-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_9560767-9735895

-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_53204-T1
Valid prediction for snap_scaffold_24-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_53213-T1
Valid prediction for GlimmerHMM_glimmerT_53191-T1
Valid prediction for HiQ_model.g35428.t1
Couldn't classify 135187, 135319
Sorry, prediction pasa_asmbl_32535.p1 fails validation.
(ATG)	 AC	133129-133184	GT	CAG
(GAA)	 AG	133839-133882	GT	AGG
(GTC)	 AG	133973-134112	GT	TGG
(GCA)	 AG	134688-134783	GT	ATG
(GCA)	 AG	134965-135086	GT	AGG
(CAC)	 AG	135187-135319	GG	GTG
-recovered pasa_asmbl_32535.p1, initial, 133129, 133184
-recovered pasa_asmbl_32535.p1, internal, 133839, 133882
-recovered pasa_asmbl_32535.p1, internal, 133973, 134112
-recovered pasa_asmbl_32535.p1, internal, 134688, 134783
-recovered pasa_asmbl_32535.p1, internal, 134965, 135086
Valid prediction for snap_scaffold_24-snap.2015-T1
Valid prediction for GlimmerHMM_glimmerT_53196-T1
Valid prediction for snap_scaffold_24-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_53190-T1
Valid prediction for GlimmerHMM_glimmerT_53192-T1
Valid prediction for snap_scaffold_24-snap.2014-T1
Valid prediction for snap_scaffold_24-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_53194-T1
Valid prediction for GlimmerHMM_glimmerT_53212-T1
Couldn't classify 119649, 119801
Sorry, prediction pasa_asmbl_32530.p2 fails validation.
(ATG)	 AG	117876-118040	GT	AGG
(GTG)	 AG	118203-118309	GT	CGG
(GTT)	 AG	118593-118714	GT	CGG
(ATC)	 AG	118879-118957	GT	AGG
(GAT)	 AG	119051-119221	GT	ATG
(GTA)	 AG	119393-119510	GT	AGG
(CTG)	 AG	119649-119801	TA	GGT
-recovered pasa_asmbl_32530.p2, initial, 117876, 118040
-recovered pasa_asmbl_32530.p2, internal, 117876, 118040
-recovered pasa_asmbl_32530.p2, internal, 118203, 118309
-recovered pasa_asmbl_32530.p2, internal, 118593, 118714
-recovered pasa_asmbl_32530.p2, internal, 118879, 118957
-recovered pasa_asmbl_32530.p2, internal, 119051, 119221
-recovered pasa_asmbl_32530.p2, internal, 119393, 119510
Valid prediction for snap_scaffold_24-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_53184-T1
Couldn't classify 119930, 119936
Sorry, prediction pasa_asmbl_32532.p1 fails validation.
(ATG)	 TC	118920-118957	GT	AGG
(GAT)	 AG	119051-119221	GT	ATG
(GTA)	 AG	119393-119510	GT	AGG
(CTG)	 AG	119649-119800	GT	AGG
(GTT)	 AG	119930-119936	GA	AGG
-recovered pasa_asmbl_32532.p1, initial, 118920, 118957
-recovered pasa_asmbl_32532.p1, internal, 119051, 119221
-recovered pasa_asmbl_32532.p1, internal, 119393, 119510
-recovered pasa_asmbl_32532.p1, internal, 119649, 119800
Valid prediction for CodingQuarry_transcript_37410-T1
Valid prediction for snap_scaffold_24-snap.2018-T1
Valid prediction for Augustus_model.g35417.t1
Valid prediction for GlimmerHMM_glimmerT_53202-T1
Valid prediction for snap_scaffold_24-snap.2032-T1
Valid prediction for snap_scaffold_24-snap.2034-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53206-T1
Valid prediction for GlimmerHMM_glimmerT_53188-T1
Valid prediction for GlimmerHMM_glimmerT_53185-T1
Valid prediction for Augustus_model.g35419.t1
Valid prediction for Augustus_model.g35421.t1
Valid prediction for snap_scaffold_24-snap.2038-T1
Valid prediction for snap_scaffold_24-snap.2025-T1
Valid prediction for snap_scaffold_24-snap.2027-T1
Valid prediction for snap_scaffold_24-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_53209-T1
Valid prediction for snap_scaffold_24-snap.2028-T1
Valid prediction for snap_scaffold_24-snap.2040-T1
Couldn't classify 121877, 121881
Sorry, prediction CodingQuarry_transcript_37412-T1 fails validation.
(ATG)	 CC	121086-121182	GC	CTG
(GCT)	 TC	121877-121881	AC	AGA
-recovered CodingQuarry_transcript_37412-T1, initial, 121086, 121182
Valid prediction for snap_scaffold_24-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_53183-T1
Valid prediction for CodingQuarry_transcript_37411-T1
Valid prediction for GlimmerHMM_glimmerT_53205-T1
Valid prediction for snap_scaffold_24-snap.2026-T1
Valid prediction for pasa_asmbl_32528.p1
Valid prediction for Augustus_model.g35425.t1
Valid prediction for GlimmerHMM_glimmerT_53210-T1
Couldn't classify 134691, 134783
Sorry, prediction pasa_asmbl_32536.p2 fails validation.
