-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_741030-916567

-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 snap_scaffold_20-snap.186-T1
Valid prediction for GlimmerHMM_glimmerT_45368-T1
Valid prediction for GlimmerHMM_glimmerT_45375-T1
Valid prediction for Augustus_model.g30134.t1
Valid prediction for CodingQuarry_transcript_30386-T1
Valid prediction for CodingQuarry_transcript_30387-T1
Valid prediction for snap_scaffold_20-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_45366-T1
Couldn't classify 94814, 94945
Couldn't classify 96002, 96088
Sorry, prediction pasa_asmbl_26382.p1 fails validation.
(CTC)	 GG	94814-94945	GT	CGG
(GAG)	 AG	95131-95279	GT	GGG
(TGG)	 AG	95711-95801	GT	AGG
(GTG)	 AG	96002-96088	AG	GCA
-recovered pasa_asmbl_26382.p1, internal, 95131, 95279
-recovered pasa_asmbl_26382.p1, internal, 95711, 95801
Valid prediction for snap_scaffold_20-snap.194-T1
Valid prediction for snap_scaffold_20-snap.172-T1
Valid prediction for GlimmerHMM_glimmerT_45381-T1
Valid prediction for Augustus_model.g30130.t1
Valid prediction for Augustus_model.g30125.t1
Valid prediction for GlimmerHMM_glimmerT_45365-T1
Valid prediction for snap_scaffold_20-snap.161-T1
Couldn't classify 44522, 44561
Sorry, prediction pasa_asmbl_26378.p1 fails validation.
(CTG)	 AC	44522-44561	GT	CGG
(GTG)	 AG	44877-44982	GT	CGG
(AGA)	 AG	46102-46393	TT	GAT
-recovered pasa_asmbl_26378.p1, terminal, 46102, 46393
-recovered pasa_asmbl_26378.p1, internal, 44877, 44982
Valid prediction for pasa_asmbl_26388.p1
Valid prediction for snap_scaffold_20-snap.170-T1
Valid prediction for snap_scaffold_20-snap.198-T1
Valid prediction for Augustus_model.g30121.t1
Valid prediction for snap_scaffold_20-snap.158-T1
Valid prediction for snap_scaffold_20-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_45369-T1
Valid prediction for snap_scaffold_20-snap.173-T1
Couldn't classify 123719, 123871
Couldn't classify 127930, 128059
Couldn't classify 128134, 128172
Couldn't classify 129474, 129583
Sorry, prediction pasa_asmbl_26393.p1 fails validation.
(ACT)	 AT	123719-123871	GT	AGG
(ATT)	 AG	124798-124900	GT	AGG
(ACC)	 AG	125014-125073	GT	GTG
(CCA)	 AG	125977-126013	GT	AGG
(TGT)	 AG	126116-126174	GT	AAG
(TCA)	 AG	126323-126394	GT	AGG
(ACA)	 AG	126558-126615	GT	CAG
(GAA)	 AG	127930-128059	AT	TCA
(ATC)	 AC	128134-128172	GT	AGG
(GAG)	 AG	128458-128556	GT	AGG
(CAA)	 AG	128875-128994	GT	ATG
(GTC)	 AG	129082-129184	GT	TGG
(ACG)	 AG	129474-129583	GA	AGG
add_exon() Sorry, pasa_asmbl_26393.p1 126116-126174-terminal-2 is invalid.
-recovered pasa_asmbl_26393.p1, terminal, 126116, 126174
-recovered pasa_asmbl_26393.p1, internal, 124798, 124900
-recovered pasa_asmbl_26393.p1, internal, 125014, 125073
-recovered pasa_asmbl_26393.p1, internal, 125977, 126013
-recovered pasa_asmbl_26393.p1, internal, 126116, 126174
-recovered pasa_asmbl_26393.p1, internal, 126323, 126394
-recovered pasa_asmbl_26393.p1, internal, 126558, 126615
-recovered pasa_asmbl_26393.p1, internal, 128458, 128556
-recovered pasa_asmbl_26393.p1, internal, 128875, 128994
-recovered pasa_asmbl_26393.p1, internal, 129082, 129184
Valid prediction for GlimmerHMM_glimmerT_45383-T1
Valid prediction for snap_scaffold_20-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_45376-T1
Valid prediction for snap_scaffold_20-snap.188-T1
Valid prediction for snap_scaffold_20-snap.166-T1
Valid prediction for snap_scaffold_20-snap.180-T1
Valid prediction for Augustus_model.g30128.t1
Valid prediction for snap_scaffold_20-snap.182-T1
Valid prediction for HiQ_model.g30129.t1
Valid prediction for Augustus_model.g30127.t1
Valid prediction for snap_scaffold_20-snap.163-T1
Valid prediction for snap_scaffold_20-snap.196-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45384-T1
Valid prediction for snap_scaffold_20-snap.157-T1
Valid prediction for snap_scaffold_20-snap.200-T1
Valid prediction for CodingQuarry_transcript_30388-T1
Couldn't classify 101944, 102111
Couldn't classify 104722, 104866
Sorry, prediction pasa_asmbl_26386.p1 fails validation.
