-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_3423134-3636999

-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_9-snap.753-T1
Valid prediction for snap_scaffold_9-snap.739-T1
Valid prediction for snap_scaffold_9-snap.756-T1
Valid prediction for Augustus_model.g14556.t1
Valid prediction for snap_scaffold_9-snap.740-T1
Valid prediction for snap_scaffold_9-snap.760-T1
Valid prediction for Augustus_model.g14546.t1
Valid prediction for snap_scaffold_9-snap.737-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_21880-T1
Valid prediction for snap_scaffold_9-snap.769-T1
Valid prediction for snap_scaffold_9-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_21871-T1
Valid prediction for snap_scaffold_9-snap.768-T1
Valid prediction for snap_scaffold_9-snap.720-T1
Valid prediction for snap_scaffold_9-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_21878-T1
Valid prediction for snap_scaffold_9-snap.730-T1
Couldn't classify 46827, 46911
Sorry, prediction pasa_asmbl_53904.p2 fails validation.
(TTC)	 CC	46827-46911	GT	CGG
(GTC)	 AG	47148-47195	GT	AGG
(CGC)	 AG	48157-48344	GG	GAG
-recovered pasa_asmbl_53904.p2, terminal, 48157, 48344
-recovered pasa_asmbl_53904.p2, internal, 47148, 47195
Valid prediction for snap_scaffold_9-snap.759-T1
Valid prediction for snap_scaffold_9-snap.750-T1
Valid prediction for snap_scaffold_9-snap.725-T1
Valid prediction for snap_scaffold_9-snap.738-T1
Valid prediction for snap_scaffold_9-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_21870-T1
Valid prediction for GlimmerHMM_glimmerT_21889-T1
Valid prediction for snap_scaffold_9-snap.721-T1
Valid prediction for Augustus_model.g14552.t1
Valid prediction for Augustus_model.g14544.t1
Valid prediction for snap_scaffold_9-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_21883-T1
Valid prediction for snap_scaffold_9-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_21874-T1
Valid prediction for Augustus_model.g14548.t1
Valid prediction for snap_scaffold_9-snap.762-T1
Valid prediction for Augustus_model.g14550.t1
Valid prediction for snap_scaffold_9-snap.764-T1
Valid prediction for snap_scaffold_9-snap.754-T1
Valid prediction for snap_scaffold_9-snap.727-T1
Valid prediction for Augustus_model.g14554.t1
Valid prediction for snap_scaffold_9-snap.751-T1
Valid prediction for snap_scaffold_9-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_21866-T1
Valid prediction for snap_scaffold_9-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_21865-T1
Valid prediction for Augustus_model.g14547.t1
Valid prediction for snap_scaffold_9-snap.724-T1
Valid prediction for snap_scaffold_9-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_21884-T1
Valid prediction for GlimmerHMM_glimmerT_21882-T1
Valid prediction for snap_scaffold_9-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_21877-T1
Valid prediction for Augustus_model.g14545.t1
Valid prediction for GlimmerHMM_glimmerT_21869-T1
Valid prediction for pasa_asmbl_53905.p1