(GAC)	 CA	134691-134783	GT	ATG
(GCA)	 AG	134965-135086	GT	AGG
(CAC)	 AG	135187-135334	GT	AGG
(GGG)	 AG	135745-135866	GT	AGG
(GCA)	 AG	136336-136393	GA	GAG
-recovered pasa_asmbl_32536.p2, terminal, 136336, 136393
-recovered pasa_asmbl_32536.p2, internal, 134965, 135086
-recovered pasa_asmbl_32536.p2, internal, 135187, 135334
-recovered pasa_asmbl_32536.p2, internal, 135745, 135866
Valid prediction for GlimmerHMM_glimmerT_53189-T1
Valid prediction for HiQ_model.g35431.t1
Valid prediction for Augustus_model.g35423.t1
Valid prediction for GlimmerHMM_glimmerT_53187-T1
Valid prediction for snap_scaffold_24-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_53203-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53208-T1
Valid prediction for snap_scaffold_24-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_53199-T1
Valid prediction for Augustus_model.g35430.t1
Valid prediction for snap_scaffold_24-snap.2045-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 GlimmerHMM_glimmerT_53193-T1
Valid prediction for GlimmerHMM_glimmerT_53195-T1
Valid prediction for GlimmerHMM_glimmerT_53201-T1
Valid prediction for snap_scaffold_24-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_53182-T1
Valid prediction for snap_scaffold_24-snap.2041-T1
Valid prediction for snap_scaffold_24-snap.2008-T1
Valid prediction for Augustus_model.g35426.t1
Valid prediction for snap_scaffold_24-snap.2035-T1
Valid prediction for Augustus_model.g35429.t1
Couldn't classify 8970, 9080
Couldn't classify 11093, 11125
Sorry, prediction pasa_asmbl_33255.p1 fails validation.
(GGC)	 AG	8970-9080	GT	AGG
(TAC)	 AG	9366-9455	GT	AGG
(CTG)	 AG	10610-10690	GT	AGG
(GGC)	 AG	10797-10904	GT	GGG
(GTT)	 AG	11093-11125	AC	AGA
-recovered pasa_asmbl_33255.p1, internal, 8970, 9080
-recovered pasa_asmbl_33255.p1, internal, 9366, 9455
-recovered pasa_asmbl_33255.p1, internal, 10610, 10690
-recovered pasa_asmbl_33255.p1, internal, 10797, 10904
Valid prediction for GlimmerHMM_glimmerT_53198-T1
Valid prediction for snap_scaffold_24-snap.2019-T1
Valid prediction for snap_scaffold_24-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_53215-T1
Valid prediction for snap_scaffold_24-snap.2010-T1
Valid prediction for snap_scaffold_24-snap.2024-T1
Valid prediction for snap_scaffold_24-snap.2039-T1
Valid prediction for snap_scaffold_24-snap.2033-T1
Valid prediction for CodingQuarry_transcript_37408-T1
Couldn't classify 20201, 20322
Sorry, prediction pasa_asmbl_33148.p1 fails validation.
(ATG)	 AG	13367-13416	GT	AAG
(GTC)	 AG	13753-13903	GT	AGG
(ATC)	 AG	14764-14961	GT	AGG
(GTG)	 AG	15062-15220	GT	TGG
(AGC)	 AG	15405-15586	GT	AGG
(GAT)	 AG	15781-15849	GT	AAG
(ATA)	 AG	15934-16007	GT	AGG
(GGG)	 AG	16150-16253	GT	TGG
(AAG)	 AG	16872-17053	GT	AAG
(GCT)	 AG	18060-18263	GT	AGG
(GAT)	 AG	19563-19716	GT	AGG
(GTG)	 AG	19963-20065	GT	AGG
(GGA)	 AG	20201-20322	CT	CCC
-recovered pasa_asmbl_33148.p1, initial, 13367, 13416
add_exon() Sorry, pasa_asmbl_33148.p1 19963-20065-terminal-3 is invalid.
