-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1519764-1755329

-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.g3950.t1
Valid prediction for snap_scaffold_3-snap.396-T1
Valid prediction for snap_scaffold_3-snap.393-T1
Valid prediction for snap_scaffold_3-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_6061-T1
Valid prediction for snap_scaffold_3-snap.401-T1
Valid prediction for GlimmerHMM_glimmerT_6059-T1
Valid prediction for GlimmerHMM_glimmerT_6073-T1
Valid prediction for CodingQuarry_transcript_46087-T1
Valid prediction for snap_scaffold_3-snap.391-T1
Valid prediction for pasa_asmbl_39861.p1
Valid prediction for GlimmerHMM_glimmerT_6049-T1
Valid prediction for GlimmerHMM_glimmerT_6048-T1
Valid prediction for GlimmerHMM_glimmerT_6051-T1
Valid prediction for snap_scaffold_3-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_6071-T1
Valid prediction for snap_scaffold_3-snap.424-T1
Couldn't classify 52375, 52423
Sorry, prediction pasa_asmbl_39865.p1 fails validation.
(GCC)	 GG	52375-52423	GT	AGG
(ATG)	 AG	52613-52984	GT	ACG
(ACT)	 AG	53580-53673	GT	AGG
(GTT)	 AG	53887-53980	AT	GAA
add_exon() Sorry, pasa_asmbl_39865.p1 52613-52984-initial-1 is invalid.
-recovered pasa_asmbl_39865.p1, initial, 52613, 52984
-recovered pasa_asmbl_39865.p1, terminal, 53887, 53980
-recovered pasa_asmbl_39865.p1, internal, 52613, 52984
-recovered pasa_asmbl_39865.p1, internal, 53580, 53673
Valid prediction for pasa_asmbl_39863.p1
Valid prediction for CodingQuarry_transcript_46084-T1
Valid prediction for snap_scaffold_3-snap.382-T1
Valid prediction for Augustus_model.g3956.t1
Valid prediction for snap_scaffold_3-snap.375-T1
Valid prediction for snap_scaffold_3-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_6055-T1
Valid prediction for Augustus_model.g3948.t1
Valid prediction for GlimmerHMM_glimmerT_6066-T1
Valid prediction for snap_scaffold_3-snap.413-T1
Couldn't classify 9108, 9109
Sorry, prediction pasa_asmbl_39859.p1 fails validation.
(ATG)	 AG	3027-3771	GT	GGG
(CGC)	 AG	5534-5652	GT	AGG
(GCC)	 AG	5811-5933	GT	AGG
(GTG)	 AG	6502-6660	GT	AGG
(GAC)	 AG	7012-7210	GT	AGG
(ATG)	 AG	7411-7513	GT	AGG
(GCT)	 AG	7623-7737	GT	AGG
(TAC)	 AG	8118-8239	GT	AAG
(CCT)	 AG	8470-8795	GT	GTG
(AGG)	 AG	9108-9109	GG	AGG
-recovered pasa_asmbl_39859.p1, initial, 3027, 3771
add_exon() Sorry, pasa_asmbl_39859.p1 7411-7513-initial-1 is invalid.
-recovered pasa_asmbl_39859.p1, initial, 7411, 7513
-recovered pasa_asmbl_39859.p1, internal, 3027, 3771
-recovered pasa_asmbl_39859.p1, internal, 5534, 5652
-recovered pasa_asmbl_39859.p1, internal, 5811, 5933
-recovered pasa_asmbl_39859.p1, internal, 6502, 6660
-recovered pasa_asmbl_39859.p1, internal, 7012, 7210
-recovered pasa_asmbl_39859.p1, internal, 7411, 7513
-recovered pasa_asmbl_39859.p1, internal, 7623, 7737
-recovered pasa_asmbl_39859.p1, internal, 8118, 8239
-recovered pasa_asmbl_39859.p1, internal, 8470, 8795
Valid prediction for CodingQuarry_transcript_46081-T1
Valid prediction for GlimmerHMM_glimmerT_6043-T1
Valid prediction for Augustus_model.g3951.t1
Valid prediction for snap_scaffold_3-snap.418-T1
Valid prediction for snap_scaffold_3-snap.386-T1
Valid prediction for snap_scaffold_3-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_6068-T1
Valid prediction for snap_scaffold_3-snap.423-T1
Valid prediction for snap_scaffold_3-snap.420-T1
Couldn't classify 9108, 9109
Sorry, prediction CodingQuarry_transcript_46077-T1 fails validation.
