-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_12578057-12774115

-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_2-snap.2426-T1
Valid prediction for HiQ_model.g3144.t1
Valid prediction for GlimmerHMM_glimmerT_4677-T1
Valid prediction for snap_scaffold_2-snap.2428-T1
Valid prediction for snap_scaffold_2-snap.2391-T1
Valid prediction for CodingQuarry_transcript_28685-T1
Valid prediction for Augustus_model.g3132.t1
Valid prediction for GlimmerHMM_glimmerT_4659-T1
Couldn't classify 59836, 59927
Sorry, prediction pasa_asmbl_24800.p1 fails validation.
(ATG)	 CG	58056-58063	GT	AGG
(TTA)	 AG	58199-58364	GT	GGG
(GGC)	 AG	58971-59142	GT	GTG
(ATA)	 AG	59263-59369	GT	AGG
(CCT)	 AG	59588-59642	GT	AGG
(AGG)	 AG	59836-59927	AA	CCA
-recovered pasa_asmbl_24800.p1, initial, 58056, 58063
-recovered pasa_asmbl_24800.p1, internal, 58199, 58364
-recovered pasa_asmbl_24800.p1, internal, 58971, 59142
-recovered pasa_asmbl_24800.p1, internal, 59263, 59369
-recovered pasa_asmbl_24800.p1, internal, 59588, 59642
Valid prediction for snap_scaffold_2-snap.2421-T1
Valid prediction for snap_scaffold_2-snap.2432-T1
Valid prediction for Augustus_model.g3147.t1
Valid prediction for GlimmerHMM_glimmerT_4678-T1
Valid prediction for GlimmerHMM_glimmerT_4682-T1
Valid prediction for Augustus_model.g3134.t1
Valid prediction for GlimmerHMM_glimmerT_4666-T1
Valid prediction for snap_scaffold_2-snap.2396-T1
Valid prediction for Augustus_model.g3149.t1
Valid prediction for snap_scaffold_2-snap.2398-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g3140.t1
Valid prediction for snap_scaffold_2-snap.2402-T1
Valid prediction for snap_scaffold_2-snap.2423-T1
Valid prediction for snap_scaffold_2-snap.2405-T1
Valid prediction for snap_scaffold_2-snap.2436-T1
Valid prediction for snap_scaffold_2-snap.2409-T1
Valid prediction for snap_scaffold_2-snap.2414-T1
Valid prediction for GlimmerHMM_glimmerT_4669-T1
Valid prediction for Augustus_model.g3143.t1
Valid prediction for snap_scaffold_2-snap.2429-T1
Couldn't classify 144091, 144173
Sorry, prediction pasa_asmbl_24805.p1 fails validation.
(GAC)	 CT	144091-144173	GT	GGG
(TGG)	 AG	144516-144610	GT	CGG
(GTC)	 AG	145571-145773	GT	TGG
(TCT)	 AG	145940-146179	GT	AGG
(CAT)	 AG	146331-146420	CC	GAC
-recovered pasa_asmbl_24805.p1, terminal, 146331, 146420
-recovered pasa_asmbl_24805.p1, internal, 144516, 144610
-recovered pasa_asmbl_24805.p1, internal, 145571, 145773
-recovered pasa_asmbl_24805.p1, internal, 145940, 146179
Valid prediction for HiQ_model.g3145.t1
Couldn't classify 131270, 131386
Sorry, prediction pasa_asmbl_24802.p1 fails validation.
(GTA)	 CA	131270-131386	GT	AGG
(GAC)	 AG	132192-132370	GT	AGG
(GGA)	 AG	133785-133944	GT	AGG
(GGA)	 AG	134709-134828	TG	GAT
-recovered pasa_asmbl_24802.p1, terminal, 134709, 134828
-recovered pasa_asmbl_24802.p1, internal, 132192, 132370
-recovered pasa_asmbl_24802.p1, internal, 133785, 133944
Valid prediction for CodingQuarry_transcript_28682-T1
Valid prediction for snap_scaffold_2-snap.2403-T1
Valid prediction for GlimmerHMM_glimmerT_4662-T1
Valid prediction for snap_scaffold_2-snap.2408-T1
Valid prediction for snap_scaffold_2-snap.2416-T1
Valid prediction for snap_scaffold_2-snap.2433-T1
Valid prediction for snap_scaffold_2-snap.2411-T1
Couldn't classify 22, 206
Sorry, prediction pasa_asmbl_24799.p1 fails validation.
(CTG)	 GC	22-206	GT	AGG
(CCG)	 AG	366-573	TC	AGT
-recovered pasa_asmbl_24799.p1, terminal, 366, 573
Valid prediction for GlimmerHMM_glimmerT_4660-T1
Valid prediction for snap_scaffold_2-snap.2393-T1
Valid prediction for snap_scaffold_2-snap.2425-T1
Valid prediction for snap_scaffold_2-snap.2395-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g3136.t1
Valid prediction for snap_scaffold_2-snap.2401-T1
Valid prediction for snap_scaffold_2-snap.2437-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_4676-T1
Couldn't classify 122999, 123060
Sorry, prediction pasa_asmbl_24002.p1 fails validation.
(ATG)	 AG	122006-122008	GT	TGG
(ATT)	 AG	122168-122301	GT	GGG
(GTA)	 AG	122404-122495	GT	ACG
(GTG)	 AG	122999-123060	CG	GCC
-recovered pasa_asmbl_24002.p1, initial, 122006, 122008
-recovered pasa_asmbl_24002.p1, internal, 122006, 122008
-recovered pasa_asmbl_24002.p1, internal, 122168, 122301
-recovered pasa_asmbl_24002.p1, internal, 122404, 122495
Valid prediction for snap_scaffold_2-snap.2424-T1
Valid prediction for snap_scaffold_2-snap.2390-T1
Valid prediction for snap_scaffold_2-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_4671-T1
Valid prediction for Augustus_model.g3146.t1
Valid prediction for GlimmerHMM_glimmerT_4658-T1
Couldn't classify 128792, 129176
Sorry, prediction pasa_asmbl_23469.p1 fails validation.
(CCA)	 CT	128792-129176	GT	CAG
(AGC)	 AG	129337-129398	GT	AGG
(GAC)	 AG	130631-130792	GT	AGG
(TAT)	 AG	130982-131110	GT	AGG
(GTG)	 AG	131353-131520	CT	GAC
-recovered pasa_asmbl_23469.p1, terminal, 131353, 131520
-recovered pasa_asmbl_23469.p1, internal, 129337, 129398
