-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_9244978-9450086

-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 Augustus_model.g6430.t1
Couldn't classify 5282, 6408
Sorry, prediction pasa_asmbl_41606.p1 fails validation.
(GAT)	 CA	5282-6408	GT	AGG
(CCC)	 AG	9167-9674	AG	AAA
-recovered pasa_asmbl_41606.p1, terminal, 9167, 9674
Valid prediction for snap_scaffold_4-snap.1985-T1
Valid prediction for Augustus_model.g6443.t1
Valid prediction for GlimmerHMM_glimmerT_9916-T1
Valid prediction for snap_scaffold_4-snap.1940-T1
Valid prediction for Augustus_model.g6429.t1
Valid prediction for GlimmerHMM_glimmerT_9920-T1
Valid prediction for snap_scaffold_4-snap.1951-T1
Valid prediction for Augustus_model.g6428.t1
Valid prediction for snap_scaffold_4-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_9904-T1
Valid prediction for snap_scaffold_4-snap.1972-T1
Valid prediction for snap_scaffold_4-snap.1949-T1
Valid prediction for snap_scaffold_4-snap.1977-T1
Valid prediction for snap_scaffold_4-snap.1947-T1
Valid prediction for snap_scaffold_4-snap.1986-T1
Valid prediction for Augustus_model.g6427.t1
Valid prediction for GlimmerHMM_glimmerT_9919-T1
Valid prediction for snap_scaffold_4-snap.1978-T1
Valid prediction for snap_scaffold_4-snap.1982-T1
Valid prediction for snap_scaffold_4-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_9915-T1
Valid prediction for GlimmerHMM_glimmerT_9898-T1
Valid prediction for snap_scaffold_4-snap.1980-T1
Valid prediction for snap_scaffold_4-snap.1957-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9895-T1
Valid prediction for snap_scaffold_4-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_9908-T1
Valid prediction for Augustus_model.g6442.t1
Valid prediction for GlimmerHMM_glimmerT_9913-T1
Valid prediction for snap_scaffold_4-snap.1968-T1
Valid prediction for snap_scaffold_4-snap.1973-T1
Valid prediction for snap_scaffold_4-snap.1939-T1
Valid prediction for Augustus_model.g6426.t1
Valid prediction for snap_scaffold_4-snap.1945-T1
Valid prediction for snap_scaffold_4-snap.1974-T1
Valid prediction for Augustus_model.g6435.t1
Valid prediction for GlimmerHMM_glimmerT_9911-T1
Valid prediction for snap_scaffold_4-snap.1961-T1
Valid prediction for Augustus_model.g6425.t1
Valid prediction for snap_scaffold_4-snap.1970-T1
Valid prediction for snap_scaffold_4-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_9914-T1
Valid prediction for snap_scaffold_4-snap.1983-T1
Valid prediction for snap_scaffold_4-snap.1953-T1
Valid prediction for snap_scaffold_4-snap.1962-T1
Valid prediction for snap_scaffold_4-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_9897-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_4-snap.1989-T1
Valid prediction for snap_scaffold_4-snap.1946-T1
Valid prediction for GlimmerHMM_glimmerT_9910-T1
Valid prediction for GlimmerHMM_glimmerT_9907-T1
Valid prediction for snap_scaffold_4-snap.1971-T1
Valid prediction for Augustus_model.g6434.t1
Valid prediction for Augustus_model.g6439.t1
Valid prediction for snap_scaffold_4-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_9896-T1
Couldn't classify 139143, 139826
Sorry, prediction pasa_asmbl_42806.p1 fails validation.
