-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_9323650-9492925

-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 CodingQuarry_transcript_13194-T1
Valid prediction for GlimmerHMM_glimmerT_32113-T1
Valid prediction for Augustus_model.g21431.t1
Valid prediction for HiQ_model.g21426.t1
Valid prediction for snap_scaffold_13-snap.1683-T1
Valid prediction for Augustus_model.g21436.t1
Valid prediction for snap_scaffold_13-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_32141-T1
Valid prediction for GlimmerHMM_glimmerT_32115-T1
Valid prediction for snap_scaffold_13-snap.1694-T1
Valid prediction for Augustus_model.g21422.t1
Valid prediction for Augustus_model.g21438.t1
Valid prediction for Augustus_model.g21434.t1
Valid prediction for GlimmerHMM_glimmerT_32122-T1
Valid prediction for GlimmerHMM_glimmerT_32128-T1
Couldn't classify 54676, 54882
Couldn't classify 55167, 55472
Sorry, prediction pasa_asmbl_11200.p1 fails validation.
(TTC)	 AC	54676-54882	GT	AAG
(TTT)	 AG	55167-55472	GG	CAG
Valid prediction for snap_scaffold_13-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_32130-T1
Valid prediction for snap_scaffold_13-snap.1693-T1
Valid prediction for snap_scaffold_13-snap.1692-T1
Valid prediction for snap_scaffold_13-snap.1679-T1
Valid prediction for Augustus_model.g21429.t1
Valid prediction for GlimmerHMM_glimmerT_32126-T1
Valid prediction for snap_scaffold_13-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_32139-T1
Valid prediction for GlimmerHMM_glimmerT_32117-T1
Valid prediction for GlimmerHMM_glimmerT_32132-T1
Valid prediction for HiQ_model.g21420.t1
Valid prediction for Augustus_model.g21439.t1
Valid prediction for snap_scaffold_13-snap.1687-T1
Valid prediction for snap_scaffold_13-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_32136-T1
Valid prediction for snap_scaffold_13-snap.1703-T1
Valid prediction for snap_scaffold_13-snap.1709-T1
Valid prediction for snap_scaffold_13-snap.1681-T1
Valid prediction for Augustus_model.g21437.t1
Valid prediction for snap_scaffold_13-snap.1699-T1
Valid prediction for snap_scaffold_13-snap.1695-T1
Valid prediction for snap_scaffold_13-snap.1698-T1
Valid prediction for snap_scaffold_13-snap.1705-T1
Valid prediction for snap_scaffold_13-snap.1708-T1
Valid prediction for GlimmerHMM_glimmerT_32124-T1
Valid prediction for snap_scaffold_13-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_32138-T1
Valid prediction for CodingQuarry_transcript_13197-T1
Valid prediction for Augustus_model.g21432.t1
Valid prediction for GlimmerHMM_glimmerT_32134-T1
Valid prediction for GlimmerHMM_glimmerT_32133-T1
Valid prediction for GlimmerHMM_glimmerT_32125-T1
Valid prediction for GlimmerHMM_glimmerT_32121-T1
Valid prediction for Augustus_model.g21435.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 pasa_asmbl_10023.p1
Valid prediction for snap_scaffold_13-snap.1696-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32123-T1
Valid prediction for snap_scaffold_13-snap.1711-T1
Valid prediction for snap_scaffold_13-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_32120-T1
Valid prediction for GlimmerHMM_glimmerT_32131-T1
Valid prediction for snap_scaffold_13-snap.1704-T1
Valid prediction for snap_scaffold_13-snap.1678-T1
Valid prediction for snap_scaffold_13-snap.1690-T1
Valid prediction for Augustus_model.g21425.t1
Valid prediction for snap_scaffold_13-snap.1680-T1
Couldn't classify 116783, 116892
Sorry, prediction pasa_asmbl_10407.p1 fails validation.
