-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_15285264-15450955

-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_12-snap.2963-T1
Valid prediction for GeneMark_model.54071_t
Valid prediction for Augustus_model.g20881.t1
Valid prediction for snap_scaffold_12-snap.2954-T1
Valid prediction for GeneMark_model.54054_t
Valid prediction for GeneMark_model.54050_t
Valid prediction for Augustus_model.g20885.t1
Valid prediction for snap_scaffold_12-snap.2953-T1
Valid prediction for snap_scaffold_12-snap.2959-T1
Valid prediction for Augustus_model.g20880.t1
Valid prediction for snap_scaffold_12-snap.2940-T1
Valid prediction for snap_scaffold_12-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_31316-T1
Valid prediction for GeneMark_model.54076_t
Couldn't classify 128173, 128253
Sorry, prediction pasa_asmbl_9092.p2 fails validation.
(GAG)	 CA	128173-128253	GT	AGG
(TAC)	 AG	128381-128538	GT	AGG
(GCC)	 AG	128648-128717	GG	GAG
add_exon() Sorry, pasa_asmbl_9092.p2 128381-128538-terminal-2 is invalid.
-recovered pasa_asmbl_9092.p2, terminal, 128381, 128538
-recovered pasa_asmbl_9092.p2, terminal, 128648, 128717
-recovered pasa_asmbl_9092.p2, internal, 128381, 128538
Valid prediction for GlimmerHMM_glimmerT_31322-T1
Valid prediction for GlimmerHMM_glimmerT_31325-T1
Valid prediction for GeneMark_model.54053_t
Valid prediction for GeneMark_model.54063_t
Valid prediction for GeneMark_model.54052_t
Valid prediction for snap_scaffold_12-snap.2968-T1
Valid prediction for GeneMark_model.54075_t
Valid prediction for GeneMark_model.54079_t
Valid prediction for GeneMark_model.54062_t
Valid prediction for GeneMark_model.54069_t
Valid prediction for GeneMark_model.54058_t
Valid prediction for snap_scaffold_12-snap.2958-T1
Valid prediction for snap_scaffold_12-snap.2965-T1
Couldn't classify 9069, 9078
Couldn't classify 9800, 9912
Sorry, prediction pasa_asmbl_9086.p1 fails validation.
(GAG)	 TG	9069-9078	GT	AGG
(AGT)	 AG	9236-9658	GT	AGG
(ACT)	 AG	9800-9912	AG	TGA
-recovered pasa_asmbl_9086.p1, internal, 9236, 9658
Valid prediction for GlimmerHMM_glimmerT_31334-T1
Valid prediction for GlimmerHMM_glimmerT_31324-T1
Valid prediction for snap_scaffold_12-snap.2941-T1
Valid prediction for snap_scaffold_12-snap.2962-T1
Valid prediction for GeneMark_model.54056_t
Valid prediction for HiQ_model.g20882.t1
Valid prediction for GeneMark_model.54065_t
Valid prediction for GeneMark_model.54047_t
Valid prediction for GeneMark_model.54082_t
Valid prediction for GeneMark_model.54049_t
Valid prediction for GlimmerHMM_glimmerT_31329-T1
Valid prediction for snap_scaffold_12-snap.2951-T1
Valid prediction for GlimmerHMM_glimmerT_31330-T1
Valid prediction for snap_scaffold_12-snap.2949-T1
Valid prediction for snap_scaffold_12-snap.2969-T1
Valid prediction for snap_scaffold_12-snap.2937-T1
Valid prediction for snap_scaffold_12-snap.2956-T1
Couldn't classify 126902, 126967
Sorry, prediction pasa_asmbl_9090.p1 fails validation.