(ATG)	 AG	3708-3771	GT	GGG
(CGC)	 AG	5534-5652	GT	AGG
(GCC)	 AG	5811-5933	GT	AGG
(GTG)	 AG	6502-6660	GT	AGG
(GAC)	 AG	7012-7210	GT	AGG
(ATG)	 AG	7411-7513	GT	AGG
(GCT)	 AG	7623-7737	GT	AGG
(TAC)	 AG	8118-8239	GT	AAG
(CCT)	 AG	8470-8795	GT	GTG
(AGG)	 AG	9108-9109	GG	AGG
-recovered CodingQuarry_transcript_46077-T1, initial, 3708, 3771
add_exon() Sorry, CodingQuarry_transcript_46077-T1 7411-7513-initial-1 is invalid.
-recovered CodingQuarry_transcript_46077-T1, initial, 7411, 7513
-recovered CodingQuarry_transcript_46077-T1, internal, 3708, 3771
-recovered CodingQuarry_transcript_46077-T1, internal, 5534, 5652
-recovered CodingQuarry_transcript_46077-T1, internal, 5811, 5933
-recovered CodingQuarry_transcript_46077-T1, internal, 6502, 6660
-recovered CodingQuarry_transcript_46077-T1, internal, 7012, 7210
-recovered CodingQuarry_transcript_46077-T1, internal, 7411, 7513
-recovered CodingQuarry_transcript_46077-T1, internal, 7623, 7737
-recovered CodingQuarry_transcript_46077-T1, internal, 8118, 8239
-recovered CodingQuarry_transcript_46077-T1, internal, 8470, 8795
Valid prediction for GlimmerHMM_glimmerT_6060-T1
Valid prediction for snap_scaffold_3-snap.376-T1
Valid prediction for snap_scaffold_3-snap.385-T1
Valid prediction for Augustus_model.g3960.t1
Valid prediction for GlimmerHMM_glimmerT_6067-T1
Valid prediction for GlimmerHMM_glimmerT_6065-T1
Valid prediction for snap_scaffold_3-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_6063-T1
Valid prediction for GlimmerHMM_glimmerT_6069-T1
Valid prediction for HiQ_model.g3944.t1
Valid prediction for GlimmerHMM_glimmerT_6057-T1
Couldn't classify 49046, 49070
Sorry, prediction pasa_asmbl_40852.p3 fails validation.
(GGC)	 CC	49046-49070	GT	AGG
(AGG)	 AG	49392-49534	GT	TGG
(CCC)	 AG	49725-49877	GT	AGG
(GTG)	 AG	50229-50297	AA	GAA
-recovered pasa_asmbl_40852.p3, terminal, 50229, 50297
-recovered pasa_asmbl_40852.p3, internal, 49392, 49534
-recovered pasa_asmbl_40852.p3, internal, 49725, 49877
Valid prediction for snap_scaffold_3-snap.389-T1
Valid prediction for snap_scaffold_3-snap.383-T1
Valid prediction for Augustus_model.g3955.t1
Valid prediction for snap_scaffold_3-snap.416-T1
Valid prediction for Augustus_model.g3961.t1
Valid prediction for snap_scaffold_3-snap.384-T1
Valid prediction for snap_scaffold_3-snap.399-T1
Valid prediction for CodingQuarry_transcript_46085-T1
Valid prediction for snap_scaffold_3-snap.421-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_6047-T1
Valid prediction for Augustus_model.g3954.t1
Valid prediction for snap_scaffold_3-snap.422-T1
Valid prediction for Augustus_model.g3958.t1
Valid prediction for snap_scaffold_3-snap.403-T1
Valid prediction for snap_scaffold_3-snap.397-T1
Valid prediction for snap_scaffold_3-snap.419-T1
Valid prediction for snap_scaffold_3-snap.404-T1
Valid prediction for snap_scaffold_3-snap.392-T1
Valid prediction for snap_scaffold_3-snap.390-T1
Valid prediction for snap_scaffold_3-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_6072-T1
Valid prediction for snap_scaffold_3-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_6062-T1
Valid prediction for snap_scaffold_3-snap.409-T1
Couldn't classify 222694, 223068
Sorry, prediction pasa_asmbl_38715.p1 fails validation.
