-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_6588877-6899143

-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_22834-T1
Valid prediction for Augustus_model.g15278.t1
Valid prediction for CodingQuarry_transcript_62058-T1
Valid prediction for GeneMark_model.39220_t
Valid prediction for Augustus_model.g15272.t1
Valid prediction for GlimmerHMM_glimmerT_22827-T1
Valid prediction for snap_scaffold_9-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_22858-T1
Valid prediction for GlimmerHMM_glimmerT_22847-T1
Valid prediction for snap_scaffold_9-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_22845-T1
Valid prediction for pasa_asmbl_54086.p1
Valid prediction for HiQ_model.g15285.t1
Valid prediction for GlimmerHMM_glimmerT_22850-T1
Valid prediction for snap_scaffold_9-snap.1431-T1
Valid prediction for GeneMark_model.39205_t
Valid prediction for pasa_asmbl_54093.p1
Valid prediction for GeneMark_model.39217_t
Valid prediction for pasa_asmbl_54731.p1
Valid prediction for Augustus_model.g15292.t1
Valid prediction for GlimmerHMM_glimmerT_22837-T1
Valid prediction for GeneMark_model.39201_t
Valid prediction for pasa_asmbl_54095.p1
Valid prediction for snap_scaffold_9-snap.1412-T1
Valid prediction for Augustus_model.g15280.t1
Valid prediction for snap_scaffold_9-snap.1399-T1
Valid prediction for GlimmerHMM_glimmerT_22853-T1
Valid prediction for snap_scaffold_9-snap.1406-T1
Valid prediction for CodingQuarry_transcript_62062-T1
Valid prediction for Augustus_model.g15289.t1
Valid prediction for GlimmerHMM_glimmerT_22835-T1
Valid prediction for snap_scaffold_9-snap.1409-T1
Valid prediction for HiQ_model.g15294.t1
Valid prediction for snap_scaffold_9-snap.1438-T1
Valid prediction for CodingQuarry_transcript_62049-T1
Valid prediction for snap_scaffold_9-snap.1425-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1422-T1
Valid prediction for Augustus_model.g15283.t1
Valid prediction for snap_scaffold_9-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_22856-T1
Valid prediction for CodingQuarry_transcript_62057-T1
Valid prediction for Augustus_model.g15273.t1
Valid prediction for Augustus_model.g15275.t1
Valid prediction for HiQ_model.g15281.t1
Valid prediction for GlimmerHMM_glimmerT_22839-T1
Valid prediction for GeneMark_model.39214_t
Couldn't classify 238068, 238221
Sorry, prediction pasa_asmbl_54091.p1 fails validation.
(GGA)	 CA	238068-238221	GT	GGG
(AGT)	 AG	238351-238425	GT	TGG
(TAA)	 AG	238534-238654	GT	AGG
(CTT)	 AG	238779-238917	GT	AGG
(GGT)	 AG	239010-239134	GT	AGG
(ATA)	 AG	239233-239665	AC	AAA
-recovered pasa_asmbl_54091.p1, terminal, 239233, 239665
-recovered pasa_asmbl_54091.p1, internal, 238351, 238425
-recovered pasa_asmbl_54091.p1, internal, 238534, 238654
-recovered pasa_asmbl_54091.p1, internal, 238779, 238917
-recovered pasa_asmbl_54091.p1, internal, 239010, 239134
Valid prediction for GeneMark_model.39227_t
Valid prediction for snap_scaffold_9-snap.1428-T1
Valid prediction for GeneMark_model.39219_t
Valid prediction for GeneMark_model.39207_t
Valid prediction for GeneMark_model.39195_t
Valid prediction for GeneMark_model.39226_t
Valid prediction for CodingQuarry_transcript_62051-T1
Valid prediction for snap_scaffold_9-snap.1393-T1
Valid prediction for HiQ_model.g15270.t1
Valid prediction for GlimmerHMM_glimmerT_22842-T1
Valid prediction for GeneMark_model.39224_t
Valid prediction for GlimmerHMM_glimmerT_22832-T1
Valid prediction for GeneMark_model.39209_t
Valid prediction for snap_scaffold_9-snap.1433-T1
Valid prediction for Augustus_model.g15282.t1
Valid prediction for Augustus_model.g15286.t1
Couldn't classify 225530, 225561
Couldn't classify 226632, 227071
Sorry, prediction pasa_asmbl_54088.p1 fails validation.
