-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_1112923-1331665

-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_4-snap.288-T1
Valid prediction for snap_scaffold_4-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_8756-T1
Valid prediction for GlimmerHMM_glimmerT_8750-T1
Valid prediction for snap_scaffold_4-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_8760-T1
Valid prediction for snap_scaffold_4-snap.294-T1
Valid prediction for snap_scaffold_4-snap.278-T1
Valid prediction for snap_scaffold_4-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_8735-T1
Valid prediction for GlimmerHMM_glimmerT_8752-T1
Valid prediction for snap_scaffold_4-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_8744-T1
Valid prediction for Augustus_model.g5652.t1
Valid prediction for snap_scaffold_4-snap.304-T1
Valid prediction for snap_scaffold_4-snap.283-T1
Valid prediction for GlimmerHMM_glimmerT_8736-T1
Valid prediction for snap_scaffold_4-snap.274-T1
Valid prediction for CodingQuarry_transcript_48876-T1
Valid prediction for GlimmerHMM_glimmerT_8743-T1
Valid prediction for snap_scaffold_4-snap.299-T1
Valid prediction for snap_scaffold_4-snap.307-T1
Valid prediction for snap_scaffold_4-snap.257-T1
Valid prediction for GlimmerHMM_glimmerT_8745-T1
Valid prediction for Augustus_model.g5653.t1
Valid prediction for snap_scaffold_4-snap.267-T1
Valid prediction for snap_scaffold_4-snap.295-T1
Valid prediction for snap_scaffold_4-snap.296-T1
Valid prediction for GlimmerHMM_glimmerT_8741-T1
Valid prediction for snap_scaffold_4-snap.281-T1
Valid prediction for snap_scaffold_4-snap.262-T1
Valid prediction for pasa_asmbl_41104.p2
Valid prediction for Augustus_model.g5656.t1
Valid prediction for Augustus_model.g5655.t1
Valid prediction for snap_scaffold_4-snap.269-T1
Valid prediction for snap_scaffold_4-snap.305-T1
Valid prediction for GlimmerHMM_glimmerT_8733-T1
Valid prediction for snap_scaffold_4-snap.263-T1
Valid prediction for Augustus_model.g5659.t1
Valid prediction for snap_scaffold_4-snap.258-T1
Valid prediction for GlimmerHMM_glimmerT_8764-T1
Valid prediction for snap_scaffold_4-snap.290-T1
Valid prediction for Augustus_model.g5658.t1
Valid prediction for GlimmerHMM_glimmerT_8739-T1
Valid prediction for snap_scaffold_4-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_8762-T1
Valid prediction for snap_scaffold_4-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_8749-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_4-snap.282-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.266-T1
Valid prediction for snap_scaffold_4-snap.292-T1
Valid prediction for snap_scaffold_4-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_8747-T1
Valid prediction for CodingQuarry_transcript_48874-T1
Couldn't classify 12954, 13077
Sorry, prediction pasa_asmbl_42364.p1 fails validation.
(GCC)	 GA	12954-13077	GT	AGG
(TCA)	 AG	13847-13897	GT	AGG
(ATG)	 AG	14926-15043	GT	AAG
(GCC)	 AG	16405-16567	GT	ATG
(GCT)	 AG	17416-17484	GT	AAG
(GTT)	 AG	17577-17737	GT	GTG
(GCG)	 AG	17963-18026	GT	AGG
(GAG)	 AG	18269-18301	CC	AAC
add_exon() Sorry, pasa_asmbl_42364.p1 14926-15043-initial-1 is invalid.
-recovered pasa_asmbl_42364.p1, initial, 14926, 15043
-recovered pasa_asmbl_42364.p1, terminal, 18269, 18301
-recovered pasa_asmbl_42364.p1, internal, 13847, 13897
-recovered pasa_asmbl_42364.p1, internal, 14926, 15043
-recovered pasa_asmbl_42364.p1, internal, 16405, 16567
-recovered pasa_asmbl_42364.p1, internal, 17416, 17484
-recovered pasa_asmbl_42364.p1, internal, 17577, 17737
-recovered pasa_asmbl_42364.p1, internal, 17963, 18026
Valid prediction for snap_scaffold_4-snap.287-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8757-T1
Valid prediction for snap_scaffold_4-snap.270-T1
Valid prediction for snap_scaffold_4-snap.306-T1
Valid prediction for Augustus_model.g5661.t1
Valid prediction for snap_scaffold_4-snap.308-T1
Valid prediction for snap_scaffold_4-snap.286-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.264-T1
Valid prediction for GlimmerHMM_glimmerT_8754-T1
Valid prediction for GlimmerHMM_glimmerT_8761-T1
Valid prediction for GlimmerHMM_glimmerT_8734-T1
Valid prediction for pasa_asmbl_41107.p2
Valid prediction for GlimmerHMM_glimmerT_8746-T1
Valid prediction for GlimmerHMM_glimmerT_8759-T1
Valid prediction for snap_scaffold_4-snap.275-T1
Valid prediction for snap_scaffold_4-snap.293-T1
Valid prediction for snap_scaffold_4-snap.280-T1
Valid prediction for GlimmerHMM_glimmerT_8740-T1
Valid prediction for HiQ_model.g5660.t1
Valid prediction for snap_scaffold_4-snap.260-T1
Valid prediction for snap_scaffold_4-snap.279-T1
Valid prediction for GlimmerHMM_glimmerT_8751-T1
Valid prediction for GlimmerHMM_glimmerT_8753-T1
Valid prediction for snap_scaffold_4-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_8755-T1
Valid prediction for HiQ_model.g5654.t1
Valid prediction for GlimmerHMM_glimmerT_8748-T1
Valid prediction for GlimmerHMM_glimmerT_8732-T1
Valid prediction for snap_scaffold_4-snap.298-T1
Valid prediction for GlimmerHMM_glimmerT_8758-T1
Valid prediction for GlimmerHMM_glimmerT_8742-T1
Valid prediction for snap_scaffold_4-snap.309-T1
Valid prediction for snap_scaffold_4-snap.273-T1
Valid prediction for snap_scaffold_4-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_8737-T1
Valid prediction for snap_scaffold_4-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_8765-T1
Valid prediction for snap_scaffold_4-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_8738-T1
Valid prediction for GlimmerHMM_glimmerT_8763-T1
Valid prediction for snap_scaffold_4-snap.302-T1
Valid prediction for snap_scaffold_4-snap.259-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.300-T1
Valid prediction for Augustus_model.g5657.t1
Valid prediction for snap_scaffold_4-snap.268-T1
Valid prediction for snap_scaffold_4-snap.285-T1
Valid prediction for snap_scaffold_4-snap.297-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23775, rend_intergenic: 7666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28511, rend_intergenic: 24953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 28826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33082, rend_intergenic: 31959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36347, rend_intergenic: 35267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37364, rend_intergenic: 36348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39117, rend_intergenic: 38832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47610, rend_intergenic: 39459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58141, rend_intergenic: 51158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75675, rend_intergenic: 66534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84258, rend_intergenic: 75728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94464, rend_intergenic: 84374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110560, rend_intergenic: 107471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120998, rend_intergenic: 110615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123892, rend_intergenic: 121418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124699, rend_intergenic: 124339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129185, rend_intergenic: 124727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137761, rend_intergenic: 129353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149907, rend_intergenic: 137888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159222, rend_intergenic: 151843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165060, rend_intergenic: 160092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181929, rend_intergenic: 166527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196582, rend_intergenic: 182912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214544, rend_intergenic: 207594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218743
-exon list size: 448


