-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_8778221-9144411

-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_56297-T1
Valid prediction for Augustus_model.g37324.t1
Valid prediction for GlimmerHMM_glimmerT_56296-T1
Valid prediction for Augustus_model.g37321.t1
Valid prediction for snap_scaffold_26-snap.2029-T1
Valid prediction for GlimmerHMM_glimmerT_56290-T1
Couldn't classify 323135, 323195
Sorry, prediction pasa_asmbl_35206.p1 fails validation.
(ATG)	 AC	314402-314509	GT	AGG
(ACC)	 AG	316043-316151	GT	AGG
(GAT)	 AG	316451-316541	GT	GGG
(GGT)	 AG	318837-318972	GT	AGG
(GGG)	 AG	321862-322011	GT	AGG
(GTG)	 AG	322130-322236	GT	AGG
(GAA)	 AG	323135-323195	GT	AGG
-recovered pasa_asmbl_35206.p1, initial, 314402, 314509
-recovered pasa_asmbl_35206.p1, internal, 316043, 316151
-recovered pasa_asmbl_35206.p1, internal, 316451, 316541
-recovered pasa_asmbl_35206.p1, internal, 318837, 318972
-recovered pasa_asmbl_35206.p1, internal, 321862, 322011
-recovered pasa_asmbl_35206.p1, internal, 322130, 322236
-recovered pasa_asmbl_35206.p1, internal, 323135, 323195
Valid prediction for CodingQuarry_transcript_40423-T1
Valid prediction for CodingQuarry_transcript_40422-T1
Valid prediction for GlimmerHMM_glimmerT_56310-T1
Valid prediction for CodingQuarry_transcript_40427-T1
Valid prediction for HiQ_model.g37325.t1
Valid prediction for snap_scaffold_26-snap.2017-T1
Valid prediction for snap_scaffold_26-snap.2019-T1
Valid prediction for Augustus_model.g37315.t1
Valid prediction for Augustus_model.g37304.t1
Valid prediction for snap_scaffold_26-snap.2042-T1
Valid prediction for snap_scaffold_26-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_56322-T1
Valid prediction for GlimmerHMM_glimmerT_56312-T1
Valid prediction for pasa_asmbl_35198.p1
Valid prediction for snap_scaffold_26-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_56294-T1
Valid prediction for GlimmerHMM_glimmerT_56323-T1
Valid prediction for snap_scaffold_26-snap.2063-T1
Valid prediction for snap_scaffold_26-snap.2015-T1
Valid prediction for Augustus_model.g37317.t1
Valid prediction for Augustus_model.g37323.t1
Valid prediction for snap_scaffold_26-snap.2026-T1
Couldn't classify 331999, 332074
Sorry, prediction pasa_asmbl_35306.p1 fails validation.
(ATG)	 GC	329014-329020	GT	TGG
(CTA)	 AG	329456-329550	GT	TGG
(GGG)	 AG	330409-330457	GT	CGG
(GTA)	 AG	330577-330649	GT	GGG
(GGG)	 AG	331999-332074	GT	CGG
-recovered pasa_asmbl_35306.p1, initial, 329014, 329020
-recovered pasa_asmbl_35306.p1, internal, 329456, 329550
-recovered pasa_asmbl_35306.p1, internal, 330409, 330457
-recovered pasa_asmbl_35306.p1, internal, 330577, 330649
-recovered pasa_asmbl_35306.p1, internal, 331999, 332074
Valid prediction for snap_scaffold_26-snap.2024-T1
Valid prediction for snap_scaffold_26-snap.2040-T1
Valid prediction for Augustus_model.g37306.t1
Valid prediction for snap_scaffold_26-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_56324-T1
Valid prediction for snap_scaffold_26-snap.2047-T1
Valid prediction for snap_scaffold_26-snap.2067-T1
Valid prediction for snap_scaffold_26-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_56327-T1
Valid prediction for GlimmerHMM_glimmerT_56315-T1
Valid prediction for snap_scaffold_26-snap.2041-T1
Valid prediction for Augustus_model.g37326.t1
Valid prediction for CodingQuarry_transcript_40421-T1
Valid prediction for GlimmerHMM_glimmerT_56325-T1
Valid prediction for Augustus_model.g37314.t1
Valid prediction for CodingQuarry_transcript_40428-T1
Valid prediction for CodingQuarry_transcript_40426-T1
Valid prediction for snap_scaffold_26-snap.2066-T1
Valid prediction for snap_scaffold_26-snap.2045-T1
Valid prediction for snap_scaffold_26-snap.2056-T1
Valid prediction for Augustus_model.g37308.t1
Valid prediction for GlimmerHMM_glimmerT_56307-T1
Valid prediction for pasa_asmbl_35192.p1
Valid prediction for pasa_asmbl_35189.p1
Valid prediction for Augustus_model.g37297.t1
Valid prediction for HiQ_model.g37309.t1
Valid prediction for HiQ_model.g37307.t1
Couldn't classify 247985, 248014
Sorry, prediction pasa_asmbl_35195.p1 fails validation.