(GCT)	 TG	225530-225561	GT	CGG
(ATG)	 AG	226020-226140	GT	CGG
(AGC)	 AG	226230-226337	GT	TGG
(ACA)	 AG	226488-226524	GT	ATG
(TGG)	 AG	226632-227071	CT	ATC
add_exon() Sorry, pasa_asmbl_54088.p1 226020-226140-initial-1 is invalid.
-recovered pasa_asmbl_54088.p1, initial, 226020, 226140
-recovered pasa_asmbl_54088.p1, internal, 226020, 226140
-recovered pasa_asmbl_54088.p1, internal, 226230, 226337
-recovered pasa_asmbl_54088.p1, internal, 226488, 226524
Valid prediction for GlimmerHMM_glimmerT_22836-T1
Valid prediction for GeneMark_model.39208_t
Valid prediction for snap_scaffold_9-snap.1414-T1
Valid prediction for snap_scaffold_9-snap.1401-T1
Valid prediction for Augustus_model.g15268.t1
Valid prediction for Augustus_model.g15279.t1
Valid prediction for GeneMark_model.39221_t
Couldn't classify 247393, 247692
Sorry, prediction pasa_asmbl_54092.p2 fails validation.
(GGC)	 GA	247393-247692	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_22851-T1
Valid prediction for GeneMark_model.39197_t
Valid prediction for GlimmerHMM_glimmerT_22848-T1
Valid prediction for pasa_asmbl_54087.p1
Valid prediction for snap_scaffold_9-snap.1416-T1
Valid prediction for CodingQuarry_transcript_62056-T1
Valid prediction for snap_scaffold_9-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_22843-T1
Valid prediction for GlimmerHMM_glimmerT_22828-T1
Valid prediction for GeneMark_model.39213_t
Valid prediction for snap_scaffold_9-snap.1427-T1
Valid prediction for HiQ_model.g15287.t1
Valid prediction for GeneMark_model.39202_t
Valid prediction for snap_scaffold_9-snap.1397-T1
Valid prediction for snap_scaffold_9-snap.1398-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1426-T1
Valid prediction for GeneMark_model.39223_t
Valid prediction for snap_scaffold_9-snap.1408-T1
Valid prediction for GlimmerHMM_glimmerT_22830-T1
Valid prediction for snap_scaffold_9-snap.1424-T1
Valid prediction for snap_scaffold_9-snap.1411-T1
Valid prediction for GeneMark_model.39216_t
Valid prediction for GlimmerHMM_glimmerT_22829-T1
Valid prediction for GlimmerHMM_glimmerT_22846-T1
Valid prediction for GeneMark_model.39231_t
Valid prediction for GeneMark_model.39200_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: -)Couldn't classify 250933, 251022
Sorry, prediction pasa_asmbl_55027.p1 fails validation.
(CGC)	 CT	250933-251022	GT	AAG
(GTT)	 AG	251106-251201	GT	TGG
(GTG)	 AG	251296-251446	GT	TGG
(AGG)	 AG	251534-251580	AA	GAA
-recovered pasa_asmbl_55027.p1, terminal, 251534, 251580
-recovered pasa_asmbl_55027.p1, internal, 251106, 251201
-recovered pasa_asmbl_55027.p1, internal, 251296, 251446
Valid prediction for HiQ_model.g15274.t1
Couldn't classify 11527, 11922
Sorry, prediction pasa_asmbl_55046.p2 fails validation.