(ACT)	 TC	116783-116892	GT	GGG
(GTT)	 AG	117322-117440	GT	AGG
(ATT)	 AG	117635-117720	GT	CGG
(GCT)	 AG	117833-117967	GT	TGG
(TTC)	 AG	118079-118191	GT	TGG
(GTG)	 AG	118274-118323	GT	GGG
(CCA)	 AG	118420-118583	GT	AGG
(CTG)	 AG	118685-118846	GT	AGG
(CCT)	 AG	118933-119010	GT	AGG
(GCT)	 AG	119101-119159	GT	CAG
(GGT)	 AG	119252-119374	GT	ACG
(ACT)	 AG	119481-119656	GT	AGG
(AGA)	 AG	119839-120042	GT	AGG
(ATA)	 AG	120209-120319	GT	GAG
(GTA)	 AG	120428-120492	GT	AGG
(CAA)	 AG	120636-120788	AG	GAA
add_exon() Sorry, pasa_asmbl_10407.p1 120209-120319-terminal-1 is invalid.
-recovered pasa_asmbl_10407.p1, terminal, 120209, 120319
-recovered pasa_asmbl_10407.p1, terminal, 120636, 120788
-recovered pasa_asmbl_10407.p1, internal, 117322, 117440
-recovered pasa_asmbl_10407.p1, internal, 117635, 117720
-recovered pasa_asmbl_10407.p1, internal, 117833, 117967
-recovered pasa_asmbl_10407.p1, internal, 118079, 118191
-recovered pasa_asmbl_10407.p1, internal, 118274, 118323
-recovered pasa_asmbl_10407.p1, internal, 118420, 118583
-recovered pasa_asmbl_10407.p1, internal, 118685, 118846
-recovered pasa_asmbl_10407.p1, internal, 118933, 119010
-recovered pasa_asmbl_10407.p1, internal, 119101, 119159
-recovered pasa_asmbl_10407.p1, internal, 119252, 119374
-recovered pasa_asmbl_10407.p1, internal, 119481, 119656
-recovered pasa_asmbl_10407.p1, internal, 119839, 120042
-recovered pasa_asmbl_10407.p1, internal, 120209, 120319
-recovered pasa_asmbl_10407.p1, internal, 120428, 120492
Valid prediction for snap_scaffold_13-snap.1697-T1
Valid prediction for snap_scaffold_13-snap.1702-T1
Valid prediction for snap_scaffold_13-snap.1712-T1
Valid prediction for Augustus_model.g21433.t1
Couldn't classify 142437, 142525
Sorry, prediction pasa_asmbl_10423.p1 fails validation.
(GTA)	 AG	142437-142525	GT	AGG
(GCC)	 AG	142602-142690	GT	TGG
(CCA)	 AG	142767-142947	GT	GGG
(ATG)	 AG	143027-143132	GT	AAG
(GTG)	 AG	143206-143291	GT	GGG
(CTG)	 AG	143397-143488	GT	AGG
(GAC)	 AG	143574-143638	GC	AAG
add_exon() Sorry, pasa_asmbl_10423.p1 143027-143132-initial-1 is invalid.