(ATG)	 CA	123757-123811	GT	TGG
(GCG)	 AG	124214-124296	GT	TGG
(GTA)	 AG	124461-124603	GT	TGG
(TCC)	 AG	125246-125327	GT	AGG
(ATA)	 AG	125487-125543	GT	AGG
(GCT)	 AG	125646-125701	GT	AAG
(ATA)	 AG	126183-126316	GT	AGG
(GTG)	 AG	126440-126520	GT	GAG
(GTT)	 AG	126699-126772	GT	AGG
(TGT)	 AG	126902-126967	TA	GGT
-recovered pasa_asmbl_9090.p1, initial, 123757, 123811
-recovered pasa_asmbl_9090.p1, internal, 124214, 124296
-recovered pasa_asmbl_9090.p1, internal, 124461, 124603
-recovered pasa_asmbl_9090.p1, internal, 125246, 125327
-recovered pasa_asmbl_9090.p1, internal, 125487, 125543
-recovered pasa_asmbl_9090.p1, internal, 125646, 125701
-recovered pasa_asmbl_9090.p1, internal, 126183, 126316
-recovered pasa_asmbl_9090.p1, internal, 126440, 126520
-recovered pasa_asmbl_9090.p1, internal, 126699, 126772
Valid prediction for HiQ_model.g20889.t1
Valid prediction for GeneMark_model.54078_t
Valid prediction for GeneMark_model.54084_t
Couldn't classify 22140, 22244
Sorry, prediction pasa_asmbl_9087.p1 fails validation.
(ATG)	 AG	18271-18367	GT	CGG
(GTC)	 AG	20777-20972	GT	TGG
(CGG)	 AG	21210-21362	GT	AAG
(GTT)	 AG	21874-22057	GT	AGG
(TGC)	 AG	22140-22244	CA	AGC
-recovered pasa_asmbl_9087.p1, initial, 18271, 18367
-recovered pasa_asmbl_9087.p1, internal, 18271, 18367
-recovered pasa_asmbl_9087.p1, internal, 20777, 20972
-recovered pasa_asmbl_9087.p1, internal, 21210, 21362
-recovered pasa_asmbl_9087.p1, internal, 21874, 22057
Valid prediction for snap_scaffold_12-snap.2973-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31320-T1
Valid prediction for snap_scaffold_12-snap.2966-T1
Valid prediction for HiQ_model.g20888.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 snap_scaffold_12-snap.2964-T1
Valid prediction for snap_scaffold_12-snap.2947-T1
Valid prediction for snap_scaffold_12-snap.2974-T1
Valid prediction for GlimmerHMM_glimmerT_31326-T1
Valid prediction for Augustus_model.g20879.t1
Valid prediction for GlimmerHMM_glimmerT_31318-T1
Couldn't classify 160610, 160675
Couldn't classify 161931, 162039
Sorry, prediction pasa_asmbl_8206.p1 fails validation.
(TTG)	 TG	160610-160675	GT	AGG
(TTA)	 AG	160802-160899	GT	GTG
(GAA)	 AG	161040-161227	GT	TGG
(AGT)	 AG	161428-161722	GT	AGG
(GGA)	 AG	161931-162039	GG	GGG
-recovered pasa_asmbl_8206.p1, internal, 160802, 160899
-recovered pasa_asmbl_8206.p1, internal, 161040, 161227
-recovered pasa_asmbl_8206.p1, internal, 161428, 161722
Valid prediction for snap_scaffold_12-snap.2972-T1
Valid prediction for snap_scaffold_12-snap.2970-T1
Couldn't classify 75898, 75928
Sorry, prediction pasa_asmbl_8208.p1 fails validation.
(TTT)	 CC	75898-75928	GT	TGG
(GGG)	 AG	76328-76497	GT	AGG
(GCG)	 AG	76778-76918	GT	AGG
(GTC)	 AG	77696-77810	GT	AGG
(ATT)	 AG	77941-78118	GT	AGG
(CAT)	 AG	78243-78454	GT	CTG
(GTC)	 AG	78584-78840	CA	GAC
-recovered pasa_asmbl_8208.p1, terminal, 78584, 78840
-recovered pasa_asmbl_8208.p1, internal, 76328, 76497
-recovered pasa_asmbl_8208.p1, internal, 76778, 76918
-recovered pasa_asmbl_8208.p1, internal, 77696, 77810
-recovered pasa_asmbl_8208.p1, internal, 77941, 78118
-recovered pasa_asmbl_8208.p1, internal, 78243, 78454
Couldn't classify 74849, 75063
Couldn't classify 75222, 75456
Sorry, prediction pasa_asmbl_8209.p1 fails validation.