(CGT)	 CG	101944-102111	GT	AGG
(GTG)	 AG	103762-103985	GT	AGG
(TGT)	 AG	104722-104866	AC	CCA
-recovered pasa_asmbl_26386.p1, internal, 103762, 103985
Valid prediction for snap_scaffold_20-snap.162-T1
Couldn't classify 121127, 121278
Couldn't classify 122250, 122282
Sorry, prediction pasa_asmbl_26391.p1 fails validation.
(ATG)	 AC	117471-117506	GT	TGG
(ATG)	 AG	117916-118074	GT	AGG
(GTG)	 AG	118473-118625	GT	AGG
(ATC)	 AG	119240-119353	GT	AGG
(GTC)	 AG	119935-120102	GT	AGG
(ACC)	 AG	120654-120801	GT	AGG
(CCA)	 AG	121127-121278	AT	ACA
(TTC)	 AC	122250-122282	AG	AGA
-recovered pasa_asmbl_26391.p1, initial, 117471, 117506
-recovered pasa_asmbl_26391.p1, initial, 117916, 118074
-recovered pasa_asmbl_26391.p1, internal, 117916, 118074
-recovered pasa_asmbl_26391.p1, internal, 118473, 118625
-recovered pasa_asmbl_26391.p1, internal, 119240, 119353
-recovered pasa_asmbl_26391.p1, internal, 119935, 120102
-recovered pasa_asmbl_26391.p1, internal, 120654, 120801
Valid prediction for snap_scaffold_20-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_45371-T1
Valid prediction for snap_scaffold_20-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_45378-T1
Valid prediction for Augustus_model.g30131.t1
Valid prediction for snap_scaffold_20-snap.179-T1
Valid prediction for snap_scaffold_20-snap.164-T1
Couldn't classify 129809, 130099
Sorry, prediction pasa_asmbl_26395.p1 fails validation.
(CCT)	 CT	129809-130099	GT	AGG
(GCT)	 AG	130456-130565	GT	CAG
(CGG)	 AG	130807-130892	GT	CAG
(ACA)	 AG	130978-131202	GT	GGG
(CTC)	 AG	131514-131683	GT	AGG
(GCT)	 AG	131898-131906	GG	GAG
-recovered pasa_asmbl_26395.p1, terminal, 131898, 131906
-recovered pasa_asmbl_26395.p1, internal, 130456, 130565
-recovered pasa_asmbl_26395.p1, internal, 130807, 130892
-recovered pasa_asmbl_26395.p1, internal, 130978, 131202
-recovered pasa_asmbl_26395.p1, internal, 131514, 131683
Valid prediction for GlimmerHMM_glimmerT_45380-T1
Valid prediction for snap_scaffold_20-snap.165-T1
Valid prediction for snap_scaffold_20-snap.169-T1
Valid prediction for snap_scaffold_20-snap.159-T1
Valid prediction for GlimmerHMM_glimmerT_45372-T1
Valid prediction for HiQ_model.g30124.t1
Valid prediction for GlimmerHMM_glimmerT_45374-T1
Valid prediction for GlimmerHMM_glimmerT_45373-T1
Valid prediction for snap_scaffold_20-snap.177-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_20-snap.178-T1
Valid prediction for Augustus_model.g30123.t1
Couldn't classify 104309, 104853
Sorry, prediction pasa_asmbl_25519.p1 fails validation.
