-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_2389332-2594296

-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_27-snap.581-T1
Couldn't classify 149631, 149809
Sorry, prediction pasa_asmbl_36089.p2 fails validation.
(ATG)	 AG	149134-149260	GT	AGG
(TTC)	 AG	149631-149809	TG	GGT
-recovered pasa_asmbl_36089.p2, initial, 149134, 149260
-recovered pasa_asmbl_36089.p2, internal, 149134, 149260
Valid prediction for snap_scaffold_27-snap.609-T1
Valid prediction for snap_scaffold_27-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_56851-T1
Valid prediction for GlimmerHMM_glimmerT_56859-T1
Valid prediction for Augustus_model.g37665.t1
Couldn't classify 39262, 39306
Couldn't classify 41620, 42072
Sorry, prediction pasa_asmbl_36083.p1 fails validation.
(TTG)	 CT	39262-39306	GT	AGG
(GTG)	 AG	39441-39482	GT	ATG
(CGT)	 AG	41620-42072	CC	GCC
-recovered pasa_asmbl_36083.p1, internal, 39441, 39482
Valid prediction for snap_scaffold_27-snap.607-T1
Valid prediction for GlimmerHMM_glimmerT_56845-T1
Valid prediction for GlimmerHMM_glimmerT_56846-T1
Valid prediction for GlimmerHMM_glimmerT_56854-T1
Valid prediction for snap_scaffold_27-snap.597-T1
Valid prediction for snap_scaffold_27-snap.602-T1
Valid prediction for Augustus_model.g37657.t1
Valid prediction for snap_scaffold_27-snap.604-T1
Couldn't classify 24604, 25407
Sorry, prediction pasa_asmbl_36079.p1 fails validation.
(ATC)	 GC	24604-25407	TA	GAT
Valid prediction for snap_scaffold_27-snap.577-T1
Valid prediction for snap_scaffold_27-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_56839-T1
Valid prediction for GlimmerHMM_glimmerT_56866-T1
Valid prediction for snap_scaffold_27-snap.591-T1
Valid prediction for CodingQuarry_transcript_41807-T1
Valid prediction for snap_scaffold_27-snap.589-T1
Valid prediction for snap_scaffold_27-snap.562-T1
Valid prediction for Augustus_model.g37654.t1
Valid prediction for GlimmerHMM_glimmerT_56842-T1
Valid prediction for GlimmerHMM_glimmerT_56833-T1
Valid prediction for snap_scaffold_27-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_56840-T1
Valid prediction for snap_scaffold_27-snap.600-T1
Valid prediction for Augustus_model.g37664.t1
Valid prediction for snap_scaffold_27-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_56863-T1
Couldn't classify 153962, 154109
Sorry, prediction pasa_asmbl_36091.p2 fails validation.
(AGG)	 CC	153962-154109	GT	AGG
(CGA)	 AG	154306-154512	GT	AGG
(GCA)	 AG	154730-154842	GT	AGG
(AAC)	 AG	155144-155253	GT	CCG
(GGC)	 AG	155356-155528	GT	GAG
(AGT)	 AG	156943-156989	AG	GAA
-recovered pasa_asmbl_36091.p2, terminal, 156943, 156989
-recovered pasa_asmbl_36091.p2, internal, 154306, 154512
-recovered pasa_asmbl_36091.p2, internal, 154730, 154842
-recovered pasa_asmbl_36091.p2, internal, 155144, 155253
-recovered pasa_asmbl_36091.p2, internal, 155356, 155528
Valid prediction for GlimmerHMM_glimmerT_56847-T1
Valid prediction for snap_scaffold_27-snap.603-T1
Valid prediction for snap_scaffold_27-snap.594-T1
Valid prediction for Augustus_model.g37669.t1
Valid prediction for GlimmerHMM_glimmerT_56850-T1
Valid prediction for GlimmerHMM_glimmerT_56834-T1
Valid prediction for Augustus_model.g37666.t1
Valid prediction for HiQ_model.g37667.t1
Valid prediction for GlimmerHMM_glimmerT_56857-T1
Valid prediction for pasa_asmbl_36087.p1
Valid prediction for snap_scaffold_27-snap.598-T1
Valid prediction for snap_scaffold_27-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_56858-T1
Valid prediction for Augustus_model.g37656.t1
Valid prediction for GlimmerHMM_glimmerT_56836-T1
Valid prediction for GlimmerHMM_glimmerT_56838-T1
Valid prediction for snap_scaffold_27-snap.573-T1
Valid prediction for Augustus_model.g37668.t1
Valid prediction for Augustus_model.g37662.t1
Valid prediction for Augustus_model.g37673.t1
Valid prediction for snap_scaffold_27-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_56861-T1
Valid prediction for snap_scaffold_27-snap.563-T1
Valid prediction for snap_scaffold_27-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_56867-T1
Valid prediction for snap_scaffold_27-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_56852-T1
Valid prediction for snap_scaffold_27-snap.558-T1
Valid prediction for snap_scaffold_27-snap.601-T1
Valid prediction for snap_scaffold_27-snap.564-T1
Valid prediction for snap_scaffold_27-snap.582-T1
Valid prediction for Augustus_model.g37671.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: -)Couldn't classify 105268, 105624
Sorry, prediction pasa_asmbl_36824.p1 fails validation.