building trellis

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27.8    
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28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
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30.4    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
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32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
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36.9    
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37.6    
37.8    
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38.7    
38.9    
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42.0    
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42.9    
43.1    
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43.6    
43.8    
44.0    
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44.7    
44.9    
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47.8    
48.0    
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48.4    
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79.6    
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81.6    
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85.3    
85.6    
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88.2    
88.4    
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88.9    
89.1    
89.3    
89.6    
89.8    
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90.4    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
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94.2    
94.4    
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95.6    
95.8    
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96.4    
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96.9    
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97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 23775, rend_intergenic: 7666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28511, rend_intergenic: 24953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 28826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33082, rend_intergenic: 31959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36347, rend_intergenic: 35267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37364, rend_intergenic: 36348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39117, rend_intergenic: 38832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47610, rend_intergenic: 39459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58141, rend_intergenic: 51158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75675, rend_intergenic: 66534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84258, rend_intergenic: 75728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94464, rend_intergenic: 84374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110560, rend_intergenic: 107471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120998, rend_intergenic: 110615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123892, rend_intergenic: 121418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124699, rend_intergenic: 124339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129185, rend_intergenic: 124727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137761, rend_intergenic: 129353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149907, rend_intergenic: 137888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159222, rend_intergenic: 151843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165060, rend_intergenic: 160092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181929, rend_intergenic: 166527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196582, rend_intergenic: 182912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214544, rend_intergenic: 207594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support