-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_1108773-1323705

-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 pasa_asmbl_2902.p1
Valid prediction for snap_scaffold_10-snap.245-T1
Valid prediction for snap_scaffold_10-snap.249-T1
Valid prediction for Augustus_model.g16060.t1
Valid prediction for snap_scaffold_10-snap.256-T1
Valid prediction for Augustus_model.g16062.t1
Valid prediction for snap_scaffold_10-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_24082-T1
Valid prediction for GlimmerHMM_glimmerT_24077-T1
Valid prediction for CodingQuarry_transcript_5280-T1
Couldn't classify 59342, 59383
Sorry, prediction pasa_asmbl_2914.p2 fails validation.
(CTG)	 CT	59342-59383	GT	TTG
(CTT)	 AG	61754-61768	GT	TGG
(GGC)	 AG	64038-64147	GT	AGG
(GGA)	 AG	64497-64629	GT	AGG
(AGT)	 AG	64783-64910	GT	AGG
(CCC)	 AG	65034-65179	GT	AGG
(GTC)	 AG	65409-65567	GT	AGG
(ATT)	 AG	67493-67500	AA	AAA
-recovered pasa_asmbl_2914.p2, terminal, 67493, 67500
-recovered pasa_asmbl_2914.p2, internal, 61754, 61768
-recovered pasa_asmbl_2914.p2, internal, 64038, 64147
-recovered pasa_asmbl_2914.p2, internal, 64497, 64629
-recovered pasa_asmbl_2914.p2, internal, 64783, 64910
-recovered pasa_asmbl_2914.p2, internal, 65034, 65179
-recovered pasa_asmbl_2914.p2, internal, 65409, 65567
Valid prediction for pasa_asmbl_2923.p1
Valid prediction for GlimmerHMM_glimmerT_24091-T1
Valid prediction for HiQ_model.g16063.t1
Valid prediction for snap_scaffold_10-snap.265-T1
Valid prediction for snap_scaffold_10-snap.257-T1
Valid prediction for GlimmerHMM_glimmerT_24089-T1
Valid prediction for GlimmerHMM_glimmerT_24090-T1
Valid prediction for snap_scaffold_10-snap.276-T1
Valid prediction for Augustus_model.g16064.t1
Couldn't classify 52528, 52656
Couldn't classify 56420, 56452
Sorry, prediction pasa_asmbl_2910.p1 fails validation.
(GCG)	 AG	52528-52656	GT	AGG
(AGG)	 AG	52852-52998	GT	GTG
(GAC)	 AG	54237-54431	GT	AGG
(CTT)	 AG	56420-56452	CC	CCC
-recovered pasa_asmbl_2910.p1, internal, 52528, 52656
-recovered pasa_asmbl_2910.p1, internal, 52852, 52998
-recovered pasa_asmbl_2910.p1, internal, 54237, 54431
Valid prediction for snap_scaffold_10-snap.280-T1
Valid prediction for HiQ_model.g16056.t1
Valid prediction for GlimmerHMM_glimmerT_24095-T1
Valid prediction for GlimmerHMM_glimmerT_24080-T1
Valid prediction for snap_scaffold_10-snap.248-T1
Valid prediction for CodingQuarry_transcript_5281-T1
Valid prediction for pasa_asmbl_2922.p2
Valid prediction for snap_scaffold_10-snap.255-T1
Couldn't classify 134495, 134709
Couldn't classify 136037, 136202
Sorry, prediction pasa_asmbl_2921.p1 fails validation.
(GCT)	 CA	134495-134709	GT	AAG
(GTG)	 AG	136037-136202	GG	TAG
Couldn't classify 8167, 8275
Sorry, prediction pasa_asmbl_2904.p1 fails validation.
(ATG)	 CA	5866-5980	GT	ATG
(CCT)	 AG	7474-7546	GT	GTG
(GTT)	 AG	7723-7848	GT	GGG
(AAT)	 AG	8167-8275	TA	AGT
-recovered pasa_asmbl_2904.p1, initial, 5866, 5980
-recovered pasa_asmbl_2904.p1, internal, 7474, 7546
-recovered pasa_asmbl_2904.p1, internal, 7723, 7848
Valid prediction for snap_scaffold_10-snap.283-T1
Valid prediction for HiQ_model.g16055.t1
Valid prediction for snap_scaffold_10-snap.263-T1
Valid prediction for GlimmerHMM_glimmerT_24076-T1
Valid prediction for snap_scaffold_10-snap.244-T1
Valid prediction for snap_scaffold_10-snap.259-T1
Valid prediction for Augustus_model.g16065.t1
Valid prediction for GlimmerHMM_glimmerT_24097-T1
Valid prediction for Augustus_model.g16061.t1
Valid prediction for snap_scaffold_10-snap.267-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g16058.t1
Valid prediction for snap_scaffold_10-snap.270-T1
Valid prediction for snap_scaffold_10-snap.272-T1
Valid prediction for Augustus_model.g16066.t1
Valid prediction for snap_scaffold_10-snap.281-T1
Valid prediction for GlimmerHMM_glimmerT_24093-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_10-snap.275-T1
Valid prediction for CodingQuarry_transcript_5279-T1
Valid prediction for snap_scaffold_10-snap.268-T1
Valid prediction for snap_scaffold_10-snap.273-T1
Valid prediction for snap_scaffold_10-snap.277-T1
Valid prediction for snap_scaffold_10-snap.266-T1
Valid prediction for snap_scaffold_10-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_24092-T1
Valid prediction for GlimmerHMM_glimmerT_24085-T1
Valid prediction for snap_scaffold_10-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_24081-T1
Valid prediction for snap_scaffold_10-snap.247-T1
Valid prediction for snap_scaffold_10-snap.271-T1
Valid prediction for snap_scaffold_10-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_24083-T1
Valid prediction for snap_scaffold_10-snap.251-T1
Valid prediction for snap_scaffold_10-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_24088-T1
Valid prediction for snap_scaffold_10-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_24094-T1
Valid prediction for snap_scaffold_10-snap.282-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24084-T1
Valid prediction for Augustus_model.g16059.t1
Valid prediction for snap_scaffold_10-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_24079-T1
Valid prediction for snap_scaffold_10-snap.258-T1
Valid prediction for snap_scaffold_10-snap.261-T1
Valid prediction for snap_scaffold_10-snap.264-T1
Valid prediction for GlimmerHMM_glimmerT_24098-T1
Valid prediction for snap_scaffold_10-snap.278-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24087-T1
Valid prediction for GlimmerHMM_glimmerT_24078-T1
Valid prediction for pasa_asmbl_4047.p1
Valid prediction for GlimmerHMM_glimmerT_24096-T1
Valid prediction for Augustus_model.g16067.t1
Valid prediction for snap_scaffold_10-snap.279-T1
Valid prediction for snap_scaffold_10-snap.250-T1
Valid prediction for snap_scaffold_10-snap.269-T1
Valid prediction for Augustus_model.g16057.t1
Valid prediction for GlimmerHMM_glimmerT_24086-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57662, rend_intergenic: 31446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59916, rend_intergenic: 58836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82775, rend_intergenic: 79610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84982, rend_intergenic: 82882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95695, rend_intergenic: 91790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120693, rend_intergenic: 118807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129591, rend_intergenic: 127519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139774, rend_intergenic: 129974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144493, rend_intergenic: 142129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146306, rend_intergenic: 145709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162431, rend_intergenic: 152699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167782, rend_intergenic: 163419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186911, rend_intergenic: 172217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209111, rend_intergenic: 206653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214933
-exon list size: 428


building trellis

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24.2    
24.4    
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24.9    
25.1    
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25.8    
26.0    
26.3    
26.5    
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27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
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30.5    
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30.9    
31.2    
31.4    
31.6    
31.9    
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32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
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34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
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37.4    
37.7    
37.9    
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38.6    
38.8    
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40.2    
40.5    
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40.9    
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41.6    
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42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
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44.0    
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44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
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46.7    
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56.7    
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75.6    
75.8    
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77.0    
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87.2    
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88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 57662, rend_intergenic: 31446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59916, rend_intergenic: 58836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82775, rend_intergenic: 79610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84982, rend_intergenic: 82882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95695, rend_intergenic: 91790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120693, rend_intergenic: 118807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129591, rend_intergenic: 127519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139774, rend_intergenic: 129974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144493, rend_intergenic: 142129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146306, rend_intergenic: 145709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162431, rend_intergenic: 152699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167782, rend_intergenic: 163419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186911, rend_intergenic: 172217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209111, rend_intergenic: 206653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support