-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_21483166-21800876

-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_2909-T1
Valid prediction for snap_scaffold_1-snap.4057-T1
Valid prediction for GlimmerHMM_glimmerT_2887-T1
Valid prediction for snap_scaffold_1-snap.4096-T1
Valid prediction for snap_scaffold_1-snap.4071-T1
Valid prediction for snap_scaffold_1-snap.4090-T1
Valid prediction for snap_scaffold_1-snap.4052-T1
Valid prediction for snap_scaffold_1-snap.4075-T1
Valid prediction for GlimmerHMM_glimmerT_2889-T1
Valid prediction for Augustus_model.g2023.t1
Valid prediction for snap_scaffold_1-snap.4073-T1
Valid prediction for snap_scaffold_1-snap.4086-T1
Valid prediction for snap_scaffold_1-snap.4061-T1
Valid prediction for snap_scaffold_1-snap.4059-T1
Valid prediction for snap_scaffold_1-snap.4044-T1
Valid prediction for GlimmerHMM_glimmerT_2895-T1
Valid prediction for GlimmerHMM_glimmerT_2905-T1
Valid prediction for snap_scaffold_1-snap.4068-T1
Valid prediction for GlimmerHMM_glimmerT_2899-T1
Valid prediction for snap_scaffold_1-snap.4085-T1
Valid prediction for snap_scaffold_1-snap.4093-T1
Valid prediction for GlimmerHMM_glimmerT_2882-T1
Valid prediction for snap_scaffold_1-snap.4050-T1
Valid prediction for snap_scaffold_1-snap.4088-T1
Valid prediction for snap_scaffold_1-snap.4091-T1
Valid prediction for snap_scaffold_1-snap.4046-T1
Valid prediction for GlimmerHMM_glimmerT_2912-T1
Couldn't classify 37991, 38156
Sorry, prediction Augustus_model.g2018.t1 fails validation.
(TCT)	 AG	37991-38156	GT	CGG
(GCG)	 AG	38445-38625	GT	GGG
(GCC)	 AG	38762-39080	TG	GAT
-recovered Augustus_model.g2018.t1, terminal, 38762, 39080
-recovered Augustus_model.g2018.t1, internal, 37991, 38156
-recovered Augustus_model.g2018.t1, internal, 38445, 38625
Valid prediction for snap_scaffold_1-snap.4065-T1
Valid prediction for GlimmerHMM_glimmerT_2900-T1
Valid prediction for snap_scaffold_1-snap.4051-T1
Valid prediction for snap_scaffold_1-snap.4080-T1
Valid prediction for GlimmerHMM_glimmerT_2883-T1
Valid prediction for snap_scaffold_1-snap.4084-T1
Valid prediction for snap_scaffold_1-snap.4089-T1
Valid prediction for snap_scaffold_1-snap.4070-T1
Valid prediction for GlimmerHMM_glimmerT_2907-T1
Valid prediction for GlimmerHMM_glimmerT_2897-T1
Valid prediction for snap_scaffold_1-snap.4054-T1
Valid prediction for snap_scaffold_1-snap.4066-T1
Valid prediction for GlimmerHMM_glimmerT_2903-T1
Valid prediction for snap_scaffold_1-snap.4077-T1
Valid prediction for snap_scaffold_1-snap.4082-T1
Valid prediction for GlimmerHMM_glimmerT_2885-T1
Valid prediction for GlimmerHMM_glimmerT_2901-T1
Valid prediction for snap_scaffold_1-snap.4098-T1
Valid prediction for snap_scaffold_1-snap.4069-T1
Valid prediction for snap_scaffold_1-snap.4048-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 Augustus_model.g2028.t1
Valid prediction for GlimmerHMM_glimmerT_2892-T1
Valid prediction for snap_scaffold_1-snap.4072-T1
Couldn't classify 83893, 83915
Couldn't classify 85502, 85579
Sorry, prediction pasa_asmbl_1248.p1 fails validation.