(GGA)	 GA	247985-248014	GT	TGG
(GAG)	 AG	248446-249383	GT	GAG
(GGA)	 AG	249497-249621	GT	AGG
(GTA)	 AG	249812-249997	GT	CGG
(CTG)	 AG	250289-250367	GT	ATG
(GTT)	 AG	250459-250583	GT	TGG
(CCA)	 AG	250696-250903	GT	TGG
(GAT)	 AG	251157-251246	GT	AGG
(GCT)	 AG	251417-251482	GT	GGG
(AAA)	 AG	251583-251668	GT	TGG
(ATA)	 AG	251768-251940	GG	AGG
-recovered pasa_asmbl_35195.p1, terminal, 251768, 251940
-recovered pasa_asmbl_35195.p1, internal, 248446, 249383
-recovered pasa_asmbl_35195.p1, internal, 249497, 249621
-recovered pasa_asmbl_35195.p1, internal, 249812, 249997
-recovered pasa_asmbl_35195.p1, internal, 250289, 250367
-recovered pasa_asmbl_35195.p1, internal, 250459, 250583
-recovered pasa_asmbl_35195.p1, internal, 250696, 250903
-recovered pasa_asmbl_35195.p1, internal, 251157, 251246
-recovered pasa_asmbl_35195.p1, internal, 251417, 251482
-recovered pasa_asmbl_35195.p1, internal, 251583, 251668
Valid prediction for snap_scaffold_26-snap.2059-T1
Valid prediction for snap_scaffold_26-snap.2065-T1
Valid prediction for GlimmerHMM_glimmerT_56299-T1
Valid prediction for GlimmerHMM_glimmerT_56326-T1
Valid prediction for GlimmerHMM_glimmerT_56318-T1
Valid prediction for snap_scaffold_26-snap.2058-T1
Valid prediction for snap_scaffold_26-snap.2039-T1
Valid prediction for pasa_asmbl_35204.p1
Valid prediction for Augustus_model.g37299.t1
Valid prediction for snap_scaffold_26-snap.2054-T1
Valid prediction for snap_scaffold_26-snap.2055-T1
Valid prediction for snap_scaffold_26-snap.2064-T1
Valid prediction for GlimmerHMM_glimmerT_56316-T1
Valid prediction for GlimmerHMM_glimmerT_56309-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_26-snap.2033-T1
Valid prediction for snap_scaffold_26-snap.2043-T1
Valid prediction for snap_scaffold_26-snap.2027-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g37300.t1
Valid prediction for GlimmerHMM_glimmerT_56302-T1
Valid prediction for GlimmerHMM_glimmerT_56313-T1
Valid prediction for CodingQuarry_transcript_40429-T1
Valid prediction for HiQ_model.g37320.t1
Valid prediction for snap_scaffold_26-snap.2025-T1
Valid prediction for snap_scaffold_26-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_56293-T1
Valid prediction for snap_scaffold_26-snap.2018-T1
Valid prediction for snap_scaffold_26-snap.2057-T1
Valid prediction for snap_scaffold_26-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_56306-T1
Valid prediction for CodingQuarry_transcript_40420-T1
Valid prediction for snap_scaffold_26-snap.2051-T1
Valid prediction for snap_scaffold_26-snap.2035-T1
Valid prediction for snap_scaffold_26-snap.2062-T1
Valid prediction for Augustus_model.g37310.t1
Valid prediction for GlimmerHMM_glimmerT_56298-T1
Valid prediction for snap_scaffold_26-snap.2034-T1
Couldn't classify 142842, 142855
Couldn't classify 143681, 143803
Sorry, prediction pasa_asmbl_35755.p1 fails validation.