(GGG)	 CC	222694-223068	CG	AGC
Valid prediction for Augustus_model.g3945.t1
Valid prediction for snap_scaffold_3-snap.379-T1
Valid prediction for Augustus_model.g3952.t1
Valid prediction for snap_scaffold_3-snap.408-T1
Valid prediction for HiQ_model.g3949.t1
Couldn't classify 218221, 218433
Couldn't classify 218610, 218709
Sorry, prediction CodingQuarry_transcript_46080-T1 fails validation.
(ATG)	 GC	214812-214986	GT	TGG
(GAT)	 AG	215572-215699	GT	AGG
(GGC)	 AG	216250-216359	GT	CAG
(CTA)	 AG	216547-216734	GT	AGG
(GTA)	 AG	217474-217716	GT	ATG
(TGT)	 AG	217818-218098	GT	CGG
(GAG)	 AG	218221-218433	TG	TAT
(AAG)	 GC	218610-218709	GT	AGG
(AGC)	 AG	218928-219121	GT	CGG
(GAG)	 AG	219306-219437	GC	AAG
-recovered CodingQuarry_transcript_46080-T1, initial, 214812, 214986
-recovered CodingQuarry_transcript_46080-T1, terminal, 219306, 219437
-recovered CodingQuarry_transcript_46080-T1, internal, 215572, 215699
-recovered CodingQuarry_transcript_46080-T1, internal, 216250, 216359
-recovered CodingQuarry_transcript_46080-T1, internal, 216547, 216734
-recovered CodingQuarry_transcript_46080-T1, internal, 217474, 217716
-recovered CodingQuarry_transcript_46080-T1, internal, 217818, 218098
-recovered CodingQuarry_transcript_46080-T1, internal, 218928, 219121
-recovered CodingQuarry_transcript_46080-T1, internal, 219306, 219437
Valid prediction for snap_scaffold_3-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_6052-T1
Valid prediction for Augustus_model.g3957.t1
Valid prediction for snap_scaffold_3-snap.414-T1
Valid prediction for snap_scaffold_3-snap.380-T1
Valid prediction for snap_scaffold_3-snap.406-T1
Valid prediction for Augustus_model.g3947.t1
Valid prediction for GlimmerHMM_glimmerT_6054-T1
Valid prediction for snap_scaffold_3-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_6044-T1
Valid prediction for GlimmerHMM_glimmerT_6045-T1
Valid prediction for CodingQuarry_transcript_46088-T1
Valid prediction for GlimmerHMM_glimmerT_6053-T1
Valid prediction for GlimmerHMM_glimmerT_6046-T1
Valid prediction for GlimmerHMM_glimmerT_6058-T1
Valid prediction for snap_scaffold_3-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_6070-T1
Valid prediction for Augustus_model.g3962.t1
Valid prediction for GlimmerHMM_glimmerT_6064-T1
Valid prediction for HiQ_model.g3946.t1
Valid prediction for Augustus_model.g3953.t1
Valid prediction for snap_scaffold_3-snap.381-T1
Valid prediction for snap_scaffold_3-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_6050-T1
Valid prediction for snap_scaffold_3-snap.394-T1
Valid prediction for snap_scaffold_3-snap.417-T1
Valid prediction for Augustus_model.g3959.t1
Valid prediction for GlimmerHMM_glimmerT_6056-T1
Couldn't classify 222001, 222324
Sorry, prediction pasa_asmbl_38716.p1 fails validation.
(ATG)	 CG	221031-221319	GT	AGG
(TTC)	 AG	221607-221722	GT	AGG
(ACT)	 AG	222001-222324	CC	CTC
-recovered pasa_asmbl_38716.p1, initial, 221031, 221319
-recovered pasa_asmbl_38716.p1, internal, 221607, 221722
Valid prediction for GlimmerHMM_glimmerT_6074-T1
Valid prediction for snap_scaffold_3-snap.388-T1
Valid prediction for CodingQuarry_transcript_46082-T1
Couldn't classify 93473, 93535
Sorry, prediction pasa_asmbl_38724.p1 fails validation.