-recovered pasa_asmbl_23469.p1, internal, 130631, 130792
-recovered pasa_asmbl_23469.p1, internal, 130982, 131110
Couldn't classify 126130, 127113
Sorry, prediction pasa_asmbl_23471.p1 fails validation.
(CAG)	 AG	126130-127113	AG	GGA
Valid prediction for snap_scaffold_2-snap.2434-T1
Valid prediction for snap_scaffold_2-snap.2392-T1
Valid prediction for snap_scaffold_2-snap.2431-T1
Valid prediction for CodingQuarry_transcript_28683-T1
Valid prediction for Augustus_model.g3135.t1
Valid prediction for GlimmerHMM_glimmerT_4661-T1
Valid prediction for GlimmerHMM_glimmerT_4668-T1
Couldn't classify 108644, 108994
Sorry, prediction pasa_asmbl_23477.p1 fails validation.
(AGG)	 GG	108644-108994	GT	AGG
Valid prediction for snap_scaffold_2-snap.2418-T1
Valid prediction for pasa_asmbl_23478.p1
Valid prediction for GlimmerHMM_glimmerT_4683-T1
Valid prediction for snap_scaffold_2-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_4673-T1
Valid prediction for snap_scaffold_2-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_4680-T1
Valid prediction for HiQ_model.g3138.t1
Couldn't classify 124919, 124929
Couldn't classify 125540, 125715
Sorry, prediction pasa_asmbl_23472.p1 fails validation.
(TTT)	 CC	124919-124929	GT	GGG
(GGA)	 AG	125022-125147	GT	AGG
(GCG)	 AG	125254-125399	GT	GGG
(TGA)	 AG	125540-125715	CC	CCC
-recovered pasa_asmbl_23472.p1, internal, 125022, 125147
-recovered pasa_asmbl_23472.p1, internal, 125254, 125399
Valid prediction for Augustus_model.g3139.t1
Valid prediction for Augustus_model.g3142.t1
Valid prediction for Augustus_model.g3133.t1
Valid prediction for GlimmerHMM_glimmerT_4664-T1
Valid prediction for snap_scaffold_2-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_4684-T1
Valid prediction for GlimmerHMM_glimmerT_4670-T1
Valid prediction for snap_scaffold_2-snap.2406-T1
Valid prediction for GlimmerHMM_glimmerT_4672-T1
Valid prediction for snap_scaffold_2-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_4681-T1
Couldn't classify 127567, 127703
Couldn't classify 127825, 128647
Sorry, prediction pasa_asmbl_23470.p1 fails validation.
(AGG)	 GC	127567-127703	GT	AGG
(GTC)	 AG	127825-128647	CC	AGC
Valid prediction for CodingQuarry_transcript_28686-T1
Valid prediction for snap_scaffold_2-snap.2417-T1
Valid prediction for pasa_asmbl_23475.p1
Valid prediction for Augustus_model.g3141.t1
Valid prediction for GlimmerHMM_glimmerT_4679-T1
Valid prediction for GlimmerHMM_glimmerT_4667-T1
Valid prediction for snap_scaffold_2-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_4665-T1
Valid prediction for snap_scaffold_2-snap.2435-T1
Valid prediction for snap_scaffold_2-snap.2427-T1
Valid prediction for snap_scaffold_2-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_4674-T1
Valid prediction for Augustus_model.g3137.t1
Valid prediction for GlimmerHMM_glimmerT_4675-T1
Valid prediction for snap_scaffold_2-snap.2400-T1
Valid prediction for Augustus_model.g3148.t1
Valid prediction for snap_scaffold_2-snap.2415-T1
Valid prediction for snap_scaffold_2-snap.2420-T1
Valid prediction for snap_scaffold_2-snap.2413-T1
Valid prediction for GlimmerHMM_glimmerT_4663-T1
Valid prediction for snap_scaffold_2-snap.2397-T1
Valid prediction for snap_scaffold_2-snap.2430-T1
Valid prediction for snap_scaffold_2-snap.2404-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8420, rend_intergenic: 4398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8971, rend_intergenic: 8815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17107, rend_intergenic: 9817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24541, rend_intergenic: 21887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25983, rend_intergenic: 24717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26977, rend_intergenic: 26179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30412, rend_intergenic: 27084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48256, rend_intergenic: 31402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74979, rend_intergenic: 67684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94918, rend_intergenic: 92914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104480, rend_intergenic: 97552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109150, rend_intergenic: 105770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120105, rend_intergenic: 117053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135290, rend_intergenic: 126333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149557, rend_intergenic: 146870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152911, rend_intergenic: 150064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167154, rend_intergenic: 159254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177342, rend_intergenic: 168695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192483, rend_intergenic: 181836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196059
-exon list size: 440


