-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_686665-952568

-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_1-snap.146-T1
Valid prediction for snap_scaffold_1-snap.157-T1
Valid prediction for Augustus_model.g85.t1
Valid prediction for CodingQuarry_transcript_2511-T1
Couldn't classify 105527, 105659
Couldn't classify 106352, 106467
Sorry, prediction pasa_asmbl_2794.p1 fails validation.
(AAG)	 CC	105527-105659	GT	CGG
(GTG)	 AG	106044-106169	GT	TGG
(GCA)	 AG	106352-106467	GT	AGG
-recovered pasa_asmbl_2794.p1, internal, 106044, 106169
-recovered pasa_asmbl_2794.p1, internal, 106352, 106467
Valid prediction for snap_scaffold_1-snap.158-T1
Valid prediction for snap_scaffold_1-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_99-T1
Valid prediction for snap_scaffold_1-snap.141-T1
Valid prediction for snap_scaffold_1-snap.137-T1
Couldn't classify 204913, 205053
Sorry, prediction pasa_asmbl_1435.p1 fails validation.
(GGC)	 AG	204913-205053	GT	AGG
(GTG)	 AG	205232-205383	GT	AGG
(GAA)	 AG	205506-205603	GT	AGG
(GTA)	 AG	205904-206014	GT	AGG
(ACG)	 AG	206672-206832	TC	GAT
add_exon() Sorry, pasa_asmbl_1435.p1 205506-205603-terminal-2 is invalid.
-recovered pasa_asmbl_1435.p1, terminal, 205506, 205603
-recovered pasa_asmbl_1435.p1, terminal, 206672, 206832
-recovered pasa_asmbl_1435.p1, internal, 204913, 205053
-recovered pasa_asmbl_1435.p1, internal, 205232, 205383
-recovered pasa_asmbl_1435.p1, internal, 205506, 205603
-recovered pasa_asmbl_1435.p1, internal, 205904, 206014
Valid prediction for GlimmerHMM_glimmerT_93-T1
Valid prediction for Augustus_model.g82.t1
Valid prediction for snap_scaffold_1-snap.152-T1
Valid prediction for Augustus_model.g78.t1
Valid prediction for GlimmerHMM_glimmerT_107-T1
Couldn't classify 130965, 131022
Couldn't classify 133567, 133725
Sorry, prediction pasa_asmbl_1414.p2 fails validation.
(AAC)	 AG	130965-131022	GT	TGG
(GCG)	 AG	131352-131563	GT	AGG
(ATC)	 AG	132245-132352	GT	AGG
(CTT)	 AG	133567-133725	GG	GAG
-recovered pasa_asmbl_1414.p2, internal, 130965, 131022
-recovered pasa_asmbl_1414.p2, internal, 131352, 131563
-recovered pasa_asmbl_1414.p2, internal, 132245, 132352
Valid prediction for Augustus_model.g99.t1
Valid prediction for Augustus_model.g80.t1
Valid prediction for snap_scaffold_1-snap.144-T1
Valid prediction for Augustus_model.g83.t1
Valid prediction for snap_scaffold_1-snap.159-T1
Couldn't classify 230475, 230628
Sorry, prediction pasa_asmbl_1437.p1 fails validation.
