-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_182449-364462

-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: +)Couldn't classify 107312, 107420
Sorry, prediction pasa_asmbl_33321.p1 fails validation.
(CAC)	 AC	107312-107420	GT	AGG
(GAC)	 AG	107648-107689	GT	AAG
(TGT)	 AG	108168-108302	GT	TGG
(AGG)	 AG	108676-108749	GT	AGG
(CCT)	 AG	108878-109033	AG	AGA
-recovered pasa_asmbl_33321.p1, terminal, 108878, 109033
-recovered pasa_asmbl_33321.p1, internal, 107648, 107689
-recovered pasa_asmbl_33321.p1, internal, 108168, 108302
-recovered pasa_asmbl_33321.p1, internal, 108676, 108749
Valid prediction for GlimmerHMM_glimmerT_53442-T1
Valid prediction for snap_scaffold_25-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_53457-T1
Valid prediction for GlimmerHMM_glimmerT_53450-T1
Valid prediction for snap_scaffold_25-snap.70-T1
Valid prediction for snap_scaffold_25-snap.74-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.66-T1
Valid prediction for snap_scaffold_25-snap.69-T1
Valid prediction for snap_scaffold_25-snap.43-T1
Valid prediction for snap_scaffold_25-snap.60-T1
Couldn't classify 166195, 166521
Sorry, prediction pasa_asmbl_33972.p2 fails validation.
(GTG)	 CT	166195-166521	TC	GAT
Valid prediction for snap_scaffold_25-snap.47-T1
Valid prediction for Augustus_model.g35552.t1
Valid prediction for GlimmerHMM_glimmerT_53463-T1
Valid prediction for Augustus_model.g35549.t1
Couldn't classify 107689, 107689
Sorry, prediction CodingQuarry_transcript_38619-T1 fails validation.
(AGT)	 GA	107689-107689	GT	AAG
(TGT)	 AG	108168-108302	GT	TGG
(AGG)	 AG	108676-108749	GT	AGG
(CCT)	 AG	108878-109033	AG	AGA
-recovered CodingQuarry_transcript_38619-T1, terminal, 108878, 109033
-recovered CodingQuarry_transcript_38619-T1, internal, 108168, 108302
-recovered CodingQuarry_transcript_38619-T1, internal, 108676, 108749
Valid prediction for Augustus_model.g35555.t1
Valid prediction for HiQ_model.g35542.t1
Valid prediction for GlimmerHMM_glimmerT_53461-T1
Valid prediction for Augustus_model.g35543.t1
Valid prediction for GlimmerHMM_glimmerT_53449-T1
Valid prediction for snap_scaffold_25-snap.64-T1
Couldn't classify 36924, 37075
Couldn't classify 37778, 37861
Couldn't classify 39470, 39559
Couldn't classify 40577, 40799
Sorry, prediction pasa_asmbl_33319.p1 fails validation.
(GGT)	 TG	36924-37075	GT	AGG
(AGA)	 AG	37778-37861	AT	ATA
(GTA)	 AC	39470-39559	GT	GGG
(CTA)	 AG	40577-40799	TC	ACT
Valid prediction for snap_scaffold_25-snap.50-T1
Valid prediction for snap_scaffold_25-snap.59-T1
Valid prediction for Augustus_model.g35551.t1
Valid prediction for snap_scaffold_25-snap.72-T1
Valid prediction for snap_scaffold_25-snap.63-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53452-T1
Valid prediction for GlimmerHMM_glimmerT_53466-T1
Valid prediction for snap_scaffold_25-snap.67-T1
Valid prediction for snap_scaffold_25-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_53448-T1
Valid prediction for GlimmerHMM_glimmerT_53447-T1
Valid prediction for snap_scaffold_25-snap.65-T1
Valid prediction for snap_scaffold_25-snap.44-T1
Valid prediction for snap_scaffold_25-snap.51-T1
Valid prediction for snap_scaffold_25-snap.54-T1
Valid prediction for GlimmerHMM_glimmerT_53460-T1
Valid prediction for GlimmerHMM_glimmerT_53441-T1
Valid prediction for snap_scaffold_25-snap.52-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: -)Couldn't classify 100963, 101101
Couldn't classify 101367, 101569
Sorry, prediction pasa_asmbl_34612.p1 fails validation.