(GCG)	 CG	142842-142855	GT	GAG
(CTA)	 AG	143035-143081	GT	CAG
(ACA)	 AG	143436-143554	GT	TGG
(GCG)	 AG	143681-143803	AG	ACA
-recovered pasa_asmbl_35755.p1, internal, 143035, 143081
-recovered pasa_asmbl_35755.p1, internal, 143436, 143554
Valid prediction for snap_scaffold_26-snap.2030-T1
Valid prediction for snap_scaffold_26-snap.2032-T1
Couldn't classify 135406, 135429
Sorry, prediction pasa_asmbl_35756.p1 fails validation.
(GAC)	 AA	135406-135429	GT	TGG
(CTT)	 AG	135809-135917	GT	TGG
(ACA)	 AG	136121-136204	GT	GGG
(GTG)	 AG	136301-136410	GT	AGG
(GAG)	 AG	136501-136633	GT	AGG
(ATG)	 AG	136711-136865	GT	GGG
(GTG)	 AG	136942-137036	GT	AGG
(ACA)	 AG	137153-137226	GT	ATG
(TGT)	 AG	137326-137438	TG	AGT
add_exon() Sorry, pasa_asmbl_35756.p1 136711-136865-initial-1 is invalid.
-recovered pasa_asmbl_35756.p1, initial, 136711, 136865
-recovered pasa_asmbl_35756.p1, terminal, 137326, 137438
-recovered pasa_asmbl_35756.p1, internal, 135809, 135917
-recovered pasa_asmbl_35756.p1, internal, 136121, 136204
-recovered pasa_asmbl_35756.p1, internal, 136301, 136410
-recovered pasa_asmbl_35756.p1, internal, 136501, 136633
-recovered pasa_asmbl_35756.p1, internal, 136711, 136865
-recovered pasa_asmbl_35756.p1, internal, 136942, 137036
-recovered pasa_asmbl_35756.p1, internal, 137153, 137226
Valid prediction for CodingQuarry_transcript_40431-T1
Valid prediction for snap_scaffold_26-snap.2049-T1
Valid prediction for Augustus_model.g37303.t1
Valid prediction for pasa_asmbl_35768.p1
Valid prediction for pasa_asmbl_35765.p1
Valid prediction for GlimmerHMM_glimmerT_56304-T1
Valid prediction for Augustus_model.g37318.t1
Valid prediction for GlimmerHMM_glimmerT_56300-T1
Valid prediction for GlimmerHMM_glimmerT_56303-T1
Valid prediction for Augustus_model.g37302.t1
Valid prediction for CodingQuarry_transcript_40424-T1
Couldn't classify 106118, 106223
Sorry, prediction pasa_asmbl_35758.p1 fails validation.