-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_9-snap.770-T1
Valid prediction for Augustus_model.g14553.t1
Valid prediction for snap_scaffold_9-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_21872-T1
Valid prediction for CodingQuarry_transcript_62136-T1
Valid prediction for snap_scaffold_9-snap.765-T1
Valid prediction for Augustus_model.g14549.t1
Valid prediction for snap_scaffold_9-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_21873-T1
Valid prediction for GlimmerHMM_glimmerT_21888-T1
Valid prediction for snap_scaffold_9-snap.772-T1
Valid prediction for pasa_asmbl_55758.p2
Valid prediction for GlimmerHMM_glimmerT_21887-T1
Valid prediction for GlimmerHMM_glimmerT_21879-T1
Couldn't classify 3670, 3978
Sorry, prediction pasa_asmbl_54917.p1 fails validation.
(CAC)	 CG	3670-3978	CA	AGC
Valid prediction for snap_scaffold_9-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_21881-T1
Valid prediction for Augustus_model.g14555.t1
Valid prediction for GlimmerHMM_glimmerT_21876-T1
Valid prediction for snap_scaffold_9-snap.755-T1
Valid prediction for HiQ_model.g14542.t1
Valid prediction for GlimmerHMM_glimmerT_21885-T1
Valid prediction for Augustus_model.g14543.t1
Couldn't classify 8284, 8463
Sorry, prediction pasa_asmbl_54913.p2 fails validation.
(ATG)	 AT	7388-7537	GT	AGG
(GTC)	 AG	8284-8463	GG	AAG
-recovered pasa_asmbl_54913.p2, initial, 7388, 7537
Valid prediction for GlimmerHMM_glimmerT_21868-T1
Valid prediction for snap_scaffold_9-snap.741-T1
Valid prediction for Augustus_model.g14551.t1
Couldn't classify 5582, 6838
Sorry, prediction pasa_asmbl_54914.p1 fails validation.
(GGG)	 GT	5582-6838	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_21875-T1
Valid prediction for snap_scaffold_9-snap.771-T1
Valid prediction for snap_scaffold_9-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_21890-T1
Valid prediction for snap_scaffold_9-snap.763-T1
Valid prediction for snap_scaffold_9-snap.752-T1
Valid prediction for snap_scaffold_9-snap.749-T1
Couldn't classify 49396, 49444
Couldn't classify 50774, 50908
Sorry, prediction pasa_asmbl_54910.p1 fails validation.
(CTC)	 AG	49396-49444	GT	CGG
(TCC)	 AG	49578-49643	GT	AGG
(GTG)	 AG	50025-50095	GT	AGG
(ATT)	 AG	50400-50456	GT	AGG
(GCT)	 AG	50774-50908	GT	AGG
-recovered pasa_asmbl_54910.p1, internal, 49396, 49444
-recovered pasa_asmbl_54910.p1, internal, 49578, 49643
-recovered pasa_asmbl_54910.p1, internal, 50025, 50095
-recovered pasa_asmbl_54910.p1, internal, 50400, 50456
-recovered pasa_asmbl_54910.p1, internal, 50774, 50908
Valid prediction for snap_scaffold_9-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_21886-T1
Valid prediction for GlimmerHMM_glimmerT_21867-T1
Valid prediction for GlimmerHMM_glimmerT_21864-T1
Valid prediction for GlimmerHMM_glimmerT_21863-T1
Valid prediction for snap_scaffold_9-snap.735-T1
Valid prediction for snap_scaffold_9-snap.731-T1
Valid prediction for Augustus_model.g14557.t1
Valid prediction for snap_scaffold_9-snap.745-T1
Couldn't classify 10618, 11652
Sorry, prediction pasa_asmbl_54912.p1 fails validation.
(GAC)	 TG	10618-11652	AA	GAA
Valid prediction for Augustus_model.g14559.t1
Valid prediction for snap_scaffold_9-snap.722-T1
Valid prediction for HiQ_model.g14558.t1
Valid prediction for snap_scaffold_9-snap.757-T1
Valid prediction for snap_scaffold_9-snap.742-T1
Valid prediction for GlimmerHMM_glimmerT_21891-T1
Valid prediction for snap_scaffold_9-snap.748-T1
Valid prediction for snap_scaffold_9-snap.733-T1
Valid prediction for snap_scaffold_9-snap.732-T1
Valid prediction for snap_scaffold_9-snap.767-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14974, rend_intergenic: 12509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24845, rend_intergenic: 15798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27509, rend_intergenic: 25226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33909, rend_intergenic: 27638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44426, rend_intergenic: 39162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47490, rend_intergenic: 45916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48344, rend_intergenic: 48086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64498, rend_intergenic: 49268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68587, rend_intergenic: 65352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76245, rend_intergenic: 68607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85135, rend_intergenic: 78118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94313, rend_intergenic: 85150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98762, rend_intergenic: 94512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105383, rend_intergenic: 100168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107353, rend_intergenic: 105510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110583, rend_intergenic: 108006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117584, rend_intergenic: 110603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131033, rend_intergenic: 117907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169648, rend_intergenic: 131064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178757, rend_intergenic: 170696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180104, rend_intergenic: 178940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185970, rend_intergenic: 180449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190476, rend_intergenic: 185999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195021, rend_intergenic: 193484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213866
-exon list size: 362


building trellis

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27.2    
27.5    
27.7    
28.0    
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28.6    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
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45.6    
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46.2    
46.4    
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47.3    
47.5    
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48.4    
48.6    
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49.5    
49.7    
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50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
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53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
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56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
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60.2    
60.4    
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85.4    
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86.3    
86.5    
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87.1    
87.4    
87.6    
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88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
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96.2    
96.4    
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97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 14974, rend_intergenic: 12509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24845, rend_intergenic: 15798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27509, rend_intergenic: 25226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33909, rend_intergenic: 27638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44426, rend_intergenic: 39162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47490, rend_intergenic: 45916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48344, rend_intergenic: 48086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64498, rend_intergenic: 49268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68587, rend_intergenic: 65352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76245, rend_intergenic: 68607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85135, rend_intergenic: 78118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94313, rend_intergenic: 85150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98762, rend_intergenic: 94512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105383, rend_intergenic: 100168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107353, rend_intergenic: 105510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110583, rend_intergenic: 108006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117584, rend_intergenic: 110603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131033, rend_intergenic: 117907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169648, rend_intergenic: 131064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178757, rend_intergenic: 170696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180104, rend_intergenic: 178940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185970, rend_intergenic: 180449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190476, rend_intergenic: 185999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195021, rend_intergenic: 193484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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