(CAG)	 CA	11527-11922	GT	GAG
Valid prediction for CodingQuarry_transcript_62055-T1
Valid prediction for snap_scaffold_9-snap.1420-T1
Valid prediction for HiQ_model.g15277.t1
Valid prediction for Augustus_model.g15295.t1
Valid prediction for GeneMark_model.39232_t
Valid prediction for GeneMark_model.39215_t
Valid prediction for GeneMark_model.39229_t
Valid prediction for CodingQuarry_transcript_62061-T1
Valid prediction for GlimmerHMM_glimmerT_22838-T1
Valid prediction for snap_scaffold_9-snap.1407-T1
Valid prediction for snap_scaffold_9-snap.1435-T1
Valid prediction for snap_scaffold_9-snap.1429-T1
Valid prediction for GlimmerHMM_glimmerT_22825-T1
Valid prediction for Augustus_model.g15284.t1
Valid prediction for HiQ_model.g15288.t1
Valid prediction for CodingQuarry_transcript_62054-T1
Valid prediction for Augustus_model.g15296.t1
Valid prediction for snap_scaffold_9-snap.1395-T1
Valid prediction for snap_scaffold_9-snap.1417-T1
Valid prediction for GeneMark_model.39233_t
Valid prediction for snap_scaffold_9-snap.1413-T1
Valid prediction for GlimmerHMM_glimmerT_22826-T1
Valid prediction for snap_scaffold_9-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_22857-T1
Valid prediction for snap_scaffold_9-snap.1394-T1
Valid prediction for GlimmerHMM_glimmerT_22849-T1
Valid prediction for snap_scaffold_9-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_22833-T1
Valid prediction for snap_scaffold_9-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_22859-T1
Valid prediction for snap_scaffold_9-snap.1440-T1
Valid prediction for GeneMark_model.39194_t
Valid prediction for Augustus_model.g15267.t1
Valid prediction for CodingQuarry_transcript_62053-T1
Valid prediction for CodingQuarry_transcript_62052-T1
Valid prediction for snap_scaffold_9-snap.1403-T1
Valid prediction for CodingQuarry_transcript_62059-T1
Valid prediction for snap_scaffold_9-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_22860-T1
Valid prediction for GlimmerHMM_glimmerT_22840-T1
Valid prediction for GeneMark_model.39218_t
Valid prediction for GeneMark_model.39225_t
Couldn't classify 170631, 170732
Couldn't classify 171364, 171448
Sorry, prediction pasa_asmbl_55742.p1 fails validation.
(GAC)	 AC	170631-170732	GT	GGG
(CCC)	 AG	170938-171016	GT	CAG
(GTG)	 AG	171140-171245	GT	TGG
(TTT)	 AG	171364-171448	AT	CCA
-recovered pasa_asmbl_55742.p1, internal, 170938, 171016
-recovered pasa_asmbl_55742.p1, internal, 171140, 171245
Valid prediction for pasa_asmbl_55043.p1
Valid prediction for GeneMark_model.39210_t
Valid prediction for HiQ_model.g15291.t1
Valid prediction for Augustus_model.g15290.t1
Valid prediction for CodingQuarry_transcript_62050-T1
Valid prediction for GlimmerHMM_glimmerT_22854-T1
Valid prediction for snap_scaffold_9-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_22841-T1
Valid prediction for GeneMark_model.39199_t
Valid prediction for snap_scaffold_9-snap.1410-T1
Valid prediction for CodingQuarry_transcript_62060-T1
Valid prediction for GeneMark_model.39211_t
Valid prediction for snap_scaffold_9-snap.1432-T1
Valid prediction for Augustus_model.g15293.t1
Valid prediction for GeneMark_model.39230_t
Valid prediction for snap_scaffold_9-snap.1405-T1
Valid prediction for snap_scaffold_9-snap.1392-T1
Valid prediction for snap_scaffold_9-snap.1400-T1
Valid prediction for GeneMark_model.39198_t
Valid prediction for snap_scaffold_9-snap.1415-T1
Valid prediction for GeneMark_model.39204_t
Valid prediction for GeneMark_model.39196_t
Valid prediction for GeneMark_model.39212_t
Valid prediction for snap_scaffold_9-snap.1439-T1
Valid prediction for Augustus_model.g15276.t1
Valid prediction for snap_scaffold_9-snap.1436-T1
Valid prediction for GeneMark_model.39203_t
Valid prediction for GlimmerHMM_glimmerT_22831-T1
Couldn't classify 149622, 149762
Sorry, prediction pasa_asmbl_55032.p1 fails validation.
