-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_1317177-1497128

-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_13-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_31077-T1
Valid prediction for snap_scaffold_13-snap.251-T1
Valid prediction for snap_scaffold_13-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_31089-T1
Valid prediction for Augustus_model.g20641.t1
Valid prediction for GlimmerHMM_glimmerT_31073-T1
Valid prediction for snap_scaffold_13-snap.264-T1
Couldn't classify 18181, 18320
Sorry, prediction pasa_asmbl_10563.p1 fails validation.
(TTC)	 TG	18181-18320	GT	ACG
(GTT)	 AG	19052-19220	GT	AGG
(TGT)	 AG	19333-19426	GT	AGG
(GTT)	 AG	19519-19626	GT	AGG
(TGT)	 AG	20169-20278	GT	GGG
(GCA)	 AG	20369-20492	GT	GGG
(TTC)	 AG	21209-21306	GT	AGG
(TGC)	 AG	21424-21528	GT	AGG
(TCT)	 AG	21624-21662	GT	AGG
(GAG)	 AG	21741-21830	CA	GAC
add_exon() Sorry, pasa_asmbl_10563.p1 19333-19426-terminal-3 is invalid.
-recovered pasa_asmbl_10563.p1, terminal, 19333, 19426
-recovered pasa_asmbl_10563.p1, terminal, 21741, 21830
-recovered pasa_asmbl_10563.p1, internal, 19052, 19220
-recovered pasa_asmbl_10563.p1, internal, 19333, 19426
-recovered pasa_asmbl_10563.p1, internal, 19519, 19626
-recovered pasa_asmbl_10563.p1, internal, 20169, 20278
-recovered pasa_asmbl_10563.p1, internal, 20369, 20492
-recovered pasa_asmbl_10563.p1, internal, 21209, 21306
-recovered pasa_asmbl_10563.p1, internal, 21424, 21528
-recovered pasa_asmbl_10563.p1, internal, 21624, 21662
Valid prediction for snap_scaffold_13-snap.259-T1
Valid prediction for Augustus_model.g20649.t1
Valid prediction for snap_scaffold_13-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_31092-T1
Valid prediction for snap_scaffold_13-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_31084-T1
Valid prediction for snap_scaffold_13-snap.267-T1
Valid prediction for snap_scaffold_13-snap.256-T1
Valid prediction for snap_scaffold_13-snap.248-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.255-T1
Valid prediction for GlimmerHMM_glimmerT_31094-T1
Valid prediction for snap_scaffold_13-snap.257-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g20644.t1
Valid prediction for snap_scaffold_13-snap.265-T1
Valid prediction for Augustus_model.g20642.t1
Valid prediction for snap_scaffold_13-snap.249-T1
Valid prediction for snap_scaffold_13-snap.260-T1
Valid prediction for snap_scaffold_13-snap.241-T1
Valid prediction for snap_scaffold_13-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_31083-T1
Valid prediction for GlimmerHMM_glimmerT_31088-T1
Valid prediction for GlimmerHMM_glimmerT_31070-T1
Valid prediction for HiQ_model.g20639.t1
Valid prediction for GlimmerHMM_glimmerT_31071-T1
Valid prediction for snap_scaffold_13-snap.240-T1
Valid prediction for snap_scaffold_13-snap.236-T1
Valid prediction for snap_scaffold_13-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_31072-T1
Valid prediction for Augustus_model.g20640.t1
Valid prediction for GlimmerHMM_glimmerT_31085-T1
Valid prediction for snap_scaffold_13-snap.268-T1
Valid prediction for Augustus_model.g20645.t1
Valid prediction for snap_scaffold_13-snap.242-T1
Couldn't classify 17909, 18072
Sorry, prediction pasa_asmbl_10561.p1 fails validation.