(ACT)	 GC	100963-101101	GT	AGG
(GCA)	 AG	101367-101569	CC	CCC
Valid prediction for CodingQuarry_transcript_38616-T1
Valid prediction for GlimmerHMM_glimmerT_53453-T1
Valid prediction for snap_scaffold_25-snap.41-T1
Couldn't classify 5450, 5492
Couldn't classify 8047, 8094
Sorry, prediction pasa_asmbl_33974.p1 fails validation.
(TCC)	 AC	5450-5492	GT	AGG
(TGG)	 AG	5615-5787	GT	AGG
(GTT)	 AG	6111-6188	GT	AGG
(ACG)	 AG	7487-7618	GT	GGG
(GGA)	 AG	8047-8094	GG	GAG
-recovered pasa_asmbl_33974.p1, internal, 5615, 5787
-recovered pasa_asmbl_33974.p1, internal, 6111, 6188
-recovered pasa_asmbl_33974.p1, internal, 7487, 7618
Valid prediction for GlimmerHMM_glimmerT_53443-T1
Valid prediction for snap_scaffold_25-snap.42-T1
Valid prediction for GlimmerHMM_glimmerT_53468-T1
Couldn't classify 150570, 150790
Sorry, prediction pasa_asmbl_33959.p1 fails validation.
(ATG)	 CA	148371-148446	GT	AGG
(CCG)	 AG	148959-149144	GT	AGG
(AGA)	 AG	150570-150790	GA	GTG
-recovered pasa_asmbl_33959.p1, initial, 148371, 148446
-recovered pasa_asmbl_33959.p1, internal, 148959, 149144
Valid prediction for GlimmerHMM_glimmerT_53464-T1
Valid prediction for HiQ_model.g35548.t1
Valid prediction for GlimmerHMM_glimmerT_53456-T1
Valid prediction for GlimmerHMM_glimmerT_53446-T1
Valid prediction for snap_scaffold_25-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_53459-T1
Couldn't classify 23546, 23768
Sorry, prediction pasa_asmbl_33970.p1 fails validation.
(CCT)	 CC	23546-23768	GT	AGG
(ATG)	 AG	23935-24001	GT	ACG
(GAA)	 AG	24097-24268	GT	AGG
(ACA)	 AG	24609-24653	GT	AGG
(ACT)	 AG	24732-24848	AC	AGA
add_exon() Sorry, pasa_asmbl_33970.p1 23935-24001-initial-1 is invalid.
-recovered pasa_asmbl_33970.p1, initial, 23935, 24001
-recovered pasa_asmbl_33970.p1, terminal, 24732, 24848
-recovered pasa_asmbl_33970.p1, internal, 23935, 24001
-recovered pasa_asmbl_33970.p1, internal, 24097, 24268
-recovered pasa_asmbl_33970.p1, internal, 24609, 24653
Valid prediction for GlimmerHMM_glimmerT_53470-T1
Valid prediction for Augustus_model.g35553.t1
Valid prediction for Augustus_model.g35544.t1
Valid prediction for GlimmerHMM_glimmerT_53458-T1
Valid prediction for Augustus_model.g35556.t1
Valid prediction for snap_scaffold_25-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_53451-T1
Valid prediction for snap_scaffold_25-snap.68-T1
Valid prediction for Augustus_model.g35554.t1
Couldn't classify 42704, 42749
Couldn't classify 44370, 44435
Sorry, prediction pasa_asmbl_33967.p1 fails validation.