(ATG)	 GA	105268-105624	GA	GCG
Valid prediction for snap_scaffold_27-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_56843-T1
Valid prediction for snap_scaffold_27-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_56832-T1
Valid prediction for HiQ_model.g37672.t1
Valid prediction for GlimmerHMM_glimmerT_56860-T1
Valid prediction for GlimmerHMM_glimmerT_56841-T1
Valid prediction for snap_scaffold_27-snap.612-T1
Valid prediction for snap_scaffold_27-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_56862-T1
Valid prediction for snap_scaffold_27-snap.561-T1
Valid prediction for Augustus_model.g37674.t1
Valid prediction for snap_scaffold_27-snap.608-T1
Valid prediction for snap_scaffold_27-snap.568-T1
Valid prediction for snap_scaffold_27-snap.595-T1
Valid prediction for snap_scaffold_27-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_56855-T1
Couldn't classify 108386, 109243
Sorry, prediction pasa_asmbl_36823.p1 fails validation.
(CCC)	 CC	108386-109243	AG	GCA
Valid prediction for snap_scaffold_27-snap.560-T1
Valid prediction for snap_scaffold_27-snap.588-T1
Valid prediction for pasa_asmbl_36827.p2
Valid prediction for snap_scaffold_27-snap.610-T1
Valid prediction for GlimmerHMM_glimmerT_56837-T1
Valid prediction for Augustus_model.g37659.t1
Valid prediction for GlimmerHMM_glimmerT_56853-T1
Valid prediction for Augustus_model.g37658.t1
Valid prediction for snap_scaffold_27-snap.571-T1
Valid prediction for snap_scaffold_27-snap.587-T1
Couldn't classify 40061, 40239
Sorry, prediction pasa_asmbl_36828.p1 fails validation.
(GAG)	 AG	40061-40239	GT	TTG
(CTC)	 AG	40514-40606	GT	AGG
(GTA)	 AG	40719-40787	GT	AGG
(GCC)	 AG	41103-41385	GT	AGG
(GAC)	 AG	44166-44225	TC	GAT
-recovered pasa_asmbl_36828.p1, terminal, 44166, 44225
-recovered pasa_asmbl_36828.p1, internal, 40061, 40239
-recovered pasa_asmbl_36828.p1, internal, 40514, 40606
-recovered pasa_asmbl_36828.p1, internal, 40719, 40787
-recovered pasa_asmbl_36828.p1, internal, 41103, 41385
Valid prediction for Augustus_model.g37660.t1
Valid prediction for CodingQuarry_transcript_41808-T1
Valid prediction for snap_scaffold_27-snap.605-T1
Valid prediction for snap_scaffold_27-snap.613-T1
Valid prediction for HiQ_model.g37661.t1
Valid prediction for GlimmerHMM_glimmerT_56865-T1
Valid prediction for GlimmerHMM_glimmerT_56864-T1
Valid prediction for snap_scaffold_27-snap.590-T1
Valid prediction for snap_scaffold_27-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_56848-T1
Valid prediction for GlimmerHMM_glimmerT_56835-T1
Valid prediction for snap_scaffold_27-snap.572-T1
Valid prediction for snap_scaffold_27-snap.592-T1
Valid prediction for snap_scaffold_27-snap.576-T1
Valid prediction for snap_scaffold_27-snap.579-T1
Valid prediction for Augustus_model.g37663.t1
Valid prediction for snap_scaffold_27-snap.586-T1
Valid prediction for snap_scaffold_27-snap.566-T1
Couldn't classify 17165, 17185
Sorry, prediction pasa_asmbl_36831.p1 fails validation.
