-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_8503380-8700329

-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.1638_t
Valid prediction for GeneMark_model.1629_t
Valid prediction for snap_scaffold_1-snap.1555-T1
Valid prediction for Augustus_model.g885.t1
Valid prediction for GeneMark_model.1635_t
Valid prediction for HiQ_model.g895.t1
Valid prediction for GlimmerHMM_glimmerT_1256-T1
Valid prediction for GeneMark_model.1631_t
Valid prediction for snap_scaffold_1-snap.1556-T1
Valid prediction for Augustus_model.g889.t1
Valid prediction for GeneMark_model.1637_t
Valid prediction for GeneMark_model.1624_t
Valid prediction for Augustus_model.g888.t1
Valid prediction for snap_scaffold_1-snap.1553-T1
Valid prediction for GeneMark_model.1640_t
Valid prediction for snap_scaffold_1-snap.1563-T1
Valid prediction for GeneMark_model.1647_t
Valid prediction for GeneMark_model.1662_t
Valid prediction for GlimmerHMM_glimmerT_1245-T1
Valid prediction for snap_scaffold_1-snap.1546-T1
Valid prediction for GeneMark_model.1645_t
Valid prediction for GlimmerHMM_glimmerT_1236-T1
Couldn't classify 77037, 77129
Couldn't classify 80032, 80111
Sorry, prediction pasa_asmbl_1930.p1 fails validation.
(AGC)	 CC	77037-77129	GT	AGG
(GAC)	 AG	78563-78694	GT	TGG
(TCA)	 AG	78810-78866	GT	AGG
(GGG)	 AG	79685-79799	GT	AGG
(TTT)	 AG	80032-80111	GT	TGG
-recovered pasa_asmbl_1930.p1, internal, 78563, 78694
-recovered pasa_asmbl_1930.p1, internal, 78810, 78866
-recovered pasa_asmbl_1930.p1, internal, 79685, 79799
-recovered pasa_asmbl_1930.p1, internal, 80032, 80111
Valid prediction for GeneMark_model.1627_t
Valid prediction for GeneMark_model.1633_t
Valid prediction for GeneMark_model.1654_t
Valid prediction for pasa_asmbl_1932.p1
Valid prediction for Augustus_model.g900.t1
Valid prediction for GeneMark_model.1649_t
Valid prediction for GlimmerHMM_glimmerT_1234-T1
Valid prediction for snap_scaffold_1-snap.1573-T1
Valid prediction for GeneMark_model.1642_t
Valid prediction for GlimmerHMM_glimmerT_1235-T1
Valid prediction for GeneMark_model.1644_t
Valid prediction for GlimmerHMM_glimmerT_1228-T1
Valid prediction for snap_scaffold_1-snap.1551-T1
Couldn't classify 81709, 81815
Sorry, prediction pasa_asmbl_1931.p1 fails validation.