-recovered pasa_asmbl_33148.p1, terminal, 19963, 20065
-recovered pasa_asmbl_33148.p1, internal, 13367, 13416
-recovered pasa_asmbl_33148.p1, internal, 13753, 13903
-recovered pasa_asmbl_33148.p1, internal, 14764, 14961
-recovered pasa_asmbl_33148.p1, internal, 15062, 15220
-recovered pasa_asmbl_33148.p1, internal, 15405, 15586
-recovered pasa_asmbl_33148.p1, internal, 15781, 15849
-recovered pasa_asmbl_33148.p1, internal, 15934, 16007
-recovered pasa_asmbl_33148.p1, internal, 16150, 16253
-recovered pasa_asmbl_33148.p1, internal, 16872, 17053
-recovered pasa_asmbl_33148.p1, internal, 18060, 18263
-recovered pasa_asmbl_33148.p1, internal, 19563, 19716
-recovered pasa_asmbl_33148.p1, internal, 19963, 20065
Valid prediction for CodingQuarry_transcript_37406-T1
Valid prediction for GlimmerHMM_glimmerT_53211-T1
Valid prediction for snap_scaffold_24-snap.2046-T1
Valid prediction for Augustus_model.g35432.t1
Valid prediction for snap_scaffold_24-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_53200-T1
Valid prediction for Augustus_model.g35422.t1
Valid prediction for snap_scaffold_24-snap.2031-T1
Valid prediction for snap_scaffold_24-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_53181-T1
Valid prediction for GlimmerHMM_glimmerT_53207-T1
Valid prediction for Augustus_model.g35418.t1
Valid prediction for snap_scaffold_24-snap.2029-T1
Valid prediction for snap_scaffold_24-snap.2036-T1
Valid prediction for snap_scaffold_24-snap.2013-T1
Valid prediction for snap_scaffold_24-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_53186-T1
Valid prediction for GlimmerHMM_glimmerT_53214-T1
Valid prediction for HiQ_model.g35420.t1
Valid prediction for Augustus_model.g35427.t1
Valid prediction for Augustus_model.g35424.t1
Couldn't classify 71830, 72044
Couldn't classify 72486, 72570
Sorry, prediction pasa_asmbl_33245.p2 fails validation.
(TCT)	 CA	71830-72044	GT	ATG
(AGA)	 AG	72486-72570	TC	TGT
Valid prediction for CodingQuarry_transcript_37407-T1
Valid prediction for snap_scaffold_24-snap.2016-T1
Couldn't classify 25336, 25419
Sorry, prediction pasa_asmbl_33147.p1 fails validation.
(ATG)	 AG	23830-23895	GT	AGG
(CTG)	 AG	24108-24211	GT	TGG
(GCC)	 AG	24402-24567	GT	AGG
(ATG)	 AG	25336-25419	AG	TTA
-recovered pasa_asmbl_33147.p1, initial, 23830, 23895
-recovered pasa_asmbl_33147.p1, internal, 23830, 23895
-recovered pasa_asmbl_33147.p1, internal, 24108, 24211
-recovered pasa_asmbl_33147.p1, internal, 24402, 24567
Valid prediction for GlimmerHMM_glimmerT_53197-T1
Couldn't classify 49630, 49728
Sorry, prediction pasa_asmbl_33143.p1 fails validation.
(ATG)	 AC	47411-47635	GT	AGG
(GCT)	 AG	47836-47952	GT	AGG
(GCA)	 AG	48120-48195	GT	AGG
(ACC)	 AG	48671-48840	GT	AGG
(GTG)	 AG	49143-49253	GT	AGG
(GAG)	 AG	49630-49728	GT	GCG
-recovered pasa_asmbl_33143.p1, initial, 47411, 47635
add_exon() Sorry, pasa_asmbl_33143.p1 48120-48195-terminal-3 is invalid.
-recovered pasa_asmbl_33143.p1, terminal, 48120, 48195
-recovered pasa_asmbl_33143.p1, internal, 47836, 47952
-recovered pasa_asmbl_33143.p1, internal, 48120, 48195
-recovered pasa_asmbl_33143.p1, internal, 48671, 48840
-recovered pasa_asmbl_33143.p1, internal, 49143, 49253
-recovered pasa_asmbl_33143.p1, internal, 49630, 49728

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4810, rend_intergenic: 1930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12925, rend_intergenic: 5654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14569, rend_intergenic: 13952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19450, rend_intergenic: 15184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31051, rend_intergenic: 28791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60343, rend_intergenic: 50491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67129, rend_intergenic: 63684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72832, rend_intergenic: 68677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75810, rend_intergenic: 72955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93670, rend_intergenic: 90087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95075, rend_intergenic: 93760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104352, rend_intergenic: 100341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123340, rend_intergenic: 116625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128793, rend_intergenic: 127130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132537, rend_intergenic: 129724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140063, rend_intergenic: 133974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166980, rend_intergenic: 147945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175129
-exon list size: 469


building trellis

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33.8    
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87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 4810, rend_intergenic: 1930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12925, rend_intergenic: 5654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14569, rend_intergenic: 13952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19450, rend_intergenic: 15184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31051, rend_intergenic: 28791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60343, rend_intergenic: 50491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67129, rend_intergenic: 63684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72832, rend_intergenic: 68677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75810, rend_intergenic: 72955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93670, rend_intergenic: 90087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95075, rend_intergenic: 93760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104352, rend_intergenic: 100341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123340, rend_intergenic: 116625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128793, rend_intergenic: 127130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132537, rend_intergenic: 129724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140063, rend_intergenic: 133974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166980, rend_intergenic: 147945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support