(GGA)	 AG	93473-93535	GT	CTG
(GGG)	 AG	93661-93711	GT	GGG
(GGT)	 AG	93951-93986	GT	AGG
(GGT)	 AG	94172-94234	GT	GGG
(GGT)	 AG	94567-94629	GT	ACG
(GGT)	 AG	94949-94981	GT	TGG
(CAA)	 AG	95082-95118	GT	CCG
(CCT)	 AG	95216-95227	GT	TGG
(GCA)	 AG	95508-96001	GT	AGG
(ATC)	 AG	96388-96490	GT	CGG
(ACT)	 AG	96786-97487	GT	CAG
(TTG)	 AG	97601-97697	GT	GAG
(GAA)	 AG	97791-97846	GT	AGG
(AAT)	 AG	98232-98492	GT	AAG
(AAG)	 AG	98684-98758	GT	GGG
(CAC)	 AG	100755-100811	GT	TGG
(CGG)	 AG	102021-102206	GT	AGG
(CAG)	 AG	102789-102829	GA	AGG
-recovered pasa_asmbl_38724.p1, terminal, 102789, 102829
-recovered pasa_asmbl_38724.p1, internal, 93473, 93535
-recovered pasa_asmbl_38724.p1, internal, 93661, 93711
-recovered pasa_asmbl_38724.p1, internal, 93951, 93986
-recovered pasa_asmbl_38724.p1, internal, 94172, 94234
-recovered pasa_asmbl_38724.p1, internal, 94567, 94629
-recovered pasa_asmbl_38724.p1, internal, 94949, 94981
-recovered pasa_asmbl_38724.p1, internal, 95082, 95118
-recovered pasa_asmbl_38724.p1, internal, 95216, 95227
-recovered pasa_asmbl_38724.p1, internal, 95508, 96001
-recovered pasa_asmbl_38724.p1, internal, 96388, 96490
-recovered pasa_asmbl_38724.p1, internal, 96786, 97487
-recovered pasa_asmbl_38724.p1, internal, 97601, 97697
-recovered pasa_asmbl_38724.p1, internal, 97791, 97846
-recovered pasa_asmbl_38724.p1, internal, 98232, 98492
-recovered pasa_asmbl_38724.p1, internal, 98684, 98758
-recovered pasa_asmbl_38724.p1, internal, 100755, 100811
-recovered pasa_asmbl_38724.p1, internal, 102021, 102206
Valid prediction for snap_scaffold_3-snap.412-T1
Valid prediction for snap_scaffold_3-snap.405-T1
Valid prediction for snap_scaffold_3-snap.378-T1
Valid prediction for pasa_asmbl_38722.p2
Valid prediction for CodingQuarry_transcript_46083-T1
Valid prediction for snap_scaffold_3-snap.387-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 64863, rend_intergenic: 64860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9789, rend_intergenic: 5461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38744, rend_intergenic: 30519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45173, rend_intergenic: 42756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47912, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53980, rend_intergenic: 47970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58312, rend_intergenic: 56439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65778, rend_intergenic: 62781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75221, rend_intergenic: 67867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120737, rend_intergenic: 112830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156243, rend_intergenic: 141770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204476, rend_intergenic: 198391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211933, rend_intergenic: 209644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218003, rend_intergenic: 215593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235566
-exon list size: 423


building trellis

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31.3    
31.5    
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32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
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34.4    
34.6    
34.8    
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37.4    
37.6    
37.9    
38.1    
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38.8    
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39.3    
39.5    
39.8    
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82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 64863, rend_intergenic: 64860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9789, rend_intergenic: 5461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38744, rend_intergenic: 30519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45173, rend_intergenic: 42756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47912, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53980, rend_intergenic: 47970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58312, rend_intergenic: 56439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65778, rend_intergenic: 62781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75221, rend_intergenic: 67867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120737, rend_intergenic: 112830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156243, rend_intergenic: 141770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204476, rend_intergenic: 198391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211933, rend_intergenic: 209644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218003, rend_intergenic: 215593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support