-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_13690163-13981736

-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 21663, 21754
Couldn't classify 24635, 24718
Sorry, prediction pasa_asmbl_6076.p1 fails validation.
(CGT)	 TC	21663-21754	GT	TGG
(GCG)	 AG	22670-22873	GT	AGG
(AGA)	 AG	23037-23183	GT	TGG
(GGT)	 AG	23462-23594	GT	CGG
(GAA)	 AG	23722-23832	GT	AGG
(TGG)	 AG	24004-24168	GT	AGG
(ATA)	 AG	24281-24415	GT	AGG
(GCC)	 AG	24635-24718	GA	CCG
-recovered pasa_asmbl_6076.p1, internal, 22670, 22873
-recovered pasa_asmbl_6076.p1, internal, 23037, 23183
-recovered pasa_asmbl_6076.p1, internal, 23462, 23594
-recovered pasa_asmbl_6076.p1, internal, 23722, 23832
-recovered pasa_asmbl_6076.p1, internal, 24004, 24168
-recovered pasa_asmbl_6076.p1, internal, 24281, 24415
Valid prediction for GlimmerHMM_glimmerT_28211-T1
Valid prediction for GlimmerHMM_glimmerT_28228-T1
Valid prediction for snap_scaffold_11-snap.2902-T1
Valid prediction for snap_scaffold_11-snap.2925-T1
Valid prediction for Augustus_model.g18698.t1
Valid prediction for GlimmerHMM_glimmerT_28212-T1
Valid prediction for Augustus_model.g18689.t1
Valid prediction for snap_scaffold_11-snap.2893-T1
Valid prediction for snap_scaffold_11-snap.2920-T1
Valid prediction for GlimmerHMM_glimmerT_28213-T1
Valid prediction for snap_scaffold_11-snap.2900-T1
Valid prediction for Augustus_model.g18696.t1
Valid prediction for snap_scaffold_11-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_28202-T1
Valid prediction for GlimmerHMM_glimmerT_28210-T1
Couldn't classify 83342, 83347
Sorry, prediction pasa_asmbl_6079.p1 fails validation.
(ATG)	 TC	81978-82080	GT	GAG
(AGT)	 AG	82526-82618	GT	AGG
(GAC)	 AG	82739-82887	GT	AGG
(GCA)	 AG	83342-83347	GA	AGG
-recovered pasa_asmbl_6079.p1, initial, 81978, 82080
-recovered pasa_asmbl_6079.p1, internal, 82526, 82618
-recovered pasa_asmbl_6079.p1, internal, 82739, 82887
Valid prediction for snap_scaffold_11-snap.2934-T1
Valid prediction for Augustus_model.g18695.t1
Valid prediction for GlimmerHMM_glimmerT_28222-T1
Valid prediction for snap_scaffold_11-snap.2906-T1
Valid prediction for Augustus_model.g18699.t1
Valid prediction for snap_scaffold_11-snap.2924-T1
Valid prediction for GlimmerHMM_glimmerT_28221-T1
Valid prediction for snap_scaffold_11-snap.2894-T1
Valid prediction for snap_scaffold_11-snap.2929-T1
Valid prediction for snap_scaffold_11-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_28229-T1
Valid prediction for snap_scaffold_11-snap.2912-T1
Valid prediction for GlimmerHMM_glimmerT_28225-T1
Valid prediction for GlimmerHMM_glimmerT_28215-T1
Valid prediction for Augustus_model.g18688.t1
Valid prediction for snap_scaffold_11-snap.2895-T1
Valid prediction for GlimmerHMM_glimmerT_28201-T1
Valid prediction for snap_scaffold_11-snap.2918-T1
Valid prediction for Augustus_model.g18692.t1
Valid prediction for snap_scaffold_11-snap.2909-T1
Valid prediction for snap_scaffold_11-snap.2890-T1
Valid prediction for snap_scaffold_11-snap.2930-T1
Valid prediction for Augustus_model.g18691.t1
Valid prediction for snap_scaffold_11-snap.2936-T1
Valid prediction for snap_scaffold_11-snap.2910-T1
Valid prediction for snap_scaffold_11-snap.2905-T1
Valid prediction for GlimmerHMM_glimmerT_28226-T1
Valid prediction for snap_scaffold_11-snap.2927-T1
Valid prediction for Augustus_model.g18686.t1
Valid prediction for snap_scaffold_11-snap.2911-T1
Couldn't classify 25169, 25398
Sorry, prediction pasa_asmbl_6077.p1 fails validation.
(CGT)	 TC	25169-25398	GT	GGG
(GGC)	 AG	25532-25682	CA	GAC
-recovered pasa_asmbl_6077.p1, terminal, 25532, 25682
Valid prediction for HiQ_model.g18685.t1
Couldn't classify 28355, 28957
Sorry, prediction pasa_asmbl_6078.p1 fails validation.
(GCT)	 CT	28355-28957	AC	AAA
Valid prediction for Augustus_model.g18687.t1
Valid prediction for GlimmerHMM_glimmerT_28219-T1
Valid prediction for snap_scaffold_11-snap.2921-T1
Valid prediction for CodingQuarry_transcript_8304-T1
Valid prediction for pasa_asmbl_6074.p1
Valid prediction for Augustus_model.g18697.t1
Valid prediction for snap_scaffold_11-snap.2938-T1
Valid prediction for snap_scaffold_11-snap.2891-T1
Valid prediction for snap_scaffold_11-snap.2928-T1
Valid prediction for Augustus_model.g18694.t1
Valid prediction for snap_scaffold_11-snap.2892-T1
Valid prediction for snap_scaffold_11-snap.2897-T1
Valid prediction for snap_scaffold_11-snap.2914-T1
Valid prediction for GlimmerHMM_glimmerT_28227-T1
Valid prediction for GlimmerHMM_glimmerT_28218-T1
Valid prediction for snap_scaffold_11-snap.2896-T1
Valid prediction for GlimmerHMM_glimmerT_28220-T1
Valid prediction for GlimmerHMM_glimmerT_28208-T1
Valid prediction for GlimmerHMM_glimmerT_28205-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_11-snap.2922-T1
Valid prediction for Augustus_model.g18693.t1
Valid prediction for snap_scaffold_11-snap.2913-T1
Valid prediction for snap_scaffold_11-snap.2908-T1
Valid prediction for GlimmerHMM_glimmerT_28224-T1
Valid prediction for snap_scaffold_11-snap.2926-T1
Valid prediction for snap_scaffold_11-snap.2919-T1
Valid prediction for snap_scaffold_11-snap.2923-T1
Valid prediction for GlimmerHMM_glimmerT_28207-T1