(ATG)	 CA	14469-14611	GT	AGG
(AAC)	 AG	15959-16007	GT	TGG
(AAT)	 AG	16537-16665	GT	ATG
(ATG)	 AG	17181-17295	GT	AGG
(CGT)	 AG	17909-18072	CC	AGC
-recovered pasa_asmbl_10561.p1, initial, 14469, 14611
-recovered pasa_asmbl_10561.p1, initial, 17181, 17295
-recovered pasa_asmbl_10561.p1, internal, 15959, 16007
-recovered pasa_asmbl_10561.p1, internal, 16537, 16665
-recovered pasa_asmbl_10561.p1, internal, 17181, 17295

-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_13-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_31095-T1
Couldn't classify 42654, 44489
Sorry, prediction pasa_asmbl_9412.p1 fails validation.
(TCC)	 CC	42654-44489	CA	ACC
Valid prediction for GlimmerHMM_glimmerT_31078-T1
Valid prediction for GlimmerHMM_glimmerT_31081-T1
Valid prediction for GlimmerHMM_glimmerT_31086-T1
Valid prediction for Augustus_model.g20652.t1
Valid prediction for snap_scaffold_13-snap.245-T1
Valid prediction for Augustus_model.g20650.t1
Valid prediction for snap_scaffold_13-snap.252-T1
Valid prediction for snap_scaffold_13-snap.269-T1
Valid prediction for snap_scaffold_13-snap.250-T1
Valid prediction for Augustus_model.g20648.t1
Valid prediction for GlimmerHMM_glimmerT_31090-T1
Valid prediction for Augustus_model.g20653.t1
Valid prediction for snap_scaffold_13-snap.266-T1
Couldn't classify 41523, 42143
Sorry, prediction pasa_asmbl_9413.p1 fails validation.
(TCT)	 CT	41523-42143	CA	CCC
Valid prediction for GlimmerHMM_glimmerT_31079-T1
Couldn't classify 120561, 120667
Sorry, prediction pasa_asmbl_9406.p1 fails validation.
(ATG)	 AT	116687-116705	GT	ATG
(GTA)	 AG	117060-117145	GT	AGG
(GCT)	 AG	117268-117342	GT	AGG
(GAA)	 AG	117681-117792	GT	GGG
(CGG)	 AG	117903-117988	GT	TGG
(CTC)	 AG	118250-118394	GT	TGG
(GCC)	 AG	118540-118607	GT	AGG
(AGT)	 AG	118811-118884	GT	CAG
(GGC)	 AG	119143-119206	GT	TGG
(GTC)	 AG	119418-119519	GT	AAG
(AAA)	 AG	119643-119768	GT	AGG
(GTG)	 AG	119989-120067	GT	TGG
(CTC)	 AG	120561-120667	GT	AGG
-recovered pasa_asmbl_9406.p1, initial, 116687, 116705
-recovered pasa_asmbl_9406.p1, internal, 117060, 117145
-recovered pasa_asmbl_9406.p1, internal, 117268, 117342
-recovered pasa_asmbl_9406.p1, internal, 117681, 117792
-recovered pasa_asmbl_9406.p1, internal, 117903, 117988
-recovered pasa_asmbl_9406.p1, internal, 118250, 118394
-recovered pasa_asmbl_9406.p1, internal, 118540, 118607
-recovered pasa_asmbl_9406.p1, internal, 118811, 118884
-recovered pasa_asmbl_9406.p1, internal, 119143, 119206
-recovered pasa_asmbl_9406.p1, internal, 119418, 119519
-recovered pasa_asmbl_9406.p1, internal, 119643, 119768
-recovered pasa_asmbl_9406.p1, internal, 119989, 120067
-recovered pasa_asmbl_9406.p1, internal, 120561, 120667
Valid prediction for snap_scaffold_13-snap.263-T1
Valid prediction for snap_scaffold_13-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_31080-T1
Couldn't classify 125899, 126067
Sorry, prediction pasa_asmbl_9401.p1 fails validation.
