-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_5843921-6038002

-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_49519-T1
Valid prediction for snap_scaffold_22-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_49508-T1
Valid prediction for pasa_asmbl_30076.p1
Valid prediction for Augustus_model.g33015.t1
Valid prediction for Augustus_model.g33030.t1
Valid prediction for CodingQuarry_transcript_34169-T1
Valid prediction for CodingQuarry_transcript_34163-T1
Valid prediction for HiQ_model.g33029.t1
Valid prediction for pasa_asmbl_30074.p1
Couldn't classify 90216, 90267
Couldn't classify 93123, 93226
Sorry, prediction CodingQuarry_transcript_34166-T1 fails validation.
(ATG)	 TG	89880-89930	GT	CAG
(CTG)	 AG	90216-90267	AT	GAA
(ATT)	 AC	93123-93226	GT	GCG
(GAT)	 AG	93502-93624	GT	TGG
(CCT)	 AG	93803-93841	GA	GAG
-recovered CodingQuarry_transcript_34166-T1, initial, 89880, 89930
add_exon() Sorry, CodingQuarry_transcript_34166-T1 90216-90267-terminal-3 is invalid.
-recovered CodingQuarry_transcript_34166-T1, terminal, 90216, 90267
-recovered CodingQuarry_transcript_34166-T1, terminal, 93803, 93841
-recovered CodingQuarry_transcript_34166-T1, internal, 93502, 93624
Valid prediction for pasa_asmbl_30084.p1
Couldn't classify 83477, 83669
Sorry, prediction pasa_asmbl_30071.p1 fails validation.
(GTT)	 GA	83477-83669	GT	AGG
(GGC)	 AG	84546-85039	GT	AGG
(GCA)	 AG	85280-85399	GT	AGG
(AGC)	 AG	85960-86029	GT	AGG
(GCA)	 AG	86481-86654	GT	ACG
(CTC)	 AG	87401-87540	AG	GAA
-recovered pasa_asmbl_30071.p1, terminal, 87401, 87540
-recovered pasa_asmbl_30071.p1, internal, 84546, 85039
-recovered pasa_asmbl_30071.p1, internal, 85280, 85399
-recovered pasa_asmbl_30071.p1, internal, 85960, 86029
-recovered pasa_asmbl_30071.p1, internal, 86481, 86654
Valid prediction for GlimmerHMM_glimmerT_49507-T1
Valid prediction for HiQ_model.g33026.t1
Valid prediction for snap_scaffold_22-snap.1120-T1
Valid prediction for snap_scaffold_22-snap.1119-T1
Valid prediction for pasa_asmbl_30428.p1
Valid prediction for Augustus_model.g33017.t1
Valid prediction for CodingQuarry_transcript_34162-T1
Valid prediction for snap_scaffold_22-snap.1101-T1
Valid prediction for snap_scaffold_22-snap.1135-T1
Couldn't classify 155942, 156110
Couldn't classify 159016, 159137
Sorry, prediction pasa_asmbl_30082.p1 fails validation.
(CTT)	 CT	155942-156110	GT	AGG
(CCA)	 AG	156291-156323	GT	AGG
(CGA)	 AG	157423-157623	GT	AGG
(CAC)	 AG	158263-158335	GT	AGG
(CTC)	 AG	158449-158492	GT	AAG
(ATT)	 AG	158733-158819	GT	AGG
(GTG)	 AG	159016-159137	AC	GTA
-recovered pasa_asmbl_30082.p1, terminal, 156291, 156323
-recovered pasa_asmbl_30082.p1, internal, 156291, 156323
-recovered pasa_asmbl_30082.p1, internal, 157423, 157623
-recovered pasa_asmbl_30082.p1, internal, 158263, 158335
-recovered pasa_asmbl_30082.p1, internal, 158449, 158492
-recovered pasa_asmbl_30082.p1, internal, 158733, 158819
Valid prediction for snap_scaffold_22-snap.1131-T1
Valid prediction for Augustus_model.g33013.t1
Valid prediction for GlimmerHMM_glimmerT_49514-T1
Valid prediction for GlimmerHMM_glimmerT_49528-T1
Valid prediction for GlimmerHMM_glimmerT_49522-T1
Valid prediction for GlimmerHMM_glimmerT_49500-T1
Valid prediction for GlimmerHMM_glimmerT_49515-T1
Valid prediction for HiQ_model.g33018.t1
Valid prediction for snap_scaffold_22-snap.1116-T1
Valid prediction for snap_scaffold_22-snap.1141-T1
Couldn't classify 173741, 174073
Sorry, prediction pasa_asmbl_30086.p1 fails validation.