(ATC)	 AC	83893-83915	GT	TTG
(CTA)	 AG	84056-84156	GT	AGG
(GAA)	 AG	84853-84950	GT	AGG
(AGA)	 AG	85502-85579	AG	GGA
-recovered pasa_asmbl_1248.p1, internal, 84056, 84156
-recovered pasa_asmbl_1248.p1, internal, 84853, 84950
Valid prediction for Augustus_model.g2019.t1
Valid prediction for snap_scaffold_1-snap.4074-T1
Valid prediction for GlimmerHMM_glimmerT_2893-T1
Valid prediction for GlimmerHMM_glimmerT_2910-T1
Valid prediction for GlimmerHMM_glimmerT_2888-T1
Valid prediction for snap_scaffold_1-snap.4045-T1
Couldn't classify 81603, 81726
Couldn't classify 82901, 82963
Sorry, prediction pasa_asmbl_1290.p1 fails validation.
(GCT)	 CG	81603-81726	GT	AGG
(TTG)	 AG	82103-82167	GT	AGG
(ACT)	 AG	82248-82307	GT	TGG
(ATA)	 AG	82901-82963	GT	TGG
-recovered pasa_asmbl_1290.p1, internal, 82103, 82167
-recovered pasa_asmbl_1290.p1, internal, 82248, 82307
-recovered pasa_asmbl_1290.p1, internal, 82901, 82963
Valid prediction for snap_scaffold_1-snap.4076-T1
Valid prediction for snap_scaffold_1-snap.4064-T1
Valid prediction for snap_scaffold_1-snap.4079-T1
Valid prediction for snap_scaffold_1-snap.4092-T1
Valid prediction for Augustus_model.g2020.t1
Valid prediction for GlimmerHMM_glimmerT_2902-T1
Valid prediction for Augustus_model.g2024.t1
Valid prediction for snap_scaffold_1-snap.4062-T1
Couldn't classify 129677, 129757
Sorry, prediction pasa_asmbl_1381.p1 fails validation.
(CAG)	 AC	129677-129757	GT	AGG
(TTC)	 AG	130139-130240	GT	AGG
(CCT)	 AG	131491-131644	GT	TGG
(CTT)	 AG	132084-132110	GT	TGG
(ATT)	 AG	132485-133668	GG	GAG
-recovered pasa_asmbl_1381.p1, terminal, 132485, 133668
-recovered pasa_asmbl_1381.p1, internal, 130139, 130240
-recovered pasa_asmbl_1381.p1, internal, 131491, 131644
-recovered pasa_asmbl_1381.p1, internal, 132084, 132110
Valid prediction for snap_scaffold_1-snap.4087-T1
Valid prediction for GlimmerHMM_glimmerT_2894-T1
Valid prediction for Augustus_model.g2026.t1
Valid prediction for snap_scaffold_1-snap.4067-T1
Valid prediction for GlimmerHMM_glimmerT_2896-T1
Valid prediction for snap_scaffold_1-snap.4053-T1
Valid prediction for Augustus_model.g2029.t1
Valid prediction for snap_scaffold_1-snap.4049-T1
Valid prediction for GlimmerHMM_glimmerT_2890-T1
Valid prediction for Augustus_model.g2025.t1
Valid prediction for snap_scaffold_1-snap.4058-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2906-T1
Valid prediction for GlimmerHMM_glimmerT_2904-T1
Valid prediction for GlimmerHMM_glimmerT_2915-T1
Valid prediction for GlimmerHMM_glimmerT_2898-T1
Valid prediction for snap_scaffold_1-snap.4081-T1
Valid prediction for Augustus_model.g2027.t1
Valid prediction for snap_scaffold_1-snap.4056-T1
Valid prediction for GlimmerHMM_glimmerT_2884-T1
Valid prediction for GlimmerHMM_glimmerT_2891-T1
Valid prediction for Augustus_model.g2022.t1
Valid prediction for snap_scaffold_1-snap.4095-T1
Valid prediction for snap_scaffold_1-snap.4083-T1
Valid prediction for Augustus_model.g2030.t1
Valid prediction for snap_scaffold_1-snap.4060-T1
Couldn't classify 104275, 104892
Sorry, prediction pasa_asmbl_1220.p1 fails validation.
(GCG)	 AG	104275-104892	GG	AGG
Valid prediction for snap_scaffold_1-snap.4055-T1
Valid prediction for snap_scaffold_1-snap.4078-T1
Couldn't classify 128278, 128436
Couldn't classify 129074, 129109
Sorry, prediction pasa_asmbl_1249.p1 fails validation.
