-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_8876761-9097440

-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 GlimmerHMM_glimmerT_4243-T1
Valid prediction for GlimmerHMM_glimmerT_4222-T1
Valid prediction for snap_scaffold_2-snap.1754-T1
Valid prediction for GlimmerHMM_glimmerT_4237-T1
Valid prediction for snap_scaffold_2-snap.1774-T1
Valid prediction for Augustus_model.g2842.t1
Valid prediction for GlimmerHMM_glimmerT_4242-T1
Valid prediction for HiQ_model.g2856.t1
Valid prediction for Augustus_model.g2844.t1
Valid prediction for snap_scaffold_2-snap.1745-T1
Valid prediction for snap_scaffold_2-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_4229-T1
Valid prediction for GlimmerHMM_glimmerT_4240-T1
Valid prediction for snap_scaffold_2-snap.1781-T1
Valid prediction for snap_scaffold_2-snap.1767-T1
Valid prediction for snap_scaffold_2-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_4228-T1
Valid prediction for GlimmerHMM_glimmerT_4230-T1
Valid prediction for pasa_asmbl_24661.p1
Valid prediction for Augustus_model.g2851.t1
Valid prediction for snap_scaffold_2-snap.1758-T1
Valid prediction for snap_scaffold_2-snap.1747-T1
Valid prediction for GlimmerHMM_glimmerT_4244-T1
Valid prediction for Augustus_model.g2861.t1
Valid prediction for Augustus_model.g2858.t1
Valid prediction for Augustus_model.g2846.t1
Valid prediction for snap_scaffold_2-snap.1768-T1
Valid prediction for snap_scaffold_2-snap.1751-T1
Valid prediction for GlimmerHMM_glimmerT_4221-T1
Valid prediction for Augustus_model.g2859.t1
Valid prediction for GlimmerHMM_glimmerT_4241-T1
Valid prediction for Augustus_model.g2860.t1
Valid prediction for snap_scaffold_2-snap.1757-T1
Valid prediction for CodingQuarry_transcript_28633-T1
Valid prediction for GlimmerHMM_glimmerT_4224-T1
Valid prediction for snap_scaffold_2-snap.1741-T1
Valid prediction for GlimmerHMM_glimmerT_4226-T1
Valid prediction for snap_scaffold_2-snap.1740-T1
Valid prediction for snap_scaffold_2-snap.1777-T1
Valid prediction for Augustus_model.g2845.t1
Valid prediction for snap_scaffold_2-snap.1770-T1
Couldn't classify 78046, 78088
Sorry, prediction pasa_asmbl_24659.p1 fails validation.
(CAT)	 AC	78046-78088	GC	GGG
(ATG)	 AG	78216-79699	GT	TGG
(AAA)	 AG	79816-79852	GT	AGG
(GAC)	 AG	79948-80033	TC	AGT
add_exon() Sorry, pasa_asmbl_24659.p1 78216-79699-initial-1 is invalid.
-recovered pasa_asmbl_24659.p1, initial, 78216, 79699
-recovered pasa_asmbl_24659.p1, terminal, 79948, 80033
-recovered pasa_asmbl_24659.p1, internal, 78216, 79699
-recovered pasa_asmbl_24659.p1, internal, 79816, 79852
Valid prediction for snap_scaffold_2-snap.1763-T1
Valid prediction for snap_scaffold_2-snap.1756-T1
Valid prediction for Augustus_model.g2852.t1
Valid prediction for snap_scaffold_2-snap.1738-T1