(CTT)	 AC	173741-174073	GG	CGG
Valid prediction for GlimmerHMM_glimmerT_49530-T1
Valid prediction for snap_scaffold_22-snap.1102-T1
Valid prediction for snap_scaffold_22-snap.1114-T1
Valid prediction for GlimmerHMM_glimmerT_49505-T1
Valid prediction for Augustus_model.g33019.t1
Valid prediction for snap_scaffold_22-snap.1133-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g33011.t1
Valid prediction for GlimmerHMM_glimmerT_49527-T1
Valid prediction for HiQ_model.g33021.t1
Valid prediction for Augustus_model.g33027.t1
Valid prediction for CodingQuarry_transcript_34167-T1
Valid prediction for CodingQuarry_transcript_34165-T1
Valid prediction for GlimmerHMM_glimmerT_49502-T1
Couldn't classify 65010, 65045
Sorry, prediction CodingQuarry_transcript_34161-T1 fails validation.
(ATG)	 TC	62877-62900	GT	AGG
(ATG)	 AG	63224-63304	GT	GGG
(ATA)	 AG	63395-63504	GT	ATG
(TTC)	 AG	63832-63982	GT	TGG
(ACG)	 AG	64209-64317	GT	AGG
(ATA)	 AG	64440-64489	GT	AGG
(CAG)	 CC	65010-65045	AG	AGA
-recovered CodingQuarry_transcript_34161-T1, initial, 62877, 62900
-recovered CodingQuarry_transcript_34161-T1, initial, 63224, 63304
-recovered CodingQuarry_transcript_34161-T1, internal, 63224, 63304
-recovered CodingQuarry_transcript_34161-T1, internal, 63395, 63504
-recovered CodingQuarry_transcript_34161-T1, internal, 63832, 63982
-recovered CodingQuarry_transcript_34161-T1, internal, 64209, 64317
-recovered CodingQuarry_transcript_34161-T1, internal, 64440, 64489
Couldn't classify 172078, 172377
Couldn't classify 172604, 173473
Sorry, prediction pasa_asmbl_30085.p1 fails validation.
(AAG)	 GT	172078-172377	GT	AGG
(GTT)	 AG	172604-173473	AG	CCA
Valid prediction for snap_scaffold_22-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_49521-T1
Valid prediction for snap_scaffold_22-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_49526-T1
Valid prediction for GlimmerHMM_glimmerT_49511-T1
Valid prediction for GlimmerHMM_glimmerT_49532-T1
Valid prediction for snap_scaffold_22-snap.1130-T1
Valid prediction for snap_scaffold_22-snap.1108-T1
Valid prediction for snap_scaffold_22-snap.1115-T1
Valid prediction for snap_scaffold_22-snap.1124-T1
Valid prediction for Augustus_model.g33031.t1
Couldn't classify 174479, 175768
Sorry, prediction pasa_asmbl_30087.p1 fails validation.
(GCC)	 AA	174479-175768	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_49529-T1
Valid prediction for GlimmerHMM_glimmerT_49523-T1
Valid prediction for GlimmerHMM_glimmerT_49501-T1
Valid prediction for snap_scaffold_22-snap.1098-T1
Valid prediction for snap_scaffold_22-snap.1139-T1
Valid prediction for snap_scaffold_22-snap.1122-T1
Valid prediction for snap_scaffold_22-snap.1106-T1
Couldn't classify 84546, 84801
Couldn't classify 84862, 85039
Sorry, prediction CodingQuarry_transcript_34164-T1 fails validation.