(CTG)	 AC	149622-149762	GT	AGG
(CGT)	 AG	149953-150028	GT	AGG
(GCT)	 AG	150175-150277	GT	GGG
(GGT)	 AG	150558-150651	GT	ATG
(GTC)	 AG	150883-150994	GT	AGG
(AAA)	 AG	151225-151331	GT	AGG
(CAA)	 AG	151479-151520	GT	AAG
(GCT)	 AG	152858-152943	GT	AGG
(GGC)	 AG	153103-153226	GT	AGG
(GAA)	 AG	153370-153503	GT	GGG
(TGC)	 AG	153645-153745	GT	AGG
(GAT)	 AG	155352-155462	GT	TGG
(ATA)	 AG	155575-155697	GT	CAG
(ATC)	 AG	155926-155956	GT	AAG
(TGA)	 AG	156080-156179	GT	TGG
(CCT)	 AG	156341-156400	GT	TGG
(CCC)	 AG	156543-156647	GT	AGG
(ATG)	 AG	157925-157939	TA	AAT
add_exon() Sorry, pasa_asmbl_55032.p1 150883-150994-terminal-3 is invalid.
-recovered pasa_asmbl_55032.p1, terminal, 150883, 150994
-recovered pasa_asmbl_55032.p1, terminal, 157925, 157939
-recovered pasa_asmbl_55032.p1, internal, 149953, 150028
-recovered pasa_asmbl_55032.p1, internal, 150175, 150277
-recovered pasa_asmbl_55032.p1, internal, 150558, 150651
-recovered pasa_asmbl_55032.p1, internal, 150883, 150994
-recovered pasa_asmbl_55032.p1, internal, 151225, 151331
-recovered pasa_asmbl_55032.p1, internal, 151479, 151520
-recovered pasa_asmbl_55032.p1, internal, 152858, 152943
-recovered pasa_asmbl_55032.p1, internal, 153103, 153226
-recovered pasa_asmbl_55032.p1, internal, 153370, 153503
-recovered pasa_asmbl_55032.p1, internal, 153645, 153745
-recovered pasa_asmbl_55032.p1, internal, 155352, 155462
-recovered pasa_asmbl_55032.p1, internal, 155575, 155697
-recovered pasa_asmbl_55032.p1, internal, 155926, 155956
-recovered pasa_asmbl_55032.p1, internal, 156080, 156179
-recovered pasa_asmbl_55032.p1, internal, 156341, 156400
-recovered pasa_asmbl_55032.p1, internal, 156543, 156647
Valid prediction for GlimmerHMM_glimmerT_22855-T1
Valid prediction for GlimmerHMM_glimmerT_22844-T1
Valid prediction for Augustus_model.g15269.t1
Valid prediction for pasa_asmbl_55029.p1
Valid prediction for Augustus_model.g15271.t1
Valid prediction for GlimmerHMM_glimmerT_22852-T1
Valid prediction for snap_scaffold_9-snap.1437-T1
Couldn't classify 50845, 50985
Sorry, prediction pasa_asmbl_55040.p1 fails validation.
(CCC)	 CG	50845-50985	GT	AGG
(GCT)	 AG	51194-51287	GT	AGG
(GAT)	 AG	51534-51680	GT	AGG
(GCC)	 AG	52227-52322	GT	TGG
(GTG)	 AG	52664-52806	AC	AAA
add_exon() Sorry, pasa_asmbl_55040.p1 51194-51287-terminal-3 is invalid.
-recovered pasa_asmbl_55040.p1, terminal, 51194, 51287
-recovered pasa_asmbl_55040.p1, terminal, 52664, 52806
-recovered pasa_asmbl_55040.p1, internal, 51194, 51287
-recovered pasa_asmbl_55040.p1, internal, 51534, 51680
-recovered pasa_asmbl_55040.p1, internal, 52227, 52322
Valid prediction for snap_scaffold_9-snap.1402-T1
Valid prediction for GeneMark_model.39228_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19473, rend_intergenic: 18204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78875, rend_intergenic: 76024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112014, rend_intergenic: 107586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148939, rend_intergenic: 141880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 310267
-exon list size: 722


building trellis

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54.3    
54.4    
54.6    
54.7    
54.8    
55.0    
55.1    
55.2    
55.4    
55.5    
55.7    
55.8    
55.9    
56.1    
56.2    
56.4    
56.5    
56.6    
56.8    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.7    
57.9    
58.0    
58.1    
58.3    
58.4    
58.6    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.5    
59.7    
59.8    
59.9    
60.1    
60.2    
60.4    
60.5    
60.6    
60.8    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.4    
62.6    
62.7    
62.8    
63.0    
63.1    
63.3    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 19473, rend_intergenic: 18204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78875, rend_intergenic: 76024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112014, rend_intergenic: 107586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148939, rend_intergenic: 141880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support