-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_7470614-7640101

-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.g790.t1
Valid prediction for Augustus_model.g775.t1
Valid prediction for GeneMark_model.1353_t
Couldn't classify 60946, 61113
Couldn't classify 63944, 64038
Sorry, prediction pasa_asmbl_1897.p1 fails validation.
(CAT)	 CC	60946-61113	GT	GGG
(ATA)	 AG	61670-61771	GT	AGG
(GGT)	 AG	62131-62190	GT	AGG
(TCT)	 AG	62460-62529	GT	AGG
(GAC)	 AG	63944-64038	TA	ACT
-recovered pasa_asmbl_1897.p1, internal, 61670, 61771
-recovered pasa_asmbl_1897.p1, internal, 62131, 62190
-recovered pasa_asmbl_1897.p1, internal, 62460, 62529
Valid prediction for snap_scaffold_1-snap.1338-T1
Valid prediction for GeneMark_model.1323_t
Valid prediction for GlimmerHMM_glimmerT_1068-T1
Valid prediction for snap_scaffold_1-snap.1342-T1
Valid prediction for GeneMark_model.1325_t
Valid prediction for snap_scaffold_1-snap.1326-T1
Valid prediction for snap_scaffold_1-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_1084-T1
Valid prediction for GlimmerHMM_glimmerT_1072-T1
Valid prediction for snap_scaffold_1-snap.1327-T1
Valid prediction for snap_scaffold_1-snap.1351-T1
Valid prediction for GeneMark_model.1368_t
Valid prediction for snap_scaffold_1-snap.1321-T1
Valid prediction for GeneMark_model.1346_t
Valid prediction for GlimmerHMM_glimmerT_1064-T1
Valid prediction for GeneMark_model.1372_t
Valid prediction for GeneMark_model.1359_t
Valid prediction for GeneMark_model.1331_t
Valid prediction for GlimmerHMM_glimmerT_1069-T1
Valid prediction for GlimmerHMM_glimmerT_1063-T1
Valid prediction for GeneMark_model.1367_t
Valid prediction for snap_scaffold_1-snap.1328-T1
Valid prediction for snap_scaffold_1-snap.1350-T1
Valid prediction for GeneMark_model.1350_t
Valid prediction for snap_scaffold_1-snap.1334-T1
Valid prediction for GeneMark_model.1355_t
Valid prediction for snap_scaffold_1-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_1073-T1
Valid prediction for GeneMark_model.1375_t
Couldn't classify 122204, 122291
Sorry, prediction pasa_asmbl_1901.p1 fails validation.
(TCT)	 AC	122204-122291	GT	AGG
(GAA)	 AG	122692-122729	GT	AGG
(ATG)	 AG	123369-123448	GT	AAG
(AGC)	 AG	126315-126359	GT	AGG
(GCG)	 AG	127054-127098	GT	AAG
(AGC)	 AG	127782-127825	GT	AGG
(GTT)	 AG	128122-128208	GT	AGG
(AGA)	 AG	129476-129561	GT	TGG
(GAG)	 AG	129656-129776	GT	AGG
(GTG)	 AG	130271-130365	GT	AGG
(GGC)	 AG	131518-131638	GT	CGG
(CGT)	 AG	133330-133418	GT	AGG
(GTC)	 AG	134572-134661	CC	AAC
-recovered pasa_asmbl_1901.p1, initial, 123369, 123448
-recovered pasa_asmbl_1901.p1, terminal, 129656, 129776
-recovered pasa_asmbl_1901.p1, terminal, 134572, 134661
-recovered pasa_asmbl_1901.p1, internal, 122692, 122729
-recovered pasa_asmbl_1901.p1, internal, 123369, 123448
-recovered pasa_asmbl_1901.p1, internal, 126315, 126359
-recovered pasa_asmbl_1901.p1, internal, 127054, 127098
-recovered pasa_asmbl_1901.p1, internal, 127782, 127825
-recovered pasa_asmbl_1901.p1, internal, 128122, 128208
-recovered pasa_asmbl_1901.p1, internal, 129476, 129561
-recovered pasa_asmbl_1901.p1, internal, 129656, 129776
-recovered pasa_asmbl_1901.p1, internal, 130271, 130365
-recovered pasa_asmbl_1901.p1, internal, 131518, 131638
-recovered pasa_asmbl_1901.p1, internal, 133330, 133418
Valid prediction for Augustus_model.g779.t1
Valid prediction for GlimmerHMM_glimmerT_1065-T1
Valid prediction for GlimmerHMM_glimmerT_1089-T1
Valid prediction for Augustus_model.g780.t1
Valid prediction for snap_scaffold_1-snap.1319-T1
Valid prediction for Augustus_model.g783.t1
Valid prediction for GeneMark_model.1363_t
Valid prediction for GlimmerHMM_glimmerT_1074-T1
Valid prediction for GeneMark_model.1333_t
Valid prediction for GlimmerHMM_glimmerT_1075-T1
Valid prediction for GeneMark_model.1340_t
Valid prediction for GeneMark_model.1342_t
Valid prediction for GeneMark_model.1327_t
Valid prediction for snap_scaffold_1-snap.1341-T1
Valid prediction for snap_scaffold_1-snap.1335-T1
Valid prediction for GlimmerHMM_glimmerT_1078-T1