building trellis

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99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 8420, rend_intergenic: 4398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8971, rend_intergenic: 8815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17107, rend_intergenic: 9817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24541, rend_intergenic: 21887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25983, rend_intergenic: 24717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26977, rend_intergenic: 26179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30412, rend_intergenic: 27084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48256, rend_intergenic: 31402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74979, rend_intergenic: 67684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94918, rend_intergenic: 92914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104480, rend_intergenic: 97552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109150, rend_intergenic: 105770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120105, rend_intergenic: 117053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135290, rend_intergenic: 126333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149557, rend_intergenic: 146870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152911, rend_intergenic: 150064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167154, rend_intergenic: 159254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177342, rend_intergenic: 168695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192483, rend_intergenic: 181836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 151940 - 196059
-exon list size: 65


building trellis

1.5    
3.0    
4.5    
6.0    
7.5    
9.0    
10.4    
11.9    
13.4    
14.9    
16.4    
17.9    
19.4    
20.9    
22.4    
23.9    
25.4    
26.9    
28.4    
29.9    
31.3    
32.8    
34.3    
35.8    
37.3    
38.8    
40.3    
41.8    
43.3    
44.8    
46.3    
47.8    
49.3    
50.7    
52.2    
53.7    
55.2    
56.7    
58.2    
59.7    
61.2    
62.7    
64.2    
65.7    
67.2    
68.7    
70.1    
71.6    
73.1    
74.6    
76.1    
77.6    
79.1    
80.6    
82.1    
83.6    
85.1    
86.6    
88.1    
89.6    
91.0    
92.5    
94.0    
95.5    
97.0    
98.5    
-found 7 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support