(GGT)	 CA	81709-81815	GT	AGG
(GCT)	 AG	81938-81980	GT	TGG
(TAC)	 AG	82073-82163	GT	CAG
(CTT)	 AG	82611-82688	GT	AGG
(GTC)	 AG	82905-82939	GG	AGG
-recovered pasa_asmbl_1931.p1, terminal, 82905, 82939
-recovered pasa_asmbl_1931.p1, internal, 81938, 81980
-recovered pasa_asmbl_1931.p1, internal, 82073, 82163
-recovered pasa_asmbl_1931.p1, internal, 82611, 82688
Valid prediction for snap_scaffold_1-snap.1542-T1
Valid prediction for snap_scaffold_1-snap.1545-T1
Valid prediction for snap_scaffold_1-snap.1540-T1
Valid prediction for snap_scaffold_1-snap.1538-T1
Valid prediction for snap_scaffold_1-snap.1548-T1
Valid prediction for snap_scaffold_1-snap.1572-T1
Valid prediction for snap_scaffold_1-snap.1543-T1
Valid prediction for snap_scaffold_1-snap.1550-T1
Valid prediction for snap_scaffold_1-snap.1570-T1
Valid prediction for GeneMark_model.1657_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 snap_scaffold_1-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_1247-T1
Valid prediction for GlimmerHMM_glimmerT_1248-T1
Valid prediction for CodingQuarry_transcript_2707-T1
Valid prediction for GlimmerHMM_glimmerT_1246-T1
Valid prediction for GeneMark_model.1621_t
Valid prediction for snap_scaffold_1-snap.1571-T1
Valid prediction for Augustus_model.g886.t1
Valid prediction for GlimmerHMM_glimmerT_1227-T1
Valid prediction for GeneMark_model.1648_t
Valid prediction for snap_scaffold_1-snap.1561-T1
Valid prediction for snap_scaffold_1-snap.1575-T1
Valid prediction for snap_scaffold_1-snap.1558-T1
Valid prediction for pasa_asmbl_466.p1
Valid prediction for GeneMark_model.1632_t
Valid prediction for pasa_asmbl_465.p1
Valid prediction for GlimmerHMM_glimmerT_1231-T1
Valid prediction for GlimmerHMM_glimmerT_1230-T1
Valid prediction for Augustus_model.g887.t1
Valid prediction for GlimmerHMM_glimmerT_1242-T1
Valid prediction for GlimmerHMM_glimmerT_1243-T1
Valid prediction for CodingQuarry_transcript_2705-T1
Valid prediction for GeneMark_model.1658_t
Valid prediction for GeneMark_model.1641_t
Couldn't classify 102761, 102784
Couldn't classify 103381, 103422
Sorry, prediction pasa_asmbl_460.p1 fails validation.
(CCT)	 AG	102761-102784	GT	GGG
(TTG)	 AG	102902-103138	GT	AGG
(ACT)	 AG	103381-103422	AT	ACA
-recovered pasa_asmbl_460.p1, internal, 102761, 102784
-recovered pasa_asmbl_460.p1, internal, 102902, 103138
Valid prediction for GeneMark_model.1652_t
Valid prediction for snap_scaffold_1-snap.1544-T1
Valid prediction for snap_scaffold_1-snap.1547-T1
Valid prediction for pasa_asmbl_473.p2
Valid prediction for GeneMark_model.1653_t
Valid prediction for snap_scaffold_1-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_1237-T1
Valid prediction for HiQ_model.g891.t1
Valid prediction for GlimmerHMM_glimmerT_1240-T1
Valid prediction for GeneMark_model.1663_t
Valid prediction for Augustus_model.g884.t1
Couldn't classify 195144, 195677
Sorry, prediction pasa_asmbl_456.p1 fails validation.
(GAT)	 CC	195144-195677	GC	TGG
Valid prediction for pasa_asmbl_485.p1
Valid prediction for snap_scaffold_1-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_1233-T1
Valid prediction for GlimmerHMM_glimmerT_1255-T1
Valid prediction for GeneMark_model.1623_t
Valid prediction for GlimmerHMM_glimmerT_1250-T1
Valid prediction for GlimmerHMM_glimmerT_1252-T1
Valid prediction for GlimmerHMM_glimmerT_1251-T1
Valid prediction for GlimmerHMM_glimmerT_1244-T1
Valid prediction for HiQ_model.g896.t1
Valid prediction for Augustus_model.g890.t1
Valid prediction for GlimmerHMM_glimmerT_1257-T1
Valid prediction for CodingQuarry_transcript_2700-T1
Valid prediction for snap_scaffold_1-snap.1539-T1
Valid prediction for GeneMark_model.1659_t
Valid prediction for GlimmerHMM_glimmerT_1254-T1
Valid prediction for snap_scaffold_1-snap.1560-T1
Valid prediction for snap_scaffold_1-snap.1568-T1
Valid prediction for GeneMark_model.1656_t
Valid prediction for pasa_asmbl_462.p1
Valid prediction for snap_scaffold_1-snap.1541-T1
Valid prediction for GlimmerHMM_glimmerT_1238-T1
Valid prediction for Augustus_model.g897.t1
Valid prediction for CodingQuarry_transcript_2703-T1