Valid prediction for GlimmerHMM_glimmerT_28217-T1
Valid prediction for GlimmerHMM_glimmerT_28223-T1
Valid prediction for GlimmerHMM_glimmerT_28203-T1
Valid prediction for GlimmerHMM_glimmerT_28209-T1
Valid prediction for pasa_asmbl_7154.p1
Valid prediction for GlimmerHMM_glimmerT_28214-T1
Valid prediction for Augustus_model.g18690.t1
Valid prediction for snap_scaffold_11-snap.2931-T1
Valid prediction for snap_scaffold_11-snap.2898-T1
Valid prediction for snap_scaffold_11-snap.2915-T1
Valid prediction for snap_scaffold_11-snap.2935-T1
Valid prediction for snap_scaffold_11-snap.2901-T1
Valid prediction for snap_scaffold_11-snap.2916-T1
Valid prediction for snap_scaffold_11-snap.2899-T1
Valid prediction for snap_scaffold_11-snap.2933-T1
Valid prediction for snap_scaffold_11-snap.2907-T1
Valid prediction for GlimmerHMM_glimmerT_28206-T1
Valid prediction for GlimmerHMM_glimmerT_28216-T1
Valid prediction for snap_scaffold_11-snap.2903-T1
Valid prediction for GlimmerHMM_glimmerT_28204-T1
Valid prediction for snap_scaffold_11-snap.2937-T1
Valid prediction for snap_scaffold_11-snap.2904-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 63087, rend_intergenic: 57453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69958, rend_intergenic: 63491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91548, rend_intergenic: 86416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132226, rend_intergenic: 128153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154617, rend_intergenic: 143150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175507, rend_intergenic: 171443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200391, rend_intergenic: 196593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203651, rend_intergenic: 200450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279607, rend_intergenic: 277620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281316, rend_intergenic: 280029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 291574
-exon list size: 348


building trellis

0.3    
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1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
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4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
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6.9    
7.1    
7.4    
7.7    
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8.9    
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10.9    
11.1    
11.4    
11.7    
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12.3    
12.6    
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13.1    
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13.7    
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14.3    
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14.9    
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16.9    
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17.7    
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18.9    
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25.7    
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27.7    
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28.3    
28.6    
28.9    
29.1    
29.4    
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30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
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39.4    
39.7    
40.0    
40.3    
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42.6    
42.9    
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44.6    
44.9    
45.1    
45.4    
45.7    
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46.6    
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47.7    
48.0    
48.3    
48.6    
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49.4    
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51.7    
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53.4    
53.7    
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54.6    
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55.7    
56.0    
56.3    
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78.6    
78.9    
79.1    
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81.7    
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84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 63087, rend_intergenic: 57453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69958, rend_intergenic: 63491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91548, rend_intergenic: 86416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132226, rend_intergenic: 128153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154617, rend_intergenic: 143150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175507, rend_intergenic: 171443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200391, rend_intergenic: 196593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203651, rend_intergenic: 200450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279607, rend_intergenic: 277620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281316, rend_intergenic: 280029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support