(CGT)	 AC	106118-106223	GT	CCG
(TAT)	 AG	106405-106494	GT	AGG
(TCC)	 AG	106854-106995	GT	AGG
(AGT)	 AG	107433-107513	GT	AGG
(GTA)	 AG	107871-108129	GG	AAG
-recovered pasa_asmbl_35758.p1, terminal, 107871, 108129
-recovered pasa_asmbl_35758.p1, internal, 106405, 106494
-recovered pasa_asmbl_35758.p1, internal, 106854, 106995
-recovered pasa_asmbl_35758.p1, internal, 107433, 107513
Valid prediction for snap_scaffold_26-snap.2052-T1
Valid prediction for Augustus_model.g37313.t1
Valid prediction for GlimmerHMM_glimmerT_56314-T1
Valid prediction for snap_scaffold_26-snap.2023-T1
Valid prediction for Augustus_model.g37311.t1
Valid prediction for GlimmerHMM_glimmerT_56311-T1
Valid prediction for CodingQuarry_transcript_40425-T1
Valid prediction for snap_scaffold_26-snap.2031-T1
Valid prediction for snap_scaffold_26-snap.2048-T1
Valid prediction for Augustus_model.g37319.t1
Valid prediction for Augustus_model.g37301.t1
Valid prediction for Augustus_model.g37312.t1
Valid prediction for snap_scaffold_26-snap.2038-T1
Valid prediction for snap_scaffold_26-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_56289-T1
Valid prediction for Augustus_model.g37322.t1
Valid prediction for GlimmerHMM_glimmerT_56321-T1
Valid prediction for snap_scaffold_26-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_56301-T1
Valid prediction for snap_scaffold_26-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_56319-T1
Valid prediction for GlimmerHMM_glimmerT_56292-T1
Valid prediction for Augustus_model.g37316.t1
Valid prediction for snap_scaffold_26-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_56305-T1
Valid prediction for Augustus_model.g37305.t1
Valid prediction for snap_scaffold_26-snap.2036-T1
Valid prediction for CodingQuarry_transcript_40430-T1
Valid prediction for GlimmerHMM_glimmerT_56291-T1
Valid prediction for GlimmerHMM_glimmerT_56308-T1
Valid prediction for Augustus_model.g37298.t1
Couldn't classify 83037, 83179
Sorry, prediction pasa_asmbl_35761.p1 fails validation.
(TCA)	 GC	83037-83179	GT	AAG
(CTC)	 AG	83286-83455	GT	TGG
(TGC)	 AG	83900-84078	GT	CAG
(CTG)	 AG	84164-84317	GT	AGG
(AGT)	 AG	84509-84599	GT	AGG
(ACT)	 AG	84735-84804	GT	AGG
(AAA)	 AG	85063-85295	GT	AGG
(TAT)	 AG	85384-86221	AA	AAA
add_exon() Sorry, pasa_asmbl_35761.p1 85063-85295-terminal-2 is invalid.
-recovered pasa_asmbl_35761.p1, terminal, 85063, 85295
-recovered pasa_asmbl_35761.p1, terminal, 85384, 86221
-recovered pasa_asmbl_35761.p1, internal, 83286, 83455
-recovered pasa_asmbl_35761.p1, internal, 83900, 84078
-recovered pasa_asmbl_35761.p1, internal, 84164, 84317
-recovered pasa_asmbl_35761.p1, internal, 84509, 84599
-recovered pasa_asmbl_35761.p1, internal, 84735, 84804
-recovered pasa_asmbl_35761.p1, internal, 85063, 85295
Valid prediction for snap_scaffold_26-snap.2061-T1
Valid prediction for snap_scaffold_26-snap.2050-T1
Valid prediction for snap_scaffold_26-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_56295-T1
Valid prediction for GlimmerHMM_glimmerT_56317-T1
Valid prediction for GlimmerHMM_glimmerT_56320-T1
Valid prediction for pasa_asmbl_35752.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23053, rend_intergenic: 18508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33874, rend_intergenic: 33760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39077, rend_intergenic: 37780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245768, rend_intergenic: 242166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262664, rend_intergenic: 258700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 366191
-exon list size: 521


building trellis

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82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 23053, rend_intergenic: 18508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33874, rend_intergenic: 33760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39077, rend_intergenic: 37780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245768, rend_intergenic: 242166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262664, rend_intergenic: 258700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support