Valid prediction for GlimmerHMM_glimmerT_1232-T1
Valid prediction for CodingQuarry_transcript_2701-T1
Valid prediction for GlimmerHMM_glimmerT_1249-T1
Valid prediction for snap_scaffold_1-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_1253-T1
Valid prediction for snap_scaffold_1-snap.1559-T1
Valid prediction for GeneMark_model.1639_t
Valid prediction for snap_scaffold_1-snap.1566-T1
Valid prediction for GeneMark_model.1625_t
Valid prediction for snap_scaffold_1-snap.1567-T1
Valid prediction for GeneMark_model.1636_t
Valid prediction for GeneMark_model.1622_t
Valid prediction for pasa_asmbl_464.p1
Valid prediction for HiQ_model.g901.t1
Valid prediction for GlimmerHMM_glimmerT_1239-T1
Valid prediction for GlimmerHMM_glimmerT_1226-T1
Valid prediction for CodingQuarry_transcript_2706-T1
Valid prediction for Augustus_model.g892.t1
Valid prediction for HiQ_model.g902.t1
Valid prediction for pasa_asmbl_486.p1
Valid prediction for CodingQuarry_transcript_2704-T1
Valid prediction for GeneMark_model.1630_t
Valid prediction for GlimmerHMM_glimmerT_1241-T1
Valid prediction for CodingQuarry_transcript_2699-T1
Valid prediction for GeneMark_model.1643_t
Valid prediction for GlimmerHMM_glimmerT_1229-T1
Valid prediction for pasa_asmbl_483.p2
Valid prediction for GeneMark_model.1628_t
Valid prediction for GeneMark_model.1660_t
Valid prediction for snap_scaffold_1-snap.1549-T1
Valid prediction for GeneMark_model.1626_t
Valid prediction for GeneMark_model.1661_t
Valid prediction for CodingQuarry_transcript_2702-T1
Valid prediction for snap_scaffold_1-snap.1569-T1
Valid prediction for Augustus_model.g899.t1
Valid prediction for GeneMark_model.1664_t
Valid prediction for GeneMark_model.1651_t
Valid prediction for snap_scaffold_1-snap.1565-T1
Valid prediction for Augustus_model.g898.t1
Couldn't classify 102044, 102187
Sorry, prediction pasa_asmbl_461.p1 fails validation.
(ATG)	 AC	101405-101611	GT	AGG
(AAC)	 AG	102044-102187	GA	GGG
-recovered pasa_asmbl_461.p1, initial, 101405, 101611
Valid prediction for snap_scaffold_1-snap.1552-T1
Valid prediction for GeneMark_model.1646_t
Valid prediction for HiQ_model.g894.t1
Valid prediction for GeneMark_model.1634_t
Valid prediction for HiQ_model.g893.t1
Valid prediction for snap_scaffold_1-snap.1574-T1
Valid prediction for GeneMark_model.1655_t
Valid prediction for CodingQuarry_transcript_2708-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26086, rend_intergenic: 22366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39336, rend_intergenic: 26495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44386, rend_intergenic: 41563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54623, rend_intergenic: 44573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72167, rend_intergenic: 57924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80618, rend_intergenic: 72919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82939, rend_intergenic: 80750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165762, rend_intergenic: 155529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174034, rend_intergenic: 165946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196950
-exon list size: 729


building trellis

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92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 26086, rend_intergenic: 22366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39336, rend_intergenic: 26495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44386, rend_intergenic: 41563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54623, rend_intergenic: 44573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72167, rend_intergenic: 57924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80618, rend_intergenic: 72919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82939, rend_intergenic: 80750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165762, rend_intergenic: 155529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174034, rend_intergenic: 165946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support