(ATG)	 CG	83624-83669	GT	AGG
(GGC)	 AG	84546-84801	CT	ACC
(CTC)	 AC	84862-85039	GT	AGG
(GCA)	 AG	85280-85399	GT	AGG
(AGC)	 AG	85960-86029	GT	AGG
(GCA)	 AG	86481-86654	GT	ACG
(CTC)	 AG	87401-87540	AG	GAA
-recovered CodingQuarry_transcript_34164-T1, initial, 83624, 83669
-recovered CodingQuarry_transcript_34164-T1, terminal, 87401, 87540
-recovered CodingQuarry_transcript_34164-T1, internal, 85280, 85399
-recovered CodingQuarry_transcript_34164-T1, internal, 85960, 86029
-recovered CodingQuarry_transcript_34164-T1, internal, 86481, 86654
Valid prediction for HiQ_model.g33014.t1
Valid prediction for snap_scaffold_22-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_49510-T1
Valid prediction for snap_scaffold_22-snap.1099-T1
Valid prediction for snap_scaffold_22-snap.1113-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g33024.t1
Valid prediction for snap_scaffold_22-snap.1138-T1
Valid prediction for snap_scaffold_22-snap.1104-T1
Valid prediction for snap_scaffold_22-snap.1112-T1
Valid prediction for snap_scaffold_22-snap.1142-T1
Valid prediction for pasa_asmbl_30072.p1
Valid prediction for GlimmerHMM_glimmerT_49512-T1
Couldn't classify 78863, 79039
Sorry, prediction pasa_asmbl_30068.p1 fails validation.
(CTC)	 AC	78863-79039	GT	CCG
(GTG)	 AG	79234-79328	GT	AAG
(GTT)	 AG	79440-79564	GT	CGG
(GTG)	 AG	79691-79929	AT	AGA
-recovered pasa_asmbl_30068.p1, terminal, 79691, 79929
-recovered pasa_asmbl_30068.p1, internal, 79234, 79328
-recovered pasa_asmbl_30068.p1, internal, 79440, 79564

-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 GlimmerHMM_glimmerT_49517-T1
Valid prediction for snap_scaffold_22-snap.1125-T1
Valid prediction for snap_scaffold_22-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_49513-T1
Valid prediction for Augustus_model.g33009.t1
Valid prediction for snap_scaffold_22-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_49503-T1
Valid prediction for Augustus_model.g33012.t1
Valid prediction for snap_scaffold_22-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_49531-T1
Couldn't classify 112953, 113318
Sorry, prediction pasa_asmbl_29293.p2 fails validation.
(TCG)	 CC	112953-113318	TG	AGT
Valid prediction for Augustus_model.g33022.t1
Valid prediction for pasa_asmbl_29298.p1
Valid prediction for GlimmerHMM_glimmerT_49518-T1
Valid prediction for Augustus_model.g33020.t1
Valid prediction for snap_scaffold_22-snap.1100-T1
Valid prediction for snap_scaffold_22-snap.1128-T1
Valid prediction for snap_scaffold_22-snap.1134-T1
Valid prediction for snap_scaffold_22-snap.1109-T1
Valid prediction for snap_scaffold_22-snap.1121-T1
Valid prediction for CodingQuarry_transcript_34168-T1
Valid prediction for snap_scaffold_22-snap.1126-T1
Valid prediction for snap_scaffold_22-snap.1111-T1
Couldn't classify 51587, 51652
Sorry, prediction pasa_asmbl_29300.p1 fails validation.
(ATC)	 GG	51587-51652	GT	CTG
(AGG)	 AG	51924-52126	GT	AGG
(GAG)	 AG	52353-52422	GT	AGG
(TTG)	 AG	52559-52653	GT	AGG
(AGG)	 AG	53220-53410	GT	AGG
(GAA)	 AG	53682-53732	GT	AGG
(ACG)	 AG	53881-54053	GT	CGG
(AAT)	 AG	54129-54238	GT	GGG
(GCT)	 AG	54410-54520	GT	CTG
(GTT)	 AG	54658-54719	GT	AGG
(GTG)	 AG	56453-56550	AA	GAA
-recovered pasa_asmbl_29300.p1, terminal, 56453, 56550
-recovered pasa_asmbl_29300.p1, internal, 51924, 52126
-recovered pasa_asmbl_29300.p1, internal, 52353, 52422
-recovered pasa_asmbl_29300.p1, internal, 52559, 52653
-recovered pasa_asmbl_29300.p1, internal, 53220, 53410
-recovered pasa_asmbl_29300.p1, internal, 53682, 53732
-recovered pasa_asmbl_29300.p1, internal, 53881, 54053
-recovered pasa_asmbl_29300.p1, internal, 54129, 54238
-recovered pasa_asmbl_29300.p1, internal, 54410, 54520
-recovered pasa_asmbl_29300.p1, internal, 54658, 54719
Valid prediction for GlimmerHMM_glimmerT_49524-T1
Valid prediction for snap_scaffold_22-snap.1097-T1
Valid prediction for snap_scaffold_22-snap.1105-T1
Valid prediction for snap_scaffold_22-snap.1096-T1
Valid prediction for Augustus_model.g33010.t1
Valid prediction for CodingQuarry_transcript_34170-T1
Valid prediction for snap_scaffold_22-snap.1132-T1
Couldn't classify 112612, 112760
Sorry, prediction pasa_asmbl_29294.p1 fails validation.
