-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_6623142-6832204

-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 GlimmerHMM_glimmerT_893-T1
Valid prediction for Augustus_model.g686.t1
Couldn't classify 126615, 126810
Sorry, prediction pasa_asmbl_1850.p1 fails validation.
(GTG)	 CA	126615-126810	GT	AGG
(CCA)	 AG	128687-128823	GT	AGG
(GAG)	 AG	129037-129207	GT	TGG
(GCC)	 AG	129351-129537	GT	GGG
(CTG)	 AG	129666-129799	GT	ATG
(TCC)	 AG	130183-130353	TG	GAT
-recovered pasa_asmbl_1850.p1, terminal, 130183, 130353
-recovered pasa_asmbl_1850.p1, internal, 128687, 128823
-recovered pasa_asmbl_1850.p1, internal, 129037, 129207
-recovered pasa_asmbl_1850.p1, internal, 129351, 129537
-recovered pasa_asmbl_1850.p1, internal, 129666, 129799
Couldn't classify 57363, 58649
Sorry, prediction pasa_asmbl_1846.p1 fails validation.
(GAC)	 GC	57363-58649	GT	AGG
(GAG)	 AG	58785-58802	GC	AAG
-recovered pasa_asmbl_1846.p1, terminal, 58785, 58802
-recovered pasa_asmbl_1846.p1, internal, 58785, 58802
Valid prediction for GlimmerHMM_glimmerT_889-T1
Valid prediction for snap_scaffold_1-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_897-T1
Valid prediction for snap_scaffold_1-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_887-T1
Valid prediction for GlimmerHMM_glimmerT_915-T1
Valid prediction for snap_scaffold_1-snap.1125-T1
Valid prediction for Augustus_model.g678.t1
Valid prediction for Augustus_model.g674.t1
Valid prediction for snap_scaffold_1-snap.1106-T1
Valid prediction for snap_scaffold_1-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_905-T1
Valid prediction for snap_scaffold_1-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_916-T1
Valid prediction for Augustus_model.g673.t1
Valid prediction for snap_scaffold_1-snap.1115-T1
Valid prediction for snap_scaffold_1-snap.1141-T1
Valid prediction for Augustus_model.g691.t1
Valid prediction for snap_scaffold_1-snap.1126-T1
Valid prediction for Augustus_model.g680.t1
Valid prediction for snap_scaffold_1-snap.1130-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_909-T1
Valid prediction for snap_scaffold_1-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_902-T1
Valid prediction for GlimmerHMM_glimmerT_922-T1
Valid prediction for snap_scaffold_1-snap.1124-T1
Valid prediction for snap_scaffold_1-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_920-T1
Valid prediction for snap_scaffold_1-snap.1114-T1
Valid prediction for snap_scaffold_1-snap.1108-T1
Valid prediction for Augustus_model.g672.t1
Valid prediction for snap_scaffold_1-snap.1138-T1
Valid prediction for snap_scaffold_1-snap.1105-T1
Valid prediction for snap_scaffold_1-snap.1119-T1
Valid prediction for Augustus_model.g692.t1
Couldn't classify 166029, 166142
Sorry, prediction pasa_asmbl_1857.p1 fails validation.
(TCC)	 AG	166029-166142	GT	AGG
(GAT)	 AG	166398-166498	GT	CGG
(ATC)	 AG	166691-166944	GT	CTG
(GCC)	 AG	167316-167632	GT	AGG
(GAG)	 AG	168508-168738	GT	AGG
(ATC)	 AG	168862-169077	TG	AAT
-recovered pasa_asmbl_1857.p1, terminal, 168862, 169077
-recovered pasa_asmbl_1857.p1, internal, 166029, 166142
-recovered pasa_asmbl_1857.p1, internal, 166398, 166498
-recovered pasa_asmbl_1857.p1, internal, 166691, 166944
-recovered pasa_asmbl_1857.p1, internal, 167316, 167632
-recovered pasa_asmbl_1857.p1, internal, 168508, 168738
Valid prediction for Augustus_model.g675.t1
Valid prediction for Augustus_model.g684.t1
Valid prediction for GlimmerHMM_glimmerT_899-T1
Valid prediction for snap_scaffold_1-snap.1098-T1
Valid prediction for Augustus_model.g676.t1
Valid prediction for GlimmerHMM_glimmerT_914-T1
Valid prediction for Augustus_model.g687.t1
Valid prediction for snap_scaffold_1-snap.1118-T1
Valid prediction for snap_scaffold_1-snap.1127-T1
Valid prediction for GlimmerHMM_glimmerT_896-T1
Valid prediction for Augustus_model.g683.t1
Valid prediction for snap_scaffold_1-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_912-T1
Valid prediction for GlimmerHMM_glimmerT_913-T1
Valid prediction for Augustus_model.g681.t1
Valid prediction for Augustus_model.g690.t1
Couldn't classify 30885, 31013
Couldn't classify 32814, 32981
Sorry, prediction pasa_asmbl_2753.p1 fails validation.
(GTG)	 AG	30885-31013	GT	CGG
(AGG)	 AG	32814-32981	CA	GCC
-recovered pasa_asmbl_2753.p1, internal, 30885, 31013
Valid prediction for Augustus_model.g685.t1
Valid prediction for snap_scaffold_1-snap.1112-T1
Valid prediction for snap_scaffold_1-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_895-T1
Valid prediction for GlimmerHMM_glimmerT_908-T1
Couldn't classify 36641, 36962
Sorry, prediction pasa_asmbl_1841.p1 fails validation.
(GGT)	 AC	36641-36962	GT	AGG
(GTC)	 AG	37486-37590	GT	AGG
(GTC)	 AG	38378-38569	GT	AGG
(GTA)	 AG	38706-38804	GT	AGG
(GTC)	 AG	39058-39170	CT	AGC
-recovered pasa_asmbl_1841.p1, terminal, 39058, 39170
-recovered pasa_asmbl_1841.p1, internal, 37486, 37590
-recovered pasa_asmbl_1841.p1, internal, 38378, 38569
-recovered pasa_asmbl_1841.p1, internal, 38706, 38804
Valid prediction for CodingQuarry_transcript_2661-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 CodingQuarry_transcript_2664-T1
Valid prediction for GlimmerHMM_glimmerT_894-T1
Valid prediction for GlimmerHMM_glimmerT_918-T1
Valid prediction for snap_scaffold_1-snap.1120-T1
Valid prediction for snap_scaffold_1-snap.1144-T1
Valid prediction for Augustus_model.g677.t1
Valid prediction for snap_scaffold_1-snap.1100-T1
Valid prediction for GlimmerHMM_glimmerT_926-T1
Valid prediction for snap_scaffold_1-snap.1111-T1
Valid prediction for snap_scaffold_1-snap.1143-T1
Valid prediction for snap_scaffold_1-snap.1131-T1
Valid prediction for snap_scaffold_1-snap.1099-T1
Valid prediction for Augustus_model.g696.t1
Valid prediction for GlimmerHMM_glimmerT_925-T1