Valid prediction for snap_scaffold_1-snap.1332-T1
Valid prediction for snap_scaffold_1-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_1080-T1
Valid prediction for GlimmerHMM_glimmerT_1070-T1
Valid prediction for CodingQuarry_transcript_2692-T1
Valid prediction for GlimmerHMM_glimmerT_1090-T1
Valid prediction for snap_scaffold_1-snap.1344-T1
Valid prediction for Augustus_model.g785.t1
Valid prediction for Augustus_model.g791.t1
Valid prediction for GeneMark_model.1348_t
Valid prediction for GeneMark_model.1361_t
Valid prediction for HiQ_model.g782.t1
Valid prediction for GeneMark_model.1335_t
Valid prediction for Augustus_model.g786.t1
Valid prediction for GeneMark_model.1344_t
Valid prediction for GeneMark_model.1329_t
Valid prediction for GeneMark_model.1365_t
Valid prediction for GeneMark_model.1343_t
Valid prediction for snap_scaffold_1-snap.1314-T1
Valid prediction for GeneMark_model.1370_t
Valid prediction for GlimmerHMM_glimmerT_1087-T1
Valid prediction for Augustus_model.g778.t1
Valid prediction for Augustus_model.g777.t1
Valid prediction for GeneMark_model.1357_t
Valid prediction for snap_scaffold_1-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_1071-T1
Valid prediction for snap_scaffold_1-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_1088-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 Augustus_model.g793.t1
Valid prediction for snap_scaffold_1-snap.1330-T1
Valid prediction for snap_scaffold_1-snap.1354-T1
Valid prediction for snap_scaffold_1-snap.1358-T1
Valid prediction for GeneMark_model.1352_t
Valid prediction for GeneMark_model.1337_t
Valid prediction for GlimmerHMM_glimmerT_1091-T1
Valid prediction for GeneMark_model.1354_t
Valid prediction for snap_scaffold_1-snap.1325-T1
Valid prediction for GeneMark_model.1336_t
Valid prediction for snap_scaffold_1-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_1092-T1
Valid prediction for GeneMark_model.1360_t
Valid prediction for snap_scaffold_1-snap.1346-T1
Valid prediction for GeneMark_model.1358_t
Valid prediction for GeneMark_model.1366_t
Valid prediction for snap_scaffold_1-snap.1323-T1
Valid prediction for GeneMark_model.1322_t
Valid prediction for GlimmerHMM_glimmerT_1081-T1
Valid prediction for Augustus_model.g781.t1
Valid prediction for snap_scaffold_1-snap.1337-T1
Valid prediction for GeneMark_model.1324_t
Valid prediction for snap_scaffold_1-snap.1331-T1
Valid prediction for GeneMark_model.1345_t
Valid prediction for GeneMark_model.1373_t
Valid prediction for GeneMark_model.1334_t
Valid prediction for GeneMark_model.1338_t
Valid prediction for snap_scaffold_1-snap.1315-T1
Valid prediction for snap_scaffold_1-snap.1348-T1
Valid prediction for GeneMark_model.1341_t
Valid prediction for GeneMark_model.1364_t
Valid prediction for Augustus_model.g794.t1
Valid prediction for snap_scaffold_1-snap.1324-T1
Valid prediction for GeneMark_model.1332_t
Valid prediction for GeneMark_model.1356_t
Valid prediction for GeneMark_model.1349_t
Valid prediction for snap_scaffold_1-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_1093-T1
Valid prediction for snap_scaffold_1-snap.1340-T1
Valid prediction for GeneMark_model.1339_t
Valid prediction for snap_scaffold_1-snap.1322-T1
Valid prediction for snap_scaffold_1-snap.1349-T1
Valid prediction for Augustus_model.g789.t1
Valid prediction for GeneMark_model.1326_t
Valid prediction for GeneMark_model.1347_t
Valid prediction for GlimmerHMM_glimmerT_1085-T1
Valid prediction for snap_scaffold_1-snap.1339-T1
Valid prediction for snap_scaffold_1-snap.1317-T1
Valid prediction for snap_scaffold_1-snap.1343-T1
Valid prediction for GeneMark_model.1328_t
Valid prediction for GeneMark_model.1374_t
Valid prediction for GlimmerHMM_glimmerT_1066-T1
Valid prediction for snap_scaffold_1-snap.1320-T1
Valid prediction for GeneMark_model.1362_t
Valid prediction for Augustus_model.g788.t1
Valid prediction for Augustus_model.g787.t1
Valid prediction for Augustus_model.g792.t1
Valid prediction for snap_scaffold_1-snap.1353-T1