(CTA)	 CC	42704-42749	GT	AGG
(ATG)	 AG	42850-42948	GT	GGG
(ATA)	 AG	43459-43550	GT	AGG
(GTG)	 AG	44370-44435	AA	ACA
-recovered pasa_asmbl_33967.p1, initial, 42850, 42948
-recovered pasa_asmbl_33967.p1, internal, 42850, 42948
-recovered pasa_asmbl_33967.p1, internal, 43459, 43550
Valid prediction for HiQ_model.g35547.t1
Valid prediction for GlimmerHMM_glimmerT_53444-T1
Valid prediction for GlimmerHMM_glimmerT_53469-T1
Valid prediction for snap_scaffold_25-snap.58-T1
Valid prediction for snap_scaffold_25-snap.49-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g35550.t1
Valid prediction for snap_scaffold_25-snap.45-T1
Valid prediction for snap_scaffold_25-snap.71-T1
Valid prediction for Augustus_model.g35541.t1
Valid prediction for snap_scaffold_25-snap.73-T1
Valid prediction for snap_scaffold_25-snap.56-T1
Couldn't classify 179198, 179385
Sorry, prediction pasa_asmbl_33955.p1 fails validation.
(ATG)	 TC	178027-178675	GT	ACG
(AGC)	 AG	179198-179385	GG	AGG
-recovered pasa_asmbl_33955.p1, initial, 178027, 178675
Valid prediction for snap_scaffold_25-snap.53-T1
Valid prediction for Augustus_model.g35546.t1
Valid prediction for Augustus_model.g35540.t1
Valid prediction for Augustus_model.g35545.t1
Valid prediction for pasa_asmbl_33965.p1
Valid prediction for pasa_asmbl_33964.p1
Valid prediction for GlimmerHMM_glimmerT_53465-T1
Valid prediction for GlimmerHMM_glimmerT_53462-T1
Valid prediction for pasa_asmbl_33957.p1
Valid prediction for GlimmerHMM_glimmerT_53445-T1
Valid prediction for GlimmerHMM_glimmerT_53454-T1
Valid prediction for GlimmerHMM_glimmerT_53455-T1
Valid prediction for snap_scaffold_25-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_53467-T1
Valid prediction for GlimmerHMM_glimmerT_53440-T1
Couldn't classify 41257, 41314
Couldn't classify 42548, 42580
Sorry, prediction pasa_asmbl_33968.p1 fails validation.
(GTT)	 TT	41257-41314	GT	TGG
(ACA)	 AG	41408-41514	GT	TAG
(CTT)	 AG	41878-41919	GT	GGG
(GAG)	 AG	42158-42250	GT	AGG
(GAC)	 AG	42548-42580	AA	TCA
-recovered pasa_asmbl_33968.p1, internal, 41408, 41514
-recovered pasa_asmbl_33968.p1, internal, 41878, 41919
-recovered pasa_asmbl_33968.p1, internal, 42158, 42250
Valid prediction for snap_scaffold_25-snap.57-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 157170, rend_intergenic: 157167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11595, rend_intergenic: 9385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16695, rend_intergenic: 12279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22003, rend_intergenic: 19381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33091, rend_intergenic: 22130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56186, rend_intergenic: 36597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60064, rend_intergenic: 58635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69793, rend_intergenic: 62186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90122, rend_intergenic: 76793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106366, rend_intergenic: 95697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109033, rend_intergenic: 109005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150643, rend_intergenic: 109496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164279, rend_intergenic: 152830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169652, rend_intergenic: 165005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178102, rend_intergenic: 172492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182014
-exon list size: 410


building trellis

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18.4    
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20.1    
20.4    
20.6    
20.9    
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23.8    
24.0    
24.3    
24.5    
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25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
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26.9    
27.2    
27.4    
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28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
51.9    
52.2    
52.4    
52.7    
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53.6    
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54.4    
54.6    
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55.3    
55.6    
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56.8    
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59.0    
59.2    
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68.4    
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68.9    
69.2    
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93.9    
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96.6    
96.8    
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97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 157170, rend_intergenic: 157167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11595, rend_intergenic: 9385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16695, rend_intergenic: 12279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22003, rend_intergenic: 19381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33091, rend_intergenic: 22130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56186, rend_intergenic: 36597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60064, rend_intergenic: 58635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69793, rend_intergenic: 62186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90122, rend_intergenic: 76793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106366, rend_intergenic: 95697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109033, rend_intergenic: 109005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150643, rend_intergenic: 109496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164279, rend_intergenic: 152830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169652, rend_intergenic: 165005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178102, rend_intergenic: 172492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support