(CCA)	 CT	17165-17185	GT	AGG
(GAA)	 AG	17344-17481	GT	TGG
(TCA)	 AG	17793-17835	GT	CGG
(GGC)	 AG	17937-18042	GT	CTG
(GTA)	 AG	18972-19104	GT	TGG
(CTC)	 AG	19536-19713	GT	AGG
(ATA)	 AG	19922-20019	GT	GGG
(AGC)	 AG	20965-21046	GT	TGG
(GTA)	 AG	21296-21449	GT	AGG
(ACA)	 AG	21785-21904	GT	AGG
(GCC)	 AG	22138-22213	GT	AGG
(TGT)	 AG	22349-22410	GT	AAG
(GCT)	 AG	22541-22619	GT	GGG
(GAG)	 AG	22709-22828	GT	ACG
(GCT)	 AG	23089-23241	CC	GAC
-recovered pasa_asmbl_36831.p1, terminal, 23089, 23241
-recovered pasa_asmbl_36831.p1, internal, 17344, 17481
-recovered pasa_asmbl_36831.p1, internal, 17793, 17835
-recovered pasa_asmbl_36831.p1, internal, 17937, 18042
-recovered pasa_asmbl_36831.p1, internal, 18972, 19104
-recovered pasa_asmbl_36831.p1, internal, 19536, 19713
-recovered pasa_asmbl_36831.p1, internal, 19922, 20019
-recovered pasa_asmbl_36831.p1, internal, 20965, 21046
-recovered pasa_asmbl_36831.p1, internal, 21296, 21449
-recovered pasa_asmbl_36831.p1, internal, 21785, 21904
-recovered pasa_asmbl_36831.p1, internal, 22138, 22213
-recovered pasa_asmbl_36831.p1, internal, 22349, 22410
-recovered pasa_asmbl_36831.p1, internal, 22541, 22619
-recovered pasa_asmbl_36831.p1, internal, 22709, 22828
Valid prediction for snap_scaffold_27-snap.580-T1
Valid prediction for Augustus_model.g37670.t1
Valid prediction for CodingQuarry_transcript_41806-T1
Couldn't classify 33998, 34022
Couldn't classify 35801, 35813
Sorry, prediction pasa_asmbl_36830.p1 fails validation.
(AAG)	 TC	33998-34022	GT	AAG
(AAC)	 AG	34610-34706	GT	TGG
(GGT)	 AG	34854-34923	GT	AGG
(CAC)	 AG	35018-35067	GT	AAG
(ACG)	 AG	35288-35410	GT	AGG
(GAA)	 AG	35523-35603	GT	CAG
(GAA)	 AG	35801-35813	GA	AGG
-recovered pasa_asmbl_36830.p1, internal, 34610, 34706
-recovered pasa_asmbl_36830.p1, internal, 34854, 34923
-recovered pasa_asmbl_36830.p1, internal, 35018, 35067
-recovered pasa_asmbl_36830.p1, internal, 35288, 35410
-recovered pasa_asmbl_36830.p1, internal, 35523, 35603
Valid prediction for GlimmerHMM_glimmerT_56849-T1
Valid prediction for Augustus_model.g37675.t1
Valid prediction for snap_scaffold_27-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_56856-T1
Valid prediction for snap_scaffold_27-snap.606-T1
Valid prediction for snap_scaffold_27-snap.584-T1
Valid prediction for Augustus_model.g37655.t1
Valid prediction for GlimmerHMM_glimmerT_56844-T1
Valid prediction for snap_scaffold_27-snap.593-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18867, rend_intergenic: 15124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35720, rend_intergenic: 33654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52401, rend_intergenic: 36865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58283, rend_intergenic: 56996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60279, rend_intergenic: 58409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68432, rend_intergenic: 65671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79146, rend_intergenic: 68436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89488, rend_intergenic: 87837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92633, rend_intergenic: 91696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130893, rend_intergenic: 129057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131201, rend_intergenic: 130917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137431, rend_intergenic: 131982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162394, rend_intergenic: 161505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180948, rend_intergenic: 177915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188310, rend_intergenic: 185209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195135, rend_intergenic: 193444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199103, rend_intergenic: 197243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204965
-exon list size: 542


building trellis

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90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 18867, rend_intergenic: 15124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35720, rend_intergenic: 33654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52401, rend_intergenic: 36865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58283, rend_intergenic: 56996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60279, rend_intergenic: 58409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68432, rend_intergenic: 65671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79146, rend_intergenic: 68436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89488, rend_intergenic: 87837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92633, rend_intergenic: 91696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130893, rend_intergenic: 129057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131201, rend_intergenic: 130917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137431, rend_intergenic: 131982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162394, rend_intergenic: 161505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180948, rend_intergenic: 177915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188310, rend_intergenic: 185209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195135, rend_intergenic: 193444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199103, rend_intergenic: 197243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support