-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 snap_scaffold_2-snap.1778-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4223-T1
Valid prediction for snap_scaffold_2-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_4238-T1
Valid prediction for snap_scaffold_2-snap.1759-T1
Valid prediction for snap_scaffold_2-snap.1773-T1
Valid prediction for snap_scaffold_2-snap.1775-T1
Valid prediction for Augustus_model.g2847.t1
Valid prediction for GlimmerHMM_glimmerT_4239-T1
Valid prediction for Augustus_model.g2843.t1
Valid prediction for pasa_asmbl_23349.p1
Valid prediction for Augustus_model.g2849.t1
Valid prediction for snap_scaffold_2-snap.1739-T1
Valid prediction for snap_scaffold_2-snap.1744-T1
Valid prediction for Augustus_model.g2850.t1
Valid prediction for GlimmerHMM_glimmerT_4236-T1
Valid prediction for GlimmerHMM_glimmerT_4235-T1
Valid prediction for GlimmerHMM_glimmerT_4232-T1
Valid prediction for snap_scaffold_2-snap.1776-T1
Valid prediction for snap_scaffold_2-snap.1769-T1
Valid prediction for Augustus_model.g2855.t1
Valid prediction for GlimmerHMM_glimmerT_4234-T1
Valid prediction for GlimmerHMM_glimmerT_4231-T1
Valid prediction for snap_scaffold_2-snap.1746-T1
Valid prediction for GlimmerHMM_glimmerT_4227-T1
Valid prediction for Augustus_model.g2853.t1
Valid prediction for snap_scaffold_2-snap.1742-T1
Valid prediction for snap_scaffold_2-snap.1752-T1
Valid prediction for snap_scaffold_2-snap.1749-T1
Valid prediction for snap_scaffold_2-snap.1780-T1
Valid prediction for snap_scaffold_2-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_4220-T1
Valid prediction for snap_scaffold_2-snap.1748-T1
Valid prediction for snap_scaffold_2-snap.1750-T1
Valid prediction for Augustus_model.g2854.t1
Valid prediction for snap_scaffold_2-snap.1765-T1
Couldn't classify 212427, 212586
Couldn't classify 216357, 216558
Sorry, prediction pasa_asmbl_23347.p1 fails validation.
(GAC)	 AG	212427-212586	GT	AGG
(ACT)	 AG	212792-212921	GT	TGG
(GTC)	 AG	214073-214207	GT	CTG
(ATT)	 AG	216357-216558	AC	CCA
-recovered pasa_asmbl_23347.p1, internal, 212427, 212586
-recovered pasa_asmbl_23347.p1, internal, 212792, 212921
-recovered pasa_asmbl_23347.p1, internal, 214073, 214207
Valid prediction for snap_scaffold_2-snap.1779-T1
Valid prediction for GlimmerHMM_glimmerT_4219-T1
Valid prediction for snap_scaffold_2-snap.1761-T1
Valid prediction for snap_scaffold_2-snap.1753-T1
Valid prediction for Augustus_model.g2848.t1
Valid prediction for snap_scaffold_2-snap.1760-T1
Valid prediction for snap_scaffold_2-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_4225-T1
Valid prediction for snap_scaffold_2-snap.1764-T1
Valid prediction for Augustus_model.g2841.t1
Valid prediction for Augustus_model.g2857.t1
Valid prediction for GlimmerHMM_glimmerT_4233-T1
Valid prediction for snap_scaffold_2-snap.1755-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7236, rend_intergenic: 3790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14560, rend_intergenic: 11221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18543, rend_intergenic: 15792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29861, rend_intergenic: 26965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33697, rend_intergenic: 31599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44292, rend_intergenic: 37928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58299, rend_intergenic: 54646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58881, rend_intergenic: 58508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118931, rend_intergenic: 114443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131228, rend_intergenic: 120749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132656, rend_intergenic: 132077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139124, rend_intergenic: 133144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154475, rend_intergenic: 144001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158610, rend_intergenic: 155684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180246, rend_intergenic: 158735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209985, rend_intergenic: 188167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216374, rend_intergenic: 213266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220680
-exon list size: 659


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 7236, rend_intergenic: 3790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14560, rend_intergenic: 11221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18543, rend_intergenic: 15792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29861, rend_intergenic: 26965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33697, rend_intergenic: 31599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44292, rend_intergenic: 37928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58299, rend_intergenic: 54646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58881, rend_intergenic: 58508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118931, rend_intergenic: 114443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131228, rend_intergenic: 120749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132656, rend_intergenic: 132077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139124, rend_intergenic: 133144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154475, rend_intergenic: 144001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158610, rend_intergenic: 155684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180246, rend_intergenic: 158735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209985, rend_intergenic: 188167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216374, rend_intergenic: 213266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support