-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_15815720-16003494

-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 snap_scaffold_1-snap.2766-T1
Valid prediction for snap_scaffold_1-snap.2786-T1
Valid prediction for Augustus_model.g1541.t1
Couldn't classify 171797, 172010
Sorry, prediction pasa_asmbl_2458.p1 fails validation.
(CAG)	 AG	171797-172010	GT	AGG
(TTC)	 AG	172182-172228	GT	ACG
(CCC)	 AG	172347-172545	GT	AGG
(CAG)	 AG	172662-172813	AC	GAA
-recovered pasa_asmbl_2458.p1, terminal, 172662, 172813
-recovered pasa_asmbl_2458.p1, internal, 171797, 172010
-recovered pasa_asmbl_2458.p1, internal, 172182, 172228
-recovered pasa_asmbl_2458.p1, internal, 172347, 172545
Valid prediction for snap_scaffold_1-snap.2751-T1
Valid prediction for GlimmerHMM_glimmerT_2092-T1
Valid prediction for snap_scaffold_1-snap.2781-T1
Valid prediction for snap_scaffold_1-snap.2776-T1
Valid prediction for HiQ_model.g1544.t1
Valid prediction for GlimmerHMM_glimmerT_2082-T1
Valid prediction for snap_scaffold_1-snap.2784-T1
Valid prediction for GlimmerHMM_glimmerT_2070-T1
Valid prediction for snap_scaffold_1-snap.2768-T1
Valid prediction for snap_scaffold_1-snap.2761-T1
Valid prediction for HiQ_model.g1547.t1
Valid prediction for Augustus_model.g1546.t1
Valid prediction for pasa_asmbl_2448.p1
Valid prediction for GlimmerHMM_glimmerT_2089-T1
Valid prediction for snap_scaffold_1-snap.2747-T1
Valid prediction for HiQ_model.g1548.t1
Valid prediction for Augustus_model.g1542.t1
Valid prediction for snap_scaffold_1-snap.2777-T1
Valid prediction for snap_scaffold_1-snap.2753-T1
Valid prediction for snap_scaffold_1-snap.2760-T1
Valid prediction for snap_scaffold_1-snap.2749-T1
Valid prediction for CodingQuarry_transcript_2948-T1
Valid prediction for GlimmerHMM_glimmerT_2090-T1
Valid prediction for snap_scaffold_1-snap.2757-T1
Valid prediction for snap_scaffold_1-snap.2750-T1
Valid prediction for snap_scaffold_1-snap.2765-T1
Valid prediction for Augustus_model.g1540.t1
Valid prediction for Augustus_model.g1539.t1
Valid prediction for GlimmerHMM_glimmerT_2067-T1
Valid prediction for snap_scaffold_1-snap.2779-T1
Valid prediction for GlimmerHMM_glimmerT_2079-T1
Valid prediction for GlimmerHMM_glimmerT_2066-T1
Valid prediction for CodingQuarry_transcript_2946-T1
Valid prediction for snap_scaffold_1-snap.2782-T1
Valid prediction for snap_scaffold_1-snap.2767-T1
Couldn't classify 61390, 61528
Sorry, prediction pasa_asmbl_2450.p1 fails validation.
(AAA)	 AC	61390-61528	GT	AGG
(GCA)	 AG	61798-61965	GT	AGG
(ACA)	 AG	62066-62109	GA	AAG
-recovered pasa_asmbl_2450.p1, terminal, 62066, 62109
-recovered pasa_asmbl_2450.p1, internal, 61798, 61965
Valid prediction for GlimmerHMM_glimmerT_2087-T1
Valid prediction for GlimmerHMM_glimmerT_2075-T1
Valid prediction for pasa_asmbl_2451.p1
Valid prediction for snap_scaffold_1-snap.2755-T1
Valid prediction for Augustus_model.g1557.t1
Valid prediction for GlimmerHMM_glimmerT_2074-T1
Valid prediction for snap_scaffold_1-snap.2770-T1
Valid prediction for HiQ_model.g1550.t1
Valid prediction for CodingQuarry_transcript_2945-T1
Valid prediction for snap_scaffold_1-snap.2759-T1
Valid prediction for GlimmerHMM_glimmerT_2086-T1
Valid prediction for Augustus_model.g1558.t1
Valid prediction for Augustus_model.g1554.t1
Valid prediction for GlimmerHMM_glimmerT_2071-T1
Valid prediction for Augustus_model.g1556.t1
Valid prediction for snap_scaffold_1-snap.2763-T1
Valid prediction for CodingQuarry_transcript_2943-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 GlimmerHMM_glimmerT_2068-T1
Valid prediction for pasa_asmbl_962.p1
Valid prediction for GlimmerHMM_glimmerT_2073-T1
Valid prediction for GlimmerHMM_glimmerT_2083-T1
Valid prediction for GlimmerHMM_glimmerT_2072-T1
Valid prediction for snap_scaffold_1-snap.2771-T1
Valid prediction for snap_scaffold_1-snap.2752-T1
Valid prediction for snap_scaffold_1-snap.2783-T1
Valid prediction for CodingQuarry_transcript_2947-T1
Valid prediction for GlimmerHMM_glimmerT_2065-T1
Valid prediction for snap_scaffold_1-snap.2787-T1
Valid prediction for snap_scaffold_1-snap.2780-T1
Valid prediction for snap_scaffold_1-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_2093-T1