-recovered pasa_asmbl_10423.p1, initial, 143027, 143132
-recovered pasa_asmbl_10423.p1, terminal, 143574, 143638
-recovered pasa_asmbl_10423.p1, internal, 142437, 142525
-recovered pasa_asmbl_10423.p1, internal, 142602, 142690
-recovered pasa_asmbl_10423.p1, internal, 142767, 142947
-recovered pasa_asmbl_10423.p1, internal, 143027, 143132
-recovered pasa_asmbl_10423.p1, internal, 143206, 143291
-recovered pasa_asmbl_10423.p1, internal, 143397, 143488
-recovered pasa_asmbl_10423.p1, internal, 143574, 143638
Valid prediction for snap_scaffold_13-snap.1688-T1
Valid prediction for snap_scaffold_13-snap.1717-T1
Valid prediction for Augustus_model.g21423.t1
Valid prediction for pasa_asmbl_10025.p1
Valid prediction for GlimmerHMM_glimmerT_32142-T1
Valid prediction for Augustus_model.g21424.t1
Valid prediction for CodingQuarry_transcript_13199-T1
Valid prediction for Augustus_model.g21428.t1
Valid prediction for GlimmerHMM_glimmerT_32127-T1
Valid prediction for GlimmerHMM_glimmerT_32129-T1
Valid prediction for snap_scaffold_13-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_32140-T1
Valid prediction for snap_scaffold_13-snap.1686-T1
Valid prediction for GlimmerHMM_glimmerT_32137-T1
Valid prediction for GlimmerHMM_glimmerT_32114-T1
Valid prediction for Augustus_model.g21430.t1
Valid prediction for snap_scaffold_13-snap.1715-T1
Valid prediction for snap_scaffold_13-snap.1701-T1
Valid prediction for Augustus_model.g21427.t1
Valid prediction for HiQ_model.g21421.t1
Valid prediction for snap_scaffold_13-snap.1684-T1
Valid prediction for snap_scaffold_13-snap.1706-T1
Couldn't classify 132730, 132794
Sorry, prediction pasa_asmbl_10027.p1 fails validation.
(GCA)	 AT	132730-132794	GT	CGG
(CCG)	 AG	132912-133052	GT	AGG
(GTA)	 AG	133340-133394	GT	CGG
(GCA)	 AG	133734-133856	GT	AGG
(CAA)	 AG	133971-134060	GT	AGG
(GTG)	 AG	134249-134376	GT	GAG
(TCG)	 AG	134570-134674	GT	AGG
(GGC)	 AG	134878-135025	GT	AGG
(GTG)	 AG	135176-135347	GT	AGG
(CAC)	 AG	135463-135614	GT	AGG
(AGT)	 AG	135826-135924	GT	AGG
(GTC)	 AG	136097-136198	CA	GAC
-recovered pasa_asmbl_10027.p1, terminal, 136097, 136198
-recovered pasa_asmbl_10027.p1, internal, 132912, 133052
-recovered pasa_asmbl_10027.p1, internal, 133340, 133394
-recovered pasa_asmbl_10027.p1, internal, 133734, 133856
-recovered pasa_asmbl_10027.p1, internal, 133971, 134060
-recovered pasa_asmbl_10027.p1, internal, 134249, 134376
-recovered pasa_asmbl_10027.p1, internal, 134570, 134674
-recovered pasa_asmbl_10027.p1, internal, 134878, 135025
-recovered pasa_asmbl_10027.p1, internal, 135176, 135347
-recovered pasa_asmbl_10027.p1, internal, 135463, 135614
-recovered pasa_asmbl_10027.p1, internal, 135826, 135924
Valid prediction for CodingQuarry_transcript_13198-T1
Valid prediction for snap_scaffold_13-snap.1689-T1
Valid prediction for snap_scaffold_13-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_32135-T1
Valid prediction for GlimmerHMM_glimmerT_32118-T1
Valid prediction for GlimmerHMM_glimmerT_32119-T1
Valid prediction for snap_scaffold_13-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_32116-T1
Valid prediction for CodingQuarry_transcript_13195-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7667, rend_intergenic: 4129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70146, rend_intergenic: 64087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95508, rend_intergenic: 87212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102066, rend_intergenic: 101614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109288, rend_intergenic: 102727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117325, rend_intergenic: 113926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124212, rend_intergenic: 118530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133425, rend_intergenic: 129094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136947, rend_intergenic: 134280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146486, rend_intergenic: 142149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169276
-exon list size: 329


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 7667, rend_intergenic: 4129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70146, rend_intergenic: 64087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95508, rend_intergenic: 87212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102066, rend_intergenic: 101614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109288, rend_intergenic: 102727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117325, rend_intergenic: 113926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124212, rend_intergenic: 118530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133425, rend_intergenic: 129094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136947, rend_intergenic: 134280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146486, rend_intergenic: 142149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support