(TTG)	 AG	125899-126067	GT	AGG
(AAT)	 AG	127905-128091	GT	AGG
(AAC)	 AG	130934-131009	GT	TGG
(GAG)	 AG	132671-132805	GT	AGG
(TGT)	 AG	133045-133142	GT	AGG
(AGA)	 AG	133488-133670	GT	AAG
(ATA)	 AG	134637-134744	GT	AAG
(GAC)	 AG	135045-135134	GT	AGG
(CAA)	 AG	135338-135464	GT	AGG
(GGC)	 AG	135909-136025	GT	AGG
(TTC)	 AG	136217-136340	GT	CGG
(ATA)	 AG	136430-136520	GT	AGG
(ATG)	 AG	137096-137198	CC	GAC
-recovered pasa_asmbl_9401.p1, terminal, 137096, 137198
-recovered pasa_asmbl_9401.p1, internal, 125899, 126067
-recovered pasa_asmbl_9401.p1, internal, 127905, 128091
-recovered pasa_asmbl_9401.p1, internal, 130934, 131009
-recovered pasa_asmbl_9401.p1, internal, 132671, 132805
-recovered pasa_asmbl_9401.p1, internal, 133045, 133142
-recovered pasa_asmbl_9401.p1, internal, 133488, 133670
-recovered pasa_asmbl_9401.p1, internal, 134637, 134744
-recovered pasa_asmbl_9401.p1, internal, 135045, 135134
-recovered pasa_asmbl_9401.p1, internal, 135338, 135464
-recovered pasa_asmbl_9401.p1, internal, 135909, 136025
-recovered pasa_asmbl_9401.p1, internal, 136217, 136340
-recovered pasa_asmbl_9401.p1, internal, 136430, 136520
Valid prediction for snap_scaffold_13-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_31087-T1
Valid prediction for GlimmerHMM_glimmerT_31074-T1
Valid prediction for GlimmerHMM_glimmerT_31076-T1
Valid prediction for GlimmerHMM_glimmerT_31093-T1
Valid prediction for Augustus_model.g20647.t1
Valid prediction for GlimmerHMM_glimmerT_31075-T1
Valid prediction for snap_scaffold_13-snap.237-T1
Valid prediction for HiQ_model.g20643.t1
Valid prediction for snap_scaffold_13-snap.262-T1
Valid prediction for Augustus_model.g20646.t1
Valid prediction for GlimmerHMM_glimmerT_31091-T1
Valid prediction for Augustus_model.g20651.t1
Couldn't classify 44733, 44960
Couldn't classify 45136, 45210
Sorry, prediction pasa_asmbl_9411.p1 fails validation.
(GGG)	 AG	44733-44960	GT	AGG
(AAG)	 AG	45136-45210	CA	ATC
-recovered pasa_asmbl_9411.p1, internal, 44733, 44960
Valid prediction for snap_scaffold_13-snap.258-T1
Valid prediction for GlimmerHMM_glimmerT_31082-T1
Valid prediction for snap_scaffold_13-snap.243-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21830, rend_intergenic: 16120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49697, rend_intergenic: 43272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93666, rend_intergenic: 88718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110084, rend_intergenic: 107978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155579, rend_intergenic: 143914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179952
-exon list size: 309


building trellis

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18.6    
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25.7    
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27.7    
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32.2    
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33.8    
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34.7    
35.0    
35.4    
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36.0    
36.3    
36.7    
37.0    
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37.6    
37.9    
38.3    
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41.2    
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42.4    
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44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
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49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
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52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
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59.2    
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60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
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63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
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69.5    
69.8    
70.1    
70.4    
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72.3    
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73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
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75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
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78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
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81.4    
81.7    
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82.3    
82.6    
83.0    
83.3    
83.6    
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88.7    
89.1    
89.4    
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90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
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94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 21830, rend_intergenic: 16120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49697, rend_intergenic: 43272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93666, rend_intergenic: 88718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110084, rend_intergenic: 107978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155579, rend_intergenic: 143914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 14468
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11644
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support