Valid prediction for pasa_asmbl_1295.p1
Valid prediction for pasa_asmbl_960.p1
Valid prediction for snap_scaffold_1-snap.2773-T1
Valid prediction for CodingQuarry_transcript_2941-T1
Valid prediction for GlimmerHMM_glimmerT_2076-T1
Valid prediction for Augustus_model.g1555.t1
Valid prediction for HiQ_model.g1543.t1
Valid prediction for snap_scaffold_1-snap.2764-T1
Valid prediction for pasa_asmbl_966.p1
Valid prediction for GlimmerHMM_glimmerT_2081-T1
Valid prediction for snap_scaffold_1-snap.2785-T1
Valid prediction for snap_scaffold_1-snap.2778-T1
Valid prediction for GlimmerHMM_glimmerT_2091-T1
Valid prediction for CodingQuarry_transcript_2944-T1
Valid prediction for GlimmerHMM_glimmerT_2088-T1
Valid prediction for snap_scaffold_1-snap.2748-T1
Valid prediction for snap_scaffold_1-snap.2769-T1
Valid prediction for Augustus_model.g1552.t1
Valid prediction for Augustus_model.g1559.t1
Valid prediction for GlimmerHMM_glimmerT_2080-T1
Valid prediction for GlimmerHMM_glimmerT_2084-T1
Valid prediction for Augustus_model.g1553.t1
Valid prediction for CodingQuarry_transcript_2942-T1
Valid prediction for snap_scaffold_1-snap.2758-T1
Valid prediction for snap_scaffold_1-snap.2762-T1
Valid prediction for Augustus_model.g1538.t1
Valid prediction for pasa_asmbl_961.p1
Valid prediction for snap_scaffold_1-snap.2772-T1
Valid prediction for Augustus_model.g1551.t1
Valid prediction for GlimmerHMM_glimmerT_2077-T1
Valid prediction for GlimmerHMM_glimmerT_2064-T1
Valid prediction for GlimmerHMM_glimmerT_2078-T1
Valid prediction for snap_scaffold_1-snap.2754-T1
Valid prediction for snap_scaffold_1-snap.2756-T1
Valid prediction for GlimmerHMM_glimmerT_2085-T1
Couldn't classify 62622, 62730
Sorry, prediction pasa_asmbl_968.p1 fails validation.
(ATG)	 TC	58790-58864	GT	AGG
(GCA)	 AG	59931-60038	GT	CGG
(CTC)	 AG	60731-60838	GT	GGG
(AAA)	 AG	61057-61129	GT	GAG
(AAT)	 AG	61890-61947	GT	TGG
(GAT)	 AG	62622-62730	GT	GGG
-recovered pasa_asmbl_968.p1, initial, 58790, 58864
-recovered pasa_asmbl_968.p1, internal, 59931, 60038
-recovered pasa_asmbl_968.p1, internal, 60731, 60838
-recovered pasa_asmbl_968.p1, internal, 61057, 61129
-recovered pasa_asmbl_968.p1, internal, 61890, 61947
-recovered pasa_asmbl_968.p1, internal, 62622, 62730
Valid prediction for HiQ_model.g1545.t1
Valid prediction for HiQ_model.g1549.t1
Valid prediction for snap_scaffold_1-snap.2775-T1
Valid prediction for GlimmerHMM_glimmerT_2069-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15876, rend_intergenic: 13877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24851, rend_intergenic: 23739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27016, rend_intergenic: 25535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91786, rend_intergenic: 81104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104157, rend_intergenic: 95316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135081, rend_intergenic: 131342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145686, rend_intergenic: 143765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161334, rend_intergenic: 159207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182206, rend_intergenic: 177257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187775
-exon list size: 325


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 15876, rend_intergenic: 13877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24851, rend_intergenic: 23739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27016, rend_intergenic: 25535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91786, rend_intergenic: 81104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104157, rend_intergenic: 95316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135081, rend_intergenic: 131342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145686, rend_intergenic: 143765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161334, rend_intergenic: 159207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182206, rend_intergenic: 177257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10336
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
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-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support