(ATG)	 CC	139143-139826	GA	GGG
Valid prediction for snap_scaffold_4-snap.1958-T1
Valid prediction for Augustus_model.g6436.t1
Valid prediction for GlimmerHMM_glimmerT_9912-T1
Valid prediction for snap_scaffold_4-snap.1952-T1
Valid prediction for Augustus_model.g6433.t1
Valid prediction for snap_scaffold_4-snap.1964-T1
Valid prediction for Augustus_model.g6432.t1
Valid prediction for snap_scaffold_4-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_9906-T1
Valid prediction for Augustus_model.g6431.t1
Valid prediction for snap_scaffold_4-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_9909-T1
Valid prediction for snap_scaffold_4-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_9903-T1
Valid prediction for GlimmerHMM_glimmerT_9921-T1
Valid prediction for GlimmerHMM_glimmerT_9917-T1
Valid prediction for GlimmerHMM_glimmerT_9902-T1
Valid prediction for Augustus_model.g6438.t1
Valid prediction for GlimmerHMM_glimmerT_9905-T1
Valid prediction for GlimmerHMM_glimmerT_9899-T1
Valid prediction for snap_scaffold_4-snap.1965-T1
Valid prediction for snap_scaffold_4-snap.1942-T1
Valid prediction for snap_scaffold_4-snap.1960-T1
Valid prediction for snap_scaffold_4-snap.1941-T1
Valid prediction for pasa_asmbl_42810.p1
Valid prediction for snap_scaffold_4-snap.1963-T1
Valid prediction for snap_scaffold_4-snap.1975-T1
Couldn't classify 155275, 155595
Sorry, prediction pasa_asmbl_41611.p1 fails validation.
(CCT)	 TC	155275-155595	CC	TCC
Valid prediction for snap_scaffold_4-snap.1966-T1
Valid prediction for snap_scaffold_4-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_9901-T1
Valid prediction for snap_scaffold_4-snap.1976-T1
Couldn't classify 81112, 81276
Sorry, prediction pasa_asmbl_42807.p1 fails validation.
(GTG)	 AA	81112-81276	GT	AGG
(ATC)	 AG	82533-82628	GT	AGG
(AGT)	 AG	82869-82996	GT	AGG
(GTT)	 AG	84386-84479	GT	CCG
(GAT)	 AG	85051-85205	GT	AGG
(GGT)	 AG	85404-85521	GT	AGG
(ATG)	 AG	85740-85940	GT	AGG
(AAC)	 AG	86047-86124	GT	TGG
(AAC)	 AG	86252-86413	GT	CGG
(GGC)	 AG	86666-86770	GT	AGG
(GCC)	 AG	86894-86989	GT	AGG
(TTC)	 AG	87135-87260	GT	AGG
(GAG)	 AG	87438-87590	GT	AGG
(ATC)	 AG	87763-87917	GT	AAG
(TCT)	 AG	88169-88295	GT	TGG
(TTC)	 AG	88763-88946	GT	AGG
(GCC)	 AG	89219-89239	GT	AGG
(GTG)	 AG	89791-89948	GT	AGG
(AAA)	 AG	90913-91094	GT	AAG
(GCT)	 AG	91279-91417	GT	AGG
(AAA)	 AG	91816-92172	GT	AGG
(AAA)	 AG	92395-92478	GT	AGG
(GAC)	 AG	92597-92701	GT	AGG
(TAT)	 AG	92855-92953	GT	AGG
(AAA)	 AG	94683-98036	GT	AGG
(ATT)	 AG	98639-104983	AT	AAA
-recovered pasa_asmbl_42807.p1, initial, 85740, 85940
-recovered pasa_asmbl_42807.p1, terminal, 98639, 104983
-recovered pasa_asmbl_42807.p1, internal, 82533, 82628
-recovered pasa_asmbl_42807.p1, internal, 82869, 82996
-recovered pasa_asmbl_42807.p1, internal, 84386, 84479
-recovered pasa_asmbl_42807.p1, internal, 85051, 85205
-recovered pasa_asmbl_42807.p1, internal, 85404, 85521
-recovered pasa_asmbl_42807.p1, internal, 85740, 85940
-recovered pasa_asmbl_42807.p1, internal, 86047, 86124
-recovered pasa_asmbl_42807.p1, internal, 86252, 86413
-recovered pasa_asmbl_42807.p1, internal, 86666, 86770
-recovered pasa_asmbl_42807.p1, internal, 86894, 86989
-recovered pasa_asmbl_42807.p1, internal, 87135, 87260
-recovered pasa_asmbl_42807.p1, internal, 87438, 87590
-recovered pasa_asmbl_42807.p1, internal, 87763, 87917
-recovered pasa_asmbl_42807.p1, internal, 88169, 88295
-recovered pasa_asmbl_42807.p1, internal, 88763, 88946
-recovered pasa_asmbl_42807.p1, internal, 89219, 89239
-recovered pasa_asmbl_42807.p1, internal, 89791, 89948
-recovered pasa_asmbl_42807.p1, internal, 90913, 91094
-recovered pasa_asmbl_42807.p1, internal, 91279, 91417
-recovered pasa_asmbl_42807.p1, internal, 91816, 92172
-recovered pasa_asmbl_42807.p1, internal, 92395, 92478
-recovered pasa_asmbl_42807.p1, internal, 92597, 92701
-recovered pasa_asmbl_42807.p1, internal, 92855, 92953
-recovered pasa_asmbl_42807.p1, internal, 94683, 98036
Valid prediction for HiQ_model.g6437.t1
Valid prediction for snap_scaffold_4-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_9900-T1
Valid prediction for GlimmerHMM_glimmerT_9918-T1
Valid prediction for Augustus_model.g6440.t1
Valid prediction for snap_scaffold_4-snap.1981-T1
Valid prediction for Augustus_model.g6444.t1
Valid prediction for snap_scaffold_4-snap.1956-T1
Couldn't classify 69103, 69147
Couldn't classify 80307, 80389
Sorry, prediction pasa_asmbl_42812.p1 fails validation.
