1
Valid prediction for snap_scaffold_28-snap.436-T1
Valid prediction for GlimmerHMM_glimmerT_59627-T1
Valid prediction for snap_scaffold_28-snap.426-T1
Valid prediction for snap_scaffold_28-snap.410-T1
Valid prediction for GeneMark_model.104067_t
Valid prediction for GlimmerHMM_glimmerT_59626-T1
Valid prediction for GlimmerHMM_glimmerT_59607-T1
Valid prediction for snap_scaffold_28-snap.442-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.104073_t
Valid prediction for snap_scaffold_28-snap.428-T1
Valid prediction for snap_scaffold_28-snap.413-T1
Valid prediction for Augustus_model.g39679.t1
Valid prediction for GeneMark_model.104051_t
Valid prediction for GeneMark_model.104078_t
Valid prediction for GeneMark_model.104075_t
Valid prediction for GlimmerHMM_glimmerT_59612-T1
Valid prediction for GeneMark_model.104064_t
Valid prediction for GeneMark_model.104058_t
Valid prediction for GeneMark_model.104046_t
Valid prediction for snap_scaffold_28-snap.407-T1
Valid prediction for GeneMark_model.104084_t
Valid prediction for GeneMark_model.104048_t
Valid prediction for snap_scaffold_28-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_59604-T1
Valid prediction for GeneMark_model.104087_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16091, rend_intergenic: 11550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41465, rend_intergenic: 36822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46767, rend_intergenic: 44644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59775, rend_intergenic: 53766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94364, rend_intergenic: 88133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111263, rend_intergenic: 110372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115646, rend_intergenic: 112709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134006, rend_intergenic: 131200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147678, rend_intergenic: 144603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148918
-exon list size: 721


building trellis

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-found 52 predictions from path traversal
Error with prediction: snap lend_intergenic: 16091, rend_intergenic: 11550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41465, rend_intergenic: 36822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46767, rend_intergenic: 44644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59775, rend_intergenic: 53766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94364, rend_intergenic: 88133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111263, rend_intergenic: 110372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115646, rend_intergenic: 112709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134006, rend_intergenic: 131200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147678, rend_intergenic: 144603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support