-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_3653398-3789483

-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_24-snap.799-T1
Valid prediction for snap_scaffold_24-snap.810-T1
Valid prediction for snap_scaffold_24-snap.806-T1
Valid prediction for GlimmerHMM_glimmerT_53592-T1
Valid prediction for pasa_asmbl_32171.p1
Valid prediction for snap_scaffold_24-snap.802-T1
Valid prediction for GeneMark_model.93530_t
Valid prediction for GeneMark_model.93560_t
Valid prediction for GlimmerHMM_glimmerT_53587-T1
Valid prediction for GlimmerHMM_glimmerT_53601-T1
Valid prediction for snap_scaffold_24-snap.817-T1
Valid prediction for Augustus_model.g35875.t1
Valid prediction for GeneMark_model.93536_t
Valid prediction for Augustus_model.g35873.t1
Valid prediction for GeneMark_model.93538_t
Valid prediction for snap_scaffold_24-snap.823-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.93540_t
Valid prediction for GeneMark_model.93554_t
Valid prediction for CodingQuarry_transcript_37212-T1
Valid prediction for GeneMark_model.93527_t
Valid prediction for GlimmerHMM_glimmerT_53594-T1
Valid prediction for snap_scaffold_24-snap.809-T1
Valid prediction for snap_scaffold_24-snap.818-T1
Valid prediction for HiQ_model.g35871.t1
Valid prediction for GeneMark_model.93542_t
Valid prediction for GlimmerHMM_glimmerT_53600-T1
Valid prediction for snap_scaffold_24-snap.819-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_37213-T1
Valid prediction for snap_scaffold_24-snap.801-T1
Valid prediction for GlimmerHMM_glimmerT_53596-T1
Valid prediction for snap_scaffold_24-snap.822-T1
Valid prediction for pasa_asmbl_32174.p1
Valid prediction for snap_scaffold_24-snap.805-T1
Valid prediction for snap_scaffold_24-snap.803-T1
Valid prediction for HiQ_model.g35877.t1
Valid prediction for Augustus_model.g35885.t1
Valid prediction for GeneMark_model.93528_t
Valid prediction for GlimmerHMM_glimmerT_53603-T1
Valid prediction for GlimmerHMM_glimmerT_53599-T1
Valid prediction for GeneMark_model.93550_t
Valid prediction for GeneMark_model.93532_t
Valid prediction for GeneMark_model.93526_t
Valid prediction for snap_scaffold_24-snap.812-T1
Valid prediction for pasa_asmbl_32169.p1
Valid prediction for snap_scaffold_24-snap.814-T1
Valid prediction for snap_scaffold_24-snap.808-T1
Valid prediction for GlimmerHMM_glimmerT_53584-T1
Valid prediction for GlimmerHMM_glimmerT_53591-T1
Valid prediction for Augustus_model.g35878.t1
Valid prediction for Augustus_model.g35880.t1
Valid prediction for GeneMark_model.93546_t
Valid prediction for HiQ_model.g35869.t1
Valid prediction for GeneMark_model.93534_t
Valid prediction for Augustus_model.g35882.t1
Valid prediction for GlimmerHMM_glimmerT_53586-T1
Valid prediction for Augustus_model.g35876.t1
Valid prediction for snap_scaffold_24-snap.804-T1
Valid prediction for Augustus_model.g35884.t1
Valid prediction for HiQ_model.g35883.t1
Valid prediction for GeneMark_model.93544_t
Valid prediction for snap_scaffold_24-snap.816-T1
Valid prediction for GeneMark_model.93556_t
Valid prediction for snap_scaffold_24-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_53590-T1
Valid prediction for GlimmerHMM_glimmerT_53598-T1
Valid prediction for GeneMark_model.93552_t
Valid prediction for GeneMark_model.93548_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 GlimmerHMM_glimmerT_53593-T1
Valid prediction for GlimmerHMM_glimmerT_53585-T1
Valid prediction for GeneMark_model.93535_t
Valid prediction for GeneMark_model.93529_t
Valid prediction for Augustus_model.g35887.t1
Valid prediction for GeneMark_model.93545_t
Couldn't classify 130495, 130552
Sorry, prediction pasa_asmbl_32824.p1 fails validation.