(ATG)	 TC	111394-111562	GT	AGG
(AGG)	 AG	112612-112760	AC	TGA
-recovered pasa_asmbl_29294.p1, initial, 111394, 111562
Valid prediction for snap_scaffold_22-snap.1118-T1
Valid prediction for Augustus_model.g33008.t1
Valid prediction for HiQ_model.g33023.t1
Valid prediction for GlimmerHMM_glimmerT_49504-T1
Valid prediction for Augustus_model.g33028.t1
Valid prediction for GlimmerHMM_glimmerT_49516-T1
Valid prediction for HiQ_model.g33016.t1
Valid prediction for HiQ_model.g33025.t1
Valid prediction for GlimmerHMM_glimmerT_49509-T1
Valid prediction for GlimmerHMM_glimmerT_49506-T1
Valid prediction for GlimmerHMM_glimmerT_49525-T1
Valid prediction for snap_scaffold_22-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_49520-T1
Couldn't classify 88908, 89061
Couldn't classify 89723, 89910
Sorry, prediction pasa_asmbl_29297.p1 fails validation.
(GAA)	 AC	88908-89061	GT	AGG
(GTG)	 AG	89167-89520	GT	GTG
(CTC)	 AG	89723-89910	CC	CCC
-recovered pasa_asmbl_29297.p1, internal, 89167, 89520
Couldn't classify 99130, 99219
Sorry, prediction pasa_asmbl_29295.p1 fails validation.
(GTG)	 TT	99130-99219	GT	AGG
(TGT)	 AG	99377-99592	GT	AGG
(AAT)	 AG	99706-99765	TG	AAT
-recovered pasa_asmbl_29295.p1, terminal, 99706, 99765
-recovered pasa_asmbl_29295.p1, internal, 99377, 99592
Valid prediction for snap_scaffold_22-snap.1103-T1
Valid prediction for snap_scaffold_22-snap.1143-T1
Valid prediction for snap_scaffold_22-snap.1127-T1
Valid prediction for snap_scaffold_22-snap.1095-T1
Couldn't classify 44023, 44078
Couldn't classify 47858, 47897
Sorry, prediction pasa_asmbl_29303.p1 fails validation.
(AGA)	 GA	44023-44078	GT	AGG
(GGC)	 AG	46314-46371	GT	AGG
(CTG)	 AG	46885-47004	GT	AGG
(GAG)	 AG	47343-47396	GT	GGG
(GAG)	 AG	47525-47583	GT	GAG
(GGA)	 AG	47858-47897	CG	AGC
-recovered pasa_asmbl_29303.p1, internal, 46314, 46371
-recovered pasa_asmbl_29303.p1, internal, 46885, 47004
-recovered pasa_asmbl_29303.p1, internal, 47343, 47396
-recovered pasa_asmbl_29303.p1, internal, 47525, 47583

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16135, rend_intergenic: 12485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24450, rend_intergenic: 20094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34257, rend_intergenic: 31628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35155, rend_intergenic: 34355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40675, rend_intergenic: 35823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47798, rend_intergenic: 43944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53513, rend_intergenic: 51805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75004, rend_intergenic: 72675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134292, rend_intergenic: 131297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140911, rend_intergenic: 137533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150057, rend_intergenic: 141650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192358, rend_intergenic: 177098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194082
-exon list size: 456


building trellis

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70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 16135, rend_intergenic: 12485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24450, rend_intergenic: 20094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34257, rend_intergenic: 31628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35155, rend_intergenic: 34355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40675, rend_intergenic: 35823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47798, rend_intergenic: 43944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53513, rend_intergenic: 51805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75004, rend_intergenic: 72675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134292, rend_intergenic: 131297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140911, rend_intergenic: 137533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150057, rend_intergenic: 141650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192358, rend_intergenic: 177098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support