Valid prediction for GlimmerHMM_glimmerT_1067-T1
Valid prediction for GeneMark_model.1351_t
Valid prediction for GeneMark_model.1371_t
Valid prediction for snap_scaffold_1-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_1077-T1
Valid prediction for GeneMark_model.1376_t
Valid prediction for Augustus_model.g776.t1
Valid prediction for GlimmerHMM_glimmerT_1086-T1
Valid prediction for GeneMark_model.1369_t
Valid prediction for Augustus_model.g784.t1
Valid prediction for snap_scaffold_1-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_1076-T1
Valid prediction for GeneMark_model.1330_t
Valid prediction for GlimmerHMM_glimmerT_1082-T1
Valid prediction for snap_scaffold_1-snap.1352-T1
Valid prediction for snap_scaffold_1-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_1083-T1
Valid prediction for GlimmerHMM_glimmerT_1079-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4387, rend_intergenic: 3754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9042, rend_intergenic: 6840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18210, rend_intergenic: 17759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19695, rend_intergenic: 18717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37037, rend_intergenic: 21935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54586, rend_intergenic: 49671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73343, rend_intergenic: 69470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85954, rend_intergenic: 76972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87344, rend_intergenic: 86912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94538, rend_intergenic: 89643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100239, rend_intergenic: 94634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106275, rend_intergenic: 101391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 114454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136671, rend_intergenic: 132564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148821, rend_intergenic: 141268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160547, rend_intergenic: 149961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163675, rend_intergenic: 161658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164374, rend_intergenic: 164368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169488
-exon list size: 792


building trellis

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73.9    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 4387, rend_intergenic: 3754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9042, rend_intergenic: 6840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18210, rend_intergenic: 17759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19695, rend_intergenic: 18717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37037, rend_intergenic: 21935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54586, rend_intergenic: 49671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73343, rend_intergenic: 69470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85954, rend_intergenic: 76972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87344, rend_intergenic: 86912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94538, rend_intergenic: 89643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100239, rend_intergenic: 94634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106275, rend_intergenic: 101391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 114454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136671, rend_intergenic: 132564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148821, rend_intergenic: 141268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160547, rend_intergenic: 149961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163675, rend_intergenic: 161658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164374, rend_intergenic: 164368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support