(ACT)	 CC	130495-130552	GT	TGG
(CTT)	 AG	130708-130773	GT	AGG
(ATC)	 AG	131242-131342	GT	AGG
(GGA)	 AG	131697-131822	GT	GGG
(AAT)	 AG	132211-132277	GT	AGG
(ATA)	 AG	132388-132468	GT	AGG
(TCC)	 AG	132563-132603	GA	AAG
add_exon() Sorry, pasa_asmbl_32824.p1 132211-132277-terminal-3 is invalid.
-recovered pasa_asmbl_32824.p1, terminal, 132211, 132277
-recovered pasa_asmbl_32824.p1, terminal, 132563, 132603
-recovered pasa_asmbl_32824.p1, internal, 130708, 130773
-recovered pasa_asmbl_32824.p1, internal, 131242, 131342
-recovered pasa_asmbl_32824.p1, internal, 131697, 131822
-recovered pasa_asmbl_32824.p1, internal, 132211, 132277
-recovered pasa_asmbl_32824.p1, internal, 132388, 132468
Valid prediction for GeneMark_model.93543_t
Couldn't classify 25378, 25481
Couldn't classify 26136, 26358
Sorry, prediction pasa_asmbl_32837.p1 fails validation.
(GAT)	 TC	25378-25481	GT	AGG
(TCT)	 AG	25571-25666	GT	AGG
(GTT)	 AG	26136-26358	GT	AGG
-recovered pasa_asmbl_32837.p1, internal, 25571, 25666
-recovered pasa_asmbl_32837.p1, internal, 26136, 26358
Valid prediction for snap_scaffold_24-snap.800-T1
Valid prediction for snap_scaffold_24-snap.807-T1
Valid prediction for GeneMark_model.93524_t
Valid prediction for GlimmerHMM_glimmerT_53602-T1
Couldn't classify 6805, 6873
Couldn't classify 10890, 11030
Sorry, prediction pasa_asmbl_32843.p1 fails validation.
(AGG)	 AG	6805-6873	GT	AGG
(GAA)	 AG	7905-7940	GT	GGG
(TTT)	 AG	8237-8302	GT	GGG
(TGT)	 AG	10090-10155	GT	AGG
(CCC)	 AG	10497-10571	GT	AGG
(CGT)	 AG	10890-11030	AT	AGA
-recovered pasa_asmbl_32843.p1, internal, 6805, 6873
-recovered pasa_asmbl_32843.p1, internal, 7905, 7940
-recovered pasa_asmbl_32843.p1, internal, 8237, 8302
-recovered pasa_asmbl_32843.p1, internal, 10090, 10155
-recovered pasa_asmbl_32843.p1, internal, 10497, 10571
Valid prediction for HiQ_model.g35879.t1
Valid prediction for snap_scaffold_24-snap.811-T1
Valid prediction for snap_scaffold_24-snap.820-T1
Valid prediction for GeneMark_model.93551_t
Valid prediction for GlimmerHMM_glimmerT_53583-T1
Valid prediction for GlimmerHMM_glimmerT_53605-T1
Valid prediction for Augustus_model.g35888.t1
Couldn't classify 63899, 63955
Couldn't classify 65088, 65192
Sorry, prediction pasa_asmbl_33273.p1 fails validation.
(AAG)	 TT	63899-63955	GT	AGG
(GTG)	 AG	64796-64951	GT	AGG
(GTG)	 AG	65088-65192	GG	TGG
-recovered pasa_asmbl_33273.p1, internal, 64796, 64951
Valid prediction for snap_scaffold_24-snap.821-T1
Valid prediction for snap_scaffold_24-snap.798-T1
Valid prediction for Augustus_model.g35870.t1
Valid prediction for GeneMark_model.93553_t
Valid prediction for GlimmerHMM_glimmerT_53595-T1
Couldn't classify 11290, 11377
Couldn't classify 13197, 13358
Sorry, prediction pasa_asmbl_32841.p1 fails validation.
(GTG)	 CA	11290-11377	GT	GGG
(GTA)	 AG	11847-11950	GT	AGG
(GCC)	 AG	12298-12405	GT	AGG
(AGC)	 AG	12810-12905	GT	AGG
(GTG)	 AG	13197-13358	GT	AGG
-recovered pasa_asmbl_32841.p1, internal, 11847, 11950
-recovered pasa_asmbl_32841.p1, internal, 12298, 12405
-recovered pasa_asmbl_32841.p1, internal, 12810, 12905
-recovered pasa_asmbl_32841.p1, internal, 13197, 13358
Valid prediction for GeneMark_model.93537_t
Valid prediction for GlimmerHMM_glimmerT_53604-T1
Valid prediction for snap_scaffold_24-snap.813-T1
Valid prediction for snap_scaffold_24-snap.824-T1
Valid prediction for GeneMark_model.93557_t
Valid prediction for Augustus_model.g35872.t1
Valid prediction for pasa_asmbl_32835.p1
Valid prediction for Augustus_model.g35881.t1
Valid prediction for GeneMark_model.93531_t
Valid prediction for GeneMark_model.93541_t
Couldn't classify 73944, 74060
Sorry, prediction pasa_asmbl_32826.p1 fails validation.