(ATG)	 AA	101400-101495	GT	AGG
(CTG)	 AG	101970-102067	GT	GGG
(CCA)	 AG	102352-102490	GT	AGG
(GTG)	 AG	103095-103201	GT	AAG
(TAC)	 AG	103459-103604	GT	AGG
(GCA)	 AG	103859-104020	GT	TGG
(GTG)	 AG	104309-104853	CA	AGC
-recovered pasa_asmbl_25519.p1, initial, 101400, 101495
-recovered pasa_asmbl_25519.p1, internal, 101970, 102067
-recovered pasa_asmbl_25519.p1, internal, 102352, 102490
-recovered pasa_asmbl_25519.p1, internal, 103095, 103201
-recovered pasa_asmbl_25519.p1, internal, 103459, 103604
-recovered pasa_asmbl_25519.p1, internal, 103859, 104020
Valid prediction for snap_scaffold_20-snap.191-T1
Valid prediction for Augustus_model.g30137.t1
Valid prediction for GlimmerHMM_glimmerT_45385-T1
Valid prediction for snap_scaffold_20-snap.155-T1
Couldn't classify 148263, 148347
Couldn't classify 149533, 149709
Sorry, prediction pasa_asmbl_25517.p1 fails validation.
(AAG)	 CC	148263-148347	GT	CAG
(CCC)	 AG	148558-148651	GT	AAG
(GTT)	 AG	149091-149193	GT	AGG
(GGT)	 AG	149533-149709	CA	GGC
-recovered pasa_asmbl_25517.p1, internal, 148558, 148651
-recovered pasa_asmbl_25517.p1, internal, 149091, 149193
Valid prediction for snap_scaffold_20-snap.160-T1
Valid prediction for Augustus_model.g30119.t1
Valid prediction for Augustus_model.g30126.t1
Valid prediction for snap_scaffold_20-snap.171-T1
Valid prediction for Augustus_model.g30132.t1
Valid prediction for snap_scaffold_20-snap.183-T1
Valid prediction for Augustus_model.g30117.t1
Couldn't classify 163244, 163512
Couldn't classify 164139, 164217
Sorry, prediction pasa_asmbl_26296.p1 fails validation.
(ACC)	 AG	163244-163512	GT	GGG
(GTT)	 AG	164139-164217	GT	AGG
-recovered pasa_asmbl_26296.p1, internal, 163244, 163512
-recovered pasa_asmbl_26296.p1, internal, 164139, 164217
Valid prediction for Augustus_model.g30122.t1
Valid prediction for GlimmerHMM_glimmerT_45370-T1
Valid prediction for Augustus_model.g30135.t1
Valid prediction for GlimmerHMM_glimmerT_45377-T1
Valid prediction for snap_scaffold_20-snap.185-T1
Valid prediction for snap_scaffold_20-snap.184-T1
Valid prediction for GlimmerHMM_glimmerT_45379-T1
Valid prediction for snap_scaffold_20-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_45362-T1
Valid prediction for Augustus_model.g30133.t1
Valid prediction for GlimmerHMM_glimmerT_45363-T1
Valid prediction for Augustus_model.g30118.t1
Valid prediction for snap_scaffold_20-snap.187-T1
Valid prediction for snap_scaffold_20-snap.168-T1
Valid prediction for snap_scaffold_20-snap.175-T1
Valid prediction for snap_scaffold_20-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_45367-T1
Valid prediction for snap_scaffold_20-snap.167-T1
Valid prediction for GlimmerHMM_glimmerT_45382-T1
Valid prediction for GlimmerHMM_glimmerT_45364-T1
Valid prediction for snap_scaffold_20-snap.176-T1
Valid prediction for Augustus_model.g30120.t1
Valid prediction for snap_scaffold_20-snap.197-T1
Valid prediction for snap_scaffold_20-snap.181-T1
Valid prediction for Augustus_model.g30136.t1
Valid prediction for snap_scaffold_20-snap.193-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20331, rend_intergenic: 8415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46466, rend_intergenic: 23591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52680, rend_intergenic: 47156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53794, rend_intergenic: 53064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74139, rend_intergenic: 61489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82068, rend_intergenic: 75865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90367, rend_intergenic: 84375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99565, rend_intergenic: 92937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111649, rend_intergenic: 101902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121991, rend_intergenic: 115994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135087, rend_intergenic: 124762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150693, rend_intergenic: 149533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154531, rend_intergenic: 151779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161453, rend_intergenic: 155655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170277, rend_intergenic: 165536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175538
-exon list size: 462


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 20331, rend_intergenic: 8415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46466, rend_intergenic: 23591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52680, rend_intergenic: 47156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53794, rend_intergenic: 53064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74139, rend_intergenic: 61489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82068, rend_intergenic: 75865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90367, rend_intergenic: 84375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99565, rend_intergenic: 92937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111649, rend_intergenic: 101902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121991, rend_intergenic: 115994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135087, rend_intergenic: 124762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150693, rend_intergenic: 149533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154531, rend_intergenic: 151779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161453, rend_intergenic: 155655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170277, rend_intergenic: 165536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support