(GGG)	 CA	128278-128436	GT	TGG
(GAT)	 AG	128751-128858	GT	AGG
(GTG)	 AG	129074-129109	AG	ACA
-recovered pasa_asmbl_1249.p1, internal, 128751, 128858
Valid prediction for CodingQuarry_transcript_3050-T1
Valid prediction for GlimmerHMM_glimmerT_2911-T1
Valid prediction for GlimmerHMM_glimmerT_2908-T1
Valid prediction for snap_scaffold_1-snap.4047-T1
Valid prediction for snap_scaffold_1-snap.4063-T1
Valid prediction for GlimmerHMM_glimmerT_2913-T1
Valid prediction for GlimmerHMM_glimmerT_2886-T1
Valid prediction for GlimmerHMM_glimmerT_2914-T1
Valid prediction for snap_scaffold_1-snap.4094-T1
Couldn't classify 101665, 101734
Couldn't classify 102847, 102990
Sorry, prediction pasa_asmbl_1303.p1 fails validation.
(CTG)	 AG	101665-101734	GT	AGG
(GCA)	 AG	102392-102528	GT	AGG
(GAC)	 AG	102847-102990	AC	CCA
add_exon() Sorry, pasa_asmbl_1303.p1 101665-101734-terminal-3 is invalid.
-recovered pasa_asmbl_1303.p1, terminal, 101665, 101734
-recovered pasa_asmbl_1303.p1, internal, 101665, 101734
-recovered pasa_asmbl_1303.p1, internal, 102392, 102528
Valid prediction for Augustus_model.g2021.t1
Valid prediction for Augustus_model.g2031.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11617, rend_intergenic: 6785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14983, rend_intergenic: 13740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15859, rend_intergenic: 15129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19118, rend_intergenic: 16822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20232, rend_intergenic: 19608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28576, rend_intergenic: 20391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39080, rend_intergenic: 38894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41755, rend_intergenic: 39123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42602, rend_intergenic: 41802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71150, rend_intergenic: 53596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73426, rend_intergenic: 71839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89773, rend_intergenic: 74264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97313, rend_intergenic: 90424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102691, rend_intergenic: 100618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110931, rend_intergenic: 103272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124214, rend_intergenic: 118572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128374, rend_intergenic: 125931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161158, rend_intergenic: 128498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162815, rend_intergenic: 161606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167988, rend_intergenic: 165725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185300, rend_intergenic: 184044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202411, rend_intergenic: 185842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205510, rend_intergenic: 202947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218271, rend_intergenic: 214179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227972, rend_intergenic: 224045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251438, rend_intergenic: 236889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255717, rend_intergenic: 254747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291612, rend_intergenic: 255776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296344, rend_intergenic: 291649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 298501, rend_intergenic: 297228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304754, rend_intergenic: 302380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307471, rend_intergenic: 305136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 317711
-exon list size: 414


building trellis

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-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 11617, rend_intergenic: 6785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14983, rend_intergenic: 13740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15859, rend_intergenic: 15129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19118, rend_intergenic: 16822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20232, rend_intergenic: 19608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28576, rend_intergenic: 20391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39080, rend_intergenic: 38894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41755, rend_intergenic: 39123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42602, rend_intergenic: 41802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71150, rend_intergenic: 53596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73426, rend_intergenic: 71839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89773, rend_intergenic: 74264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97313, rend_intergenic: 90424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102691, rend_intergenic: 100618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110931, rend_intergenic: 103272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124214, rend_intergenic: 118572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128374, rend_intergenic: 125931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161158, rend_intergenic: 128498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162815, rend_intergenic: 161606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167988, rend_intergenic: 165725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185300, rend_intergenic: 184044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202411, rend_intergenic: 185842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205510, rend_intergenic: 202947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218271, rend_intergenic: 214179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227972, rend_intergenic: 224045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251438, rend_intergenic: 236889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255717, rend_intergenic: 254747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291612, rend_intergenic: 255776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296344, rend_intergenic: 291649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 298501, rend_intergenic: 297228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304754, rend_intergenic: 302380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307471, rend_intergenic: 305136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support