(ATG)	 GC	73258-73357	GT	AAG
(GCT)	 AG	73459-73622	GT	AGG
(ATC)	 AG	73944-74060	CA	GCC
-recovered pasa_asmbl_32826.p1, initial, 73258, 73357
-recovered pasa_asmbl_32826.p1, internal, 73459, 73622
Valid prediction for GeneMark_model.93539_t
Valid prediction for GeneMark_model.93555_t
Valid prediction for GeneMark_model.93558_t
Valid prediction for CodingQuarry_transcript_37211-T1
Valid prediction for GlimmerHMM_glimmerT_53597-T1
Valid prediction for GlimmerHMM_glimmerT_53589-T1
Couldn't classify 27771, 27798
Sorry, prediction pasa_asmbl_32831.p1 fails validation.
(GGG)	 TA	27771-27798	GT	TGG
(GCA)	 AG	27883-28044	GT	CTG
(CCT)	 AG	28167-28237	GT	AGG
(ATC)	 AG	28430-28590	GT	AGG
(GCT)	 AG	28680-28741	GT	CAG
(GTT)	 AG	29241-29432	GT	AGG
(GTG)	 AG	29711-29825	GT	AAG
(ATG)	 AG	30005-30149	GT	ATG
(TAC)	 AG	30458-30577	GT	AGG
(GCG)	 AG	30946-31071	GT	AGG
(ATC)	 AG	31402-31500	GT	AGG
(AAA)	 AG	31782-31864	GT	AGG
(GTA)	 AG	31943-32084	GT	AGG
(AGG)	 AG	33255-33374	GT	GGG
(TTC)	 AG	33978-34192	GT	CGG
(TGG)	 AG	34980-35104	GT	GTG
(CCA)	 AG	35256-35397	GT	CTG
(GTC)	 AG	35828-35978	GT	AGG
(ATG)	 AG	36127-36222	GT	CAG
(ACC)	 AG	36414-36517	GT	CGG
(GGT)	 AG	37306-37419	GT	AAG
(GGT)	 AG	39595-39802	GT	GGG
(GGA)	 AG	40596-40685	GT	AGG
(AAC)	 AG	41051-41153	GT	GCG
(CTC)	 AG	41381-41499	GT	AGG
(GTG)	 AG	41661-41774	GT	AGG
(ACC)	 AG	41977-42042	GT	TGG
(GTG)	 AG	42517-42583	GT	GGG
(CTC)	 AG	43390-43468	GT	AAG
(GTG)	 AG	43671-43746	GC	AGG
(ATG)	 AG	44200-44286	GT	AGG
(GAC)	 AG	44645-44755	GT	AGG
(GGT)	 AG	45033-45095	CA	AGC
add_exon() Sorry, pasa_asmbl_32831.p1 30005-30149-initial-1 is invalid.
-recovered pasa_asmbl_32831.p1, initial, 30005, 30149
-recovered pasa_asmbl_32831.p1, initial, 36127, 36222
-recovered pasa_asmbl_32831.p1, initial, 44200, 44286
add_exon() Sorry, pasa_asmbl_32831.p1 29241-29432-terminal-1 is invalid.