(ATG)	 AT	227591-227609	GT	CGG
(AGT)	 AG	228050-228075	GT	AGG
(GAA)	 AG	228222-228394	GT	TGG
(TTG)	 AG	228708-228848	GT	CTG
(AGA)	 AG	229186-229348	GT	AGG
(ATC)	 AG	229977-230086	GT	AGG
(CTG)	 AG	230252-230371	GT	AGG
(AAC)	 AG	230475-230628	GT	CGG
-recovered pasa_asmbl_1437.p1, initial, 227591, 227609
-recovered pasa_asmbl_1437.p1, internal, 228050, 228075
-recovered pasa_asmbl_1437.p1, internal, 228222, 228394
-recovered pasa_asmbl_1437.p1, internal, 228708, 228848
-recovered pasa_asmbl_1437.p1, internal, 229186, 229348
-recovered pasa_asmbl_1437.p1, internal, 229977, 230086
-recovered pasa_asmbl_1437.p1, internal, 230252, 230371
-recovered pasa_asmbl_1437.p1, internal, 230475, 230628
Valid prediction for snap_scaffold_1-snap.165-T1
Valid prediction for Augustus_model.g86.t1
Valid prediction for snap_scaffold_1-snap.164-T1
Valid prediction for HiQ_model.g95.t1
Valid prediction for Augustus_model.g94.t1
Valid prediction for Augustus_model.g84.t1
Valid prediction for GlimmerHMM_glimmerT_110-T1
Valid prediction for GlimmerHMM_glimmerT_109-T1
Valid prediction for snap_scaffold_1-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_118-T1
Valid prediction for snap_scaffold_1-snap.133-T1
Valid prediction for snap_scaffold_1-snap.167-T1
Valid prediction for Augustus_model.g88.t1
Valid prediction for snap_scaffold_1-snap.143-T1
Valid prediction for snap_scaffold_1-snap.139-T1
Valid prediction for snap_scaffold_1-snap.172-T1
Valid prediction for GlimmerHMM_glimmerT_97-T1
Valid prediction for pasa_asmbl_1436.p2
Couldn't classify 112291, 112474
Couldn't classify 113647, 113736
Sorry, prediction pasa_asmbl_1412.p1 fails validation.
(GCT)	 CA	112291-112474	GT	TGG
(GTC)	 AG	113012-113226	GT	AGG
(AAA)	 AG	113647-113736	AC	GCA
-recovered pasa_asmbl_1412.p1, internal, 113012, 113226
Valid prediction for snap_scaffold_1-snap.134-T1
Couldn't classify 164131, 164297
Sorry, prediction pasa_asmbl_1428.p1 fails validation.
(GGG)	 CC	164131-164297	GT	ATG
(GTA)	 AG	164726-164900	GT	AGG
(GCA)	 AG	166672-166819	GT	GGG
(TGT)	 AG	166897-167038	GT	ATG
(CAT)	 AG	167527-167611	GT	TGG
(ATT)	 AG	167856-167987	GT	CCG
(GGA)	 AG	168157-168315	GT	TTG
(GTA)	 AG	168424-168549	GT	TGG
(ATC)	 AG	168743-168859	AG	GAA
-recovered pasa_asmbl_1428.p1, terminal, 168743, 168859
-recovered pasa_asmbl_1428.p1, internal, 164726, 164900
-recovered pasa_asmbl_1428.p1, internal, 166672, 166819
-recovered pasa_asmbl_1428.p1, internal, 166897, 167038
-recovered pasa_asmbl_1428.p1, internal, 167527, 167611
-recovered pasa_asmbl_1428.p1, internal, 167856, 167987
-recovered pasa_asmbl_1428.p1, internal, 168157, 168315
-recovered pasa_asmbl_1428.p1, internal, 168424, 168549
Valid prediction for snap_scaffold_1-snap.153-T1
Valid prediction for snap_scaffold_1-snap.130-T1
Valid prediction for CodingQuarry_transcript_2509-T1
Valid prediction for CodingQuarry_transcript_2508-T1
Valid prediction for GlimmerHMM_glimmerT_96-T1
Valid prediction for Augustus_model.g81.t1
Valid prediction for HiQ_model.g92.t1
Couldn't classify 202079, 202149
Couldn't classify 204604, 204630
Sorry, prediction pasa_asmbl_1434.p3 fails validation.
(TTC)	 AG	202079-202149	GT	CAG
(GAG)	 AG	203523-203667	GT	AGG
(GGA)	 AG	204292-204432	GT	AGG
(TCC)	 AG	204604-204630	TC	GCT
-recovered pasa_asmbl_1434.p3, internal, 202079, 202149
-recovered pasa_asmbl_1434.p3, internal, 203523, 203667
-recovered pasa_asmbl_1434.p3, internal, 204292, 204432
Valid prediction for GlimmerHMM_glimmerT_116-T1
Valid prediction for snap_scaffold_1-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_98-T1
Valid prediction for HiQ_model.g89.t1
Valid prediction for Augustus_model.g79.t1
Valid prediction for GlimmerHMM_glimmerT_104-T1
Valid prediction for snap_scaