-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_11749601-12003470

-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 Augustus_model.g8424.t1
Valid prediction for CodingQuarry_transcript_52266-T1
Valid prediction for snap_scaffold_5-snap.2207-T1
Valid prediction for CodingQuarry_transcript_52263-T1
Valid prediction for snap_scaffold_5-snap.2199-T1
Valid prediction for HiQ_model.g8434.t1
Valid prediction for snap_scaffold_5-snap.2202-T1
Valid prediction for snap_scaffold_5-snap.2176-T1
Valid prediction for GlimmerHMM_glimmerT_12719-T1
Valid prediction for GlimmerHMM_glimmerT_12716-T1
Valid prediction for snap_scaffold_5-snap.2205-T1
Valid prediction for snap_scaffold_5-snap.2180-T1
Valid prediction for snap_scaffold_5-snap.2204-T1
Couldn't classify 90389, 90469
Couldn't classify 91650, 91719
Sorry, prediction pasa_asmbl_45764.p1 fails validation.
(CGT)	 CT	90389-90469	GT	AGG
(GTG)	 AG	91334-91548	GT	AGG
(CCC)	 AG	91650-91719	GC	AGG
-recovered pasa_asmbl_45764.p1, internal, 91334, 91548
-recovered pasa_asmbl_45764.p1, internal, 91650, 91719
Valid prediction for GlimmerHMM_glimmerT_12731-T1
Valid prediction for GlimmerHMM_glimmerT_12730-T1
Couldn't classify 21991, 22018
Couldn't classify 23117, 23172
Sorry, prediction pasa_asmbl_46422.p1 fails validation.
(GCC)	 AT	21991-22018	GT	TGG
(ATG)	 AG	22143-22271	GT	GGG
(ATG)	 AG	22841-22966	GT	AGG
(ATG)	 AG	23117-23172	TC	GGT
-recovered pasa_asmbl_46422.p1, initial, 22143, 22271
add_exon() Sorry, pasa_asmbl_46422.p1 22841-22966-initial-1 is invalid.
-recovered pasa_asmbl_46422.p1, initial, 22841, 22966
-recovered pasa_asmbl_46422.p1, internal, 22143, 22271
-recovered pasa_asmbl_46422.p1, internal, 22841, 22966
Valid prediction for Augustus_model.g8418.t1
Valid prediction for snap_scaffold_5-snap.2187-T1
Valid prediction for GlimmerHMM_glimmerT_12728-T1
Valid prediction for CodingQuarry_transcript_52268-T1
Valid prediction for GlimmerHMM_glimmerT_12725-T1
Valid prediction for HiQ_model.g8432.t1
Valid prediction for pasa_asmbl_45762.p1
Valid prediction for GlimmerHMM_glimmerT_12714-T1
Couldn't classify 161004, 161155
Couldn't classify 161246, 161432
Sorry, prediction pasa_asmbl_46449.p1 fails validation.
(AGA)	 CC	161004-161155	GT	AGG
(ATG)	 AG	161246-161432	GG	CCG
Valid prediction for snap_scaffold_5-snap.2190-T1
Valid prediction for snap_scaffold_5-snap.2177-T1
Valid prediction for snap_scaffold_5-snap.2192-T1
Valid prediction for Augustus_model.g8427.t1
Valid prediction for snap_scaffold_5-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_12741-T1
Valid prediction for snap_scaffold_5-snap.2191-T1
Valid prediction for snap_scaffold_5-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_12736-T1
Valid prediction for Augustus_model.g8420.t1
Valid prediction for snap_scaffold_5-snap.2174-T1
Valid prediction for pasa_asmbl_45781.p1
Valid prediction for GlimmerHMM_glimmerT_12722-T1
Valid prediction for GlimmerHMM_glimmerT_12732-T1
Valid prediction for Augustus_model.g8423.t1
Valid prediction for Augustus_model.g8430.t1
Valid prediction for GlimmerHMM_glimmerT_12740-T1
Valid prediction for GlimmerHMM_glimmerT_12734-T1
Valid prediction for Augustus_model.g8421.t1
Valid prediction for snap_scaffold_5-snap.2208-T1
Valid prediction for Augustus_model.g8416.t1
Valid prediction for CodingQuarry_transcript_52265-T1
Valid prediction for Augustus_model.g8419.t1
Valid prediction for Augustus_model.g8426.t1
Couldn't classify 162668, 162725
Sorry, prediction pasa_asmbl_45772.p1 fails validation.
(CCG)	 AT	162668-162725	GT	AGG
(ACG)	 AG	163447-163586	GT	GAG
(TTC)	 AG	163719-163875	GT	AGG
(GAC)	 AG	164842-164907	GT	GGG
(AGG)	 AG	165019-165134	GC	GAG
-recovered pasa_asmbl_45772.p1, terminal, 165019, 165134
-recovered pasa_asmbl_45772.p1, internal, 163447, 163586
-recovered pasa_asmbl_45772.p1, internal, 163719, 163875
-recovered pasa_asmbl_45772.p1, internal, 164842, 164907
-recovered pasa_asmbl_45772.p1, internal, 165019, 165134
Valid prediction for GlimmerHMM_glimmerT_12738-T1
Valid prediction for Augustus_model.g8429.t1
Valid prediction for GlimmerHMM_glimmerT_12717-T1
Valid prediction for Augustus_model.g8435.t1
Valid prediction for GlimmerHMM_glimmerT_12713-T1
Valid prediction for Augustus_model.g8422.t1
Valid prediction for snap_scaffold_5-snap.2175-T1
Valid prediction for snap_scaffold_5-snap.2194-T1
Valid prediction for GlimmerHMM_glimmerT_12737-T1
Valid prediction for GlimmerHMM_glimmerT_12739-T1
Valid prediction for Augustus_model.g8431.t1
Valid prediction for GlimmerHMM_glimmerT_12715-T1
Valid prediction for Augustus_model.g8410.t1
Valid prediction for Augustus_model.g8411.t1
Valid prediction for snap_scaffold_5-snap.2183-T1
Valid prediction for GlimmerHMM_glimmerT_12726-T1
Valid prediction for snap_scaffold_5-snap.2206-T1
Couldn't classify 144333, 144398
Couldn't classify 148190, 148210
Sorry, prediction pasa_asmbl_46437.p1 fails validation.
(TTT)	 TC	144333-144398	GT	GGG
(AAG)	 AG	145293-145394	GT	CGG
(GCC)	 AG	145557-145691	GT	AGG
(AGG)	 AG	147162-147302	GT	AGG
(GAC)	 AG	148190-148210	GT	CAG
-recovered pasa_asmbl_46437.p1, internal, 145293, 145394
-recovered pasa_asmbl_46437.p1, internal, 145557, 145691
-recovered pasa_asmbl_46437.p1, internal, 147162, 147302
-recovered pasa_asmbl_46437.p1, internal, 148190, 148210
Couldn't classify 7794, 8432
Sorry, prediction pasa_asmbl_45757.p1 fails validation.
(CCC)	 CA	7794-8432	GG	CAG
Valid prediction for snap_scaffold_5-snap.2196-T1
Valid prediction for Augustus_model.g8413.t1
Valid prediction for GlimmerHMM_glimmerT_12735-T1
Valid prediction for snap_scaffold_5-snap.2201-T1
Valid prediction for snap_scaffold_5-snap.2198-T1
Valid prediction for snap_scaffold_5-snap.2209-T1
Couldn't classify 91873, 91896
Couldn't classify 94680, 95165
Sorry, prediction pasa_asmbl_45765.p1 fails validation.
(AAG)	 AG	91873-91896	GT	AGG
(ATG)	 AG	93930-94187	GT	AGG
(GTG)	 AG	94307-94510	GT	AGG
(GTG)	 AG	94680-95165	AC	GCA
-recovered pasa_asmbl_45765.p1, initial, 93930, 94187
-recovered pasa_asmbl_45765.p1, internal, 91873, 91896
-recovered pasa_asmbl_45765.p1, internal, 93930, 94187
-recovered pasa_asmbl_45765.p1, internal, 94307, 94510

-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 Augustus_model.g8412.t1
Valid prediction for Augustus_model.g8417.t1
Valid prediction for GlimmerHMM_glimmerT_12718-T1
Valid prediction for snap_scaffold_5-snap.2181-T1
Valid prediction for snap_scaffold_5-snap.2195-T1
Valid prediction for CodingQuarry_transcript_52267-T1
Valid prediction for snap_scaffold_5-snap.2179-T1
Valid prediction for Augustus_model.g8428.t1
Valid prediction for CodingQuarry_transcript_52264-T1
Valid prediction for snap_scaffold_5-snap.2200-T1
Valid prediction for GlimmerHMM_glimmerT_12721-T1
Valid prediction for HiQ_model.g8433.t1
Valid prediction for GlimmerHMM_glimmerT_12723-T1
Valid prediction for snap_scaffold_5-snap.2178-T1
Valid prediction for GlimmerHMM_glimmerT_12720-T1
Valid prediction for snap_scaffold_5-snap.2211-T1
Valid prediction for HiQ_model.g8415.t1
Valid prediction for snap_scaffold_5-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_12733-T1
Valid prediction for Augustus_model.g8436.t1
Valid prediction for snap_scaffold_5-snap.2184-T1
Valid prediction for Augustus_model.g8414.t1
Valid prediction for pasa_asmbl_44428.p1
Valid prediction for snap_scaffold_5-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_12742-T1
Valid prediction for snap_scaffold_5-snap.2203-T1
Valid prediction for CodingQuarry_transcript_52269-T1
Couldn't classify 191390, 191491
Sorry, prediction pasa_asmbl_44425.p1 fails validation.
(TTT)	 AG	191390-191491	GT	TGG
(CAC)	 AG	191934-192049	GT	TGG
(GGT)	 AG	192159-192340	GT	TGG
(GTT)	 AG	192561-192586	GG	GAG
-recovered pasa_asmbl_44425.p1, terminal, 192561, 192586
-recovered pasa_asmbl_44425.p1, internal, 191390, 191491
-recovered pasa_asmbl_44425.p1, internal, 191934, 192049
-recovered pasa_asmbl_44425.p1, internal, 192159, 192340
Valid prediction for snap_scaffold_5-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_12724-T1
Valid prediction for snap_scaffold_5-snap.2210-T1
Valid prediction for snap_scaffold_5-snap.2188-T1
Valid prediction for pasa_asmbl_44426.p1
Valid prediction for Augustus_model.g8425.t1
Valid prediction for GlimmerHMM_glimmerT_12729-T1
Valid prediction for snap_scaffold_5-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_12727-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 74132, rend_intergenic: 73325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78871, rend_intergenic: 75494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88685, rend_intergenic: 79331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122244, rend_intergenic: 111171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131072, rend_intergenic: 122928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142630, rend_intergenic: 131702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154966, rend_intergenic: 142630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182444, rend_intergenic: 182240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186605, rend_intergenic: 182882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253870
-exon list size: 431


building trellis

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31.9    
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32.3    
32.6    
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33.0    
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34.9    
35.1    
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35.6    
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36.0    
36.3    
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37.2    
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38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
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48.0    
48.3    
48.5    
48.7    
49.0    
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50.1    
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50.6    
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92.4    
92.6    
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96.1    
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96.8    
97.0    
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97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 74132, rend_intergenic: 73325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78871, rend_intergenic: 75494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88685, rend_intergenic: 79331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122244, rend_intergenic: 111171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131072, rend_intergenic: 122928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142630, rend_intergenic: 131702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154966, rend_intergenic: 142630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182444, rend_intergenic: 182240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186605, rend_intergenic: 182882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support