-recovered pasa_asmbl_32831.p1, terminal, 29241, 29432
-recovered pasa_asmbl_32831.p1, terminal, 45033, 45095
-recovered pasa_asmbl_32831.p1, internal, 27883, 28044
-recovered pasa_asmbl_32831.p1, internal, 28167, 28237
-recovered pasa_asmbl_32831.p1, internal, 28430, 28590
-recovered pasa_asmbl_32831.p1, internal, 28680, 28741
-recovered pasa_asmbl_32831.p1, internal, 29241, 29432
-recovered pasa_asmbl_32831.p1, internal, 29711, 29825
-recovered pasa_asmbl_32831.p1, internal, 30005, 30149
-recovered pasa_asmbl_32831.p1, internal, 30458, 30577
-recovered pasa_asmbl_32831.p1, internal, 30946, 31071
-recovered pasa_asmbl_32831.p1, internal, 31402, 31500
-recovered pasa_asmbl_32831.p1, internal, 31782, 31864
-recovered pasa_asmbl_32831.p1, internal, 31943, 32084
-recovered pasa_asmbl_32831.p1, internal, 33255, 33374
-recovered pasa_asmbl_32831.p1, internal, 33978, 34192
-recovered pasa_asmbl_32831.p1, internal, 34980, 35104
-recovered pasa_asmbl_32831.p1, internal, 35256, 35397
-recovered pasa_asmbl_32831.p1, internal, 35828, 35978
-recovered pasa_asmbl_32831.p1, internal, 36127, 36222
-recovered pasa_asmbl_32831.p1, internal, 36414, 36517
-recovered pasa_asmbl_32831.p1, internal, 37306, 37419
-recovered pasa_asmbl_32831.p1, internal, 39595, 39802
-recovered pasa_asmbl_32831.p1, internal, 40596, 40685
-recovered pasa_asmbl_32831.p1, internal, 41051, 41153
-recovered pasa_asmbl_32831.p1, internal, 41381, 41499
-recovered pasa_asmbl_32831.p1, internal, 41661, 41774
-recovered pasa_asmbl_32831.p1, internal, 41977, 42042
-recovered pasa_asmbl_32831.p1, internal, 42517, 42583
-recovered pasa_asmbl_32831.p1, internal, 43390, 43468
-recovered pasa_asmbl_32831.p1, internal, 43671, 43746
-recovered pasa_asmbl_32831.p1, internal, 44200, 44286
-recovered pasa_asmbl_32831.p1, internal, 44645, 44755
Valid prediction for GeneMark_model.93549_t
Valid prediction for GlimmerHMM_glimmerT_53588-T1
Couldn't classify 66243, 66341
Couldn't classify 68214, 68298
Sorry, prediction pasa_asmbl_32828.p1 fails validation.
(GGC)	 CT	66243-66341	GT	AGG
(GAG)	 AG	66619-66882	GT	AGG
(ATA)	 AG	66971-67114	GT	AGG
(GAT)	 AG	67613-67810	GT	ACG
(GTG)	 AG	67894-68072	GT	GGG
(TTT)	 AG	68214-68298	GA	GAG
-recovered pasa_asmbl_32828.p1, internal, 66619, 66882
-recovered pasa_asmbl_32828.p1, internal, 66971, 67114
-recovered pasa_asmbl_32828.p1, internal, 67613, 67810
-recovered pasa_asmbl_32828.p1, internal, 67894, 68072
Valid prediction for GeneMark_model.93547_t
Valid prediction for Augustus_model.g35874.t1
Couldn't classify 23735, 23911
Sorry, prediction pasa_asmbl_32839.p1 fails validation.
(ATG)	 AG	19466-19521	GT	AGG
(GTC)	 AG	20224-20290	GT	AGG
(GAC)	 AG	20553-20663	GT	AGG
(GCC)	 AG	20768-20866	GT	TGG
(CTG)	 AG	21181-21354	GT	AGG
(GAG)	 AG	22980-23065	GT	AGG
(GAT)	 AG	23445-23553	GT	AGG
(AAG)	 AG	23735-23911	TC	GCT
-recovered pasa_asmbl_32839.p1, initial, 19466, 19521
-recovered pasa_asmbl_32839.p1, internal, 19466, 19521
-recovered pasa_asmbl_32839.p1, internal, 20224, 20290
-recovered pasa_asmbl_32839.p1, internal, 20553, 20663
-recovered pasa_asmbl_32839.p1, internal, 20768, 20866
-recovered pasa_asmbl_32839.p1, internal, 21181, 21354
-recovered pasa_asmbl_32839.p1, internal, 22980, 23065
-recovered pasa_asmbl_32839.p1, internal, 23445, 23553
Valid prediction for Augustus_model.g35886.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10427, rend_intergenic: 9201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66686, rend_intergenic: 64942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72185, rend_intergenic: 67676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87280, rend_intergenic: 82135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130620, rend_intergenic: 88830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136086
-exon list size: 542


building trellis

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67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 10427, rend_intergenic: 9201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66686, rend_intergenic: 64942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72185, rend_intergenic: 67676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87280, rend_intergenic: 82135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130620, rend_intergenic: 88830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support