(CTG)	 TC	74849-75063	GT	AGG
(ACC)	 AG	75222-75456	CT	TGC
Valid prediction for GlimmerHMM_glimmerT_31335-T1
Valid prediction for GlimmerHMM_glimmerT_31323-T1
Valid prediction for GeneMark_model.54059_t
Valid prediction for snap_scaffold_12-snap.2967-T1
Valid prediction for Augustus_model.g20887.t1
Valid prediction for GeneMark_model.54080_t
Valid prediction for GlimmerHMM_glimmerT_31315-T1
Valid prediction for GlimmerHMM_glimmerT_31328-T1
Valid prediction for snap_scaffold_12-snap.2943-T1
Valid prediction for GeneMark_model.54070_t
Valid prediction for GeneMark_model.54086_t
Valid prediction for CodingQuarry_transcript_10467-T1
Valid prediction for Augustus_model.g20886.t1
Valid prediction for GeneMark_model.54045_t
Valid prediction for snap_scaffold_12-snap.2942-T1
Valid prediction for GeneMark_model.54066_t
Valid prediction for snap_scaffold_12-snap.2945-T1
Valid prediction for snap_scaffold_12-snap.2952-T1
Couldn't classify 3505, 3544
Sorry, prediction pasa_asmbl_8224.p1 fails validation.
(AGA)	 AC	3505-3544	GT	AGG
(GTT)	 AG	5086-5180	GT	AGG
(GGC)	 AG	6023-6129	GT	AGG
(ATC)	 AG	6414-6504	GT	AGG
(CAG)	 AG	7169-7327	GT	AGG
(ATG)	 AG	7483-7600	GT	CAG
(CCA)	 AG	7722-7877	GT	GGG
(GCG)	 AG	8382-8525	GT	AGG
(GCA)	 AG	8979-9113	GT	CGG
(TTC)	 AG	9782-9882	GT	AGG
(TCG)	 AG	10539-10688	GT	ATG
(ATC)	 AG	13187-13346	GT	TGG
(CCT)	 AG	14640-14779	GT	AGG
(GTG)	 AG	14867-14950	TG	GAT
-recovered pasa_asmbl_8224.p1, initial, 7483, 7600
-recovered pasa_asmbl_8224.p1, terminal, 14867, 14950
-recovered pasa_asmbl_8224.p1, internal, 5086, 5180
-recovered pasa_asmbl_8224.p1, internal, 6023, 6129
-recovered pasa_asmbl_8224.p1, internal, 6414, 6504
-recovered pasa_asmbl_8224.p1, internal, 7169, 7327
-recovered pasa_asmbl_8224.p1, internal, 7483, 7600
-recovered pasa_asmbl_8224.p1, internal, 7722, 7877
-recovered pasa_asmbl_8224.p1, internal, 8382, 8525
-recovered pasa_asmbl_8224.p1, internal, 8979, 9113
-recovered pasa_asmbl_8224.p1, internal, 9782, 9882
-recovered pasa_asmbl_8224.p1, internal, 10539, 10688
-recovered pasa_asmbl_8224.p1, internal, 13187, 13346
-recovered pasa_asmbl_8224.p1, internal, 14640, 14779
Valid prediction for snap_scaffold_12-snap.2938-T1
Valid prediction for snap_scaffold_12-snap.2955-T1
Valid prediction for GeneMark_model.54067_t
Valid prediction for GlimmerHMM_glimmerT_31331-T1
Valid prediction for GeneMark_model.54060_t
Valid prediction for snap_scaffold_12-snap.2948-T1
Valid prediction for GeneMark_model.54081_t
Valid prediction for GeneMark_model.54057_t
Valid prediction for GlimmerHMM_glimmerT_31333-T1
Valid prediction for GeneMark_model.54074_t
Valid prediction for GeneMark_model.54072_t
Valid prediction for GlimmerHMM_glimmerT_31319-T1
Valid prediction for GeneMark_model.54077_t
Valid prediction for Augustus_model.g20883.t1
Valid prediction for GeneMark_model.54083_t
Valid prediction for snap_scaffold_12-snap.2950-T1
Valid prediction for snap_scaffold_12-snap.2936-T1
Valid prediction for snap_scaffold_12-snap.2944-T1
Valid prediction for GeneMark_model.54048_t
Valid prediction for GeneMark_model.54055_t
Valid prediction for GeneMark_model.54051_t
Valid prediction for GeneMark_model.54064_t
Valid prediction for GeneMark_model.54073_t
Valid prediction for snap_scaffold_12-snap.2957-T1
Valid prediction for snap_scaffold_12-snap.2946-T1
Valid prediction for Augustus_model.g20878.t1
Valid prediction for HiQ_model.g20891.t1
Valid prediction for snap_scaffold_12-snap.2935-T1
Valid prediction for snap_scaffold_12-snap.2961-T1
Valid prediction for GlimmerHMM_glimmerT_31317-T1
Valid prediction for GeneMark_model.54061_t