Valid prediction for GlimmerHMM_glimmerT_906-T1
Valid prediction for pasa_asmbl_377.p1
Valid prediction for Augustus_model.g688.t1
Valid prediction for snap_scaffold_1-snap.1135-T1
Valid prediction for snap_scaffold_1-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_888-T1
Valid prediction for GlimmerHMM_glimmerT_890-T1
Valid prediction for GlimmerHMM_glimmerT_911-T1
Valid prediction for GlimmerHMM_glimmerT_904-T1
Valid prediction for snap_scaffold_1-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_923-T1
Valid prediction for snap_scaffold_1-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_919-T1
Valid prediction for snap_scaffold_1-snap.1117-T1
Valid prediction for snap_scaffold_1-snap.1122-T1
Valid prediction for snap_scaffold_1-snap.1113-T1
Valid prediction for snap_scaffold_1-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_891-T1
Valid prediction for snap_scaffold_1-snap.1140-T1
Valid prediction for Augustus_model.g693.t1
Valid prediction for GlimmerHMM_glimmerT_898-T1
Valid prediction for HiQ_model.g694.t1
Valid prediction for snap_scaffold_1-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_921-T1
Valid prediction for snap_scaffold_1-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_901-T1
Valid prediction for GlimmerHMM_glimmerT_903-T1
Valid prediction for snap_scaffold_1-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_910-T1
Valid prediction for GlimmerHMM_glimmerT_907-T1
Valid prediction for Augustus_model.g689.t1
Valid prediction for Augustus_model.g671.t1
Valid prediction for pasa_asmbl_378.p1
Couldn't classify 112434, 112916
Sorry, prediction pasa_asmbl_1849.p1 fails validation.
(GCG)	 CC	112434-112916	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_917-T1
Valid prediction for pasa_asmbl_380.p1
Valid prediction for Augustus_model.g679.t1
Valid prediction for GlimmerHMM_glimmerT_900-T1
Valid prediction for snap_scaffold_1-snap.1109-T1
Valid prediction for CodingQuarry_transcript_2665-T1
Valid prediction for snap_scaffold_1-snap.1142-T1
Valid prediction for snap_scaffold_1-snap.1136-T1
Valid prediction for snap_scaffold_1-snap.1133-T1
Valid prediction for CodingQuarry_transcript_2666-T1
Valid prediction for snap_scaffold_1-snap.1121-T1
Valid prediction for Augustus_model.g682.t1
Valid prediction for GlimmerHMM_glimmerT_892-T1
Valid prediction for Augustus_model.g695.t1
Valid prediction for snap_scaffold_1-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_924-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12790, rend_intergenic: 2886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18144, rend_intergenic: 13364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27080, rend_intergenic: 25118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35002, rend_intergenic: 27827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39281, rend_intergenic: 38149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46324, rend_intergenic: 44830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67126, rend_intergenic: 64464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74467, rend_intergenic: 69925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97651, rend_intergenic: 91286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149821, rend_intergenic: 147641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156163, rend_intergenic: 149928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161489, rend_intergenic: 160101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169077, rend_intergenic: 163198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204371, rend_intergenic: 202794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209063
-exon list size: 465


building trellis

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29.6    
29.8    
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30.2    
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30.6    
30.8    
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32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
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35.5    
35.8    
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36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
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39.6    
39.8    
40.0    
40.3    
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40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
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42.6    
42.8    
43.0    
43.3    
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44.8    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 12790, rend_intergenic: 2886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18144, rend_intergenic: 13364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27080, rend_intergenic: 25118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35002, rend_intergenic: 27827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39281, rend_intergenic: 38149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46324, rend_intergenic: 44830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67126, rend_intergenic: 64464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74467, rend_intergenic: 69925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97651, rend_intergenic: 91286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149821, rend_intergenic: 147641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156163, rend_intergenic: 149928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161489, rend_intergenic: 160101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169077, rend_intergenic: 163198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204371, rend_intergenic: 202794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support