(CAG)	 TC	69103-69147	GT	AGG
(CAC)	 AG	71574-71588	GT	CGG
(GCC)	 AG	72991-73080	GT	TGG
(CCC)	 AG	75244-75321	GT	AGG
(GTC)	 AG	75606-75698	GT	AGG
(ATC)	 AG	77045-77211	GT	CGG
(GCC)	 AG	79931-80046	GT	AGG
(ATG)	 AG	80307-80389	GT	ATG
-recovered pasa_asmbl_42812.p1, initial, 80307, 80389
-recovered pasa_asmbl_42812.p1, internal, 71574, 71588
-recovered pasa_asmbl_42812.p1, internal, 72991, 73080
-recovered pasa_asmbl_42812.p1, internal, 75244, 75321
-recovered pasa_asmbl_42812.p1, internal, 75606, 75698
-recovered pasa_asmbl_42812.p1, internal, 77045, 77211
-recovered pasa_asmbl_42812.p1, internal, 79931, 80046
-recovered pasa_asmbl_42812.p1, internal, 80307, 80389
Valid prediction for snap_scaffold_4-snap.1954-T1
Valid prediction for snap_scaffold_4-snap.1969-T1
Valid prediction for Augustus_model.g6441.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16806, rend_intergenic: 2641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24888, rend_intergenic: 22619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29527, rend_intergenic: 25700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33862, rend_intergenic: 31728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37747, rend_intergenic: 36052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41947, rend_intergenic: 38915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49639, rend_intergenic: 45033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52484, rend_intergenic: 49716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53824, rend_intergenic: 53588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55756, rend_intergenic: 54384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61379, rend_intergenic: 58663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65967, rend_intergenic: 64283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69078, rend_intergenic: 65981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90147, rend_intergenic: 76499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95997, rend_intergenic: 91066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117952, rend_intergenic: 115096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126416, rend_intergenic: 125974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129146, rend_intergenic: 127895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136775, rend_intergenic: 130810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143466, rend_intergenic: 138906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158522, rend_intergenic: 146084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165871, rend_intergenic: 163810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202030, rend_intergenic: 167562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205109
-exon list size: 503


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 16806, rend_intergenic: 2641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24888, rend_intergenic: 22619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29527, rend_intergenic: 25700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33862, rend_intergenic: 31728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37747, rend_intergenic: 36052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41947, rend_intergenic: 38915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49639, rend_intergenic: 45033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52484, rend_intergenic: 49716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53824, rend_intergenic: 53588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55756, rend_intergenic: 54384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61379, rend_intergenic: 58663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65967, rend_intergenic: 64283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69078, rend_intergenic: 65981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90147, rend_intergenic: 76499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95997, rend_intergenic: 91066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117952, rend_intergenic: 115096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126416, rend_intergenic: 125974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129146, rend_intergenic: 127895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136775, rend_intergenic: 130810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143466, rend_intergenic: 138906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158522, rend_intergenic: 146084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165871, rend_intergenic: 163810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202030, rend_intergenic: 167562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support