Couldn't classify 26069, 26280
Sorry, prediction pasa_asmbl_8217.p1 fails validation.
(ATG)	 AC	23730-23737	GT	CAG
(CGT)	 AG	23880-24042	GT	GAG
(ACT)	 AG	24131-24196	GT	AGG
(TGT)	 AG	25220-25361	GT	GAG
(AGG)	 AG	25470-25493	GT	AGG
(AGG)	 AG	25853-25972	GT	GGG
(ACC)	 AG	26069-26280	CC	CCC
-recovered pasa_asmbl_8217.p1, initial, 23730, 23737
-recovered pasa_asmbl_8217.p1, internal, 23880, 24042
-recovered pasa_asmbl_8217.p1, internal, 24131, 24196
-recovered pasa_asmbl_8217.p1, internal, 25220, 25361
-recovered pasa_asmbl_8217.p1, internal, 25470, 25493
-recovered pasa_asmbl_8217.p1, internal, 25853, 25972
Valid prediction for snap_scaffold_12-snap.2939-T1
Valid prediction for GlimmerHMM_glimmerT_31332-T1
Valid prediction for HiQ_model.g20890.t1
Valid prediction for Augustus_model.g20884.t1
Valid prediction for GeneMark_model.54068_t
Valid prediction for GlimmerHMM_glimmerT_31321-T1
Valid prediction for GeneMark_model.54085_t
Valid prediction for GlimmerHMM_glimmerT_31327-T1
Valid prediction for snap_scaffold_12-snap.2960-T1
Valid prediction for GeneMark_model.54046_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16451, rend_intergenic: 10289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21578, rend_intergenic: 16971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26075, rend_intergenic: 21776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55880, rend_intergenic: 54953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61025, rend_intergenic: 59741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65903, rend_intergenic: 62203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70067, rend_intergenic: 66359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79355, rend_intergenic: 76754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85644, rend_intergenic: 79764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138385, rend_intergenic: 131763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152752, rend_intergenic: 150963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155526, rend_intergenic: 153053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159479, rend_intergenic: 156364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163800, rend_intergenic: 159533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165692
-exon list size: 613


building trellis

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69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 16451, rend_intergenic: 10289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21578, rend_intergenic: 16971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26075, rend_intergenic: 21776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55880, rend_intergenic: 54953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61025, rend_intergenic: 59741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65903, rend_intergenic: 62203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70067, rend_intergenic: 66359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79355, rend_intergenic: 76754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85644, rend_intergenic: 79764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138385, rend_intergenic: 131763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152752, rend_intergenic: 150963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155526, rend_intergenic: 153053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159479, rend_intergenic: 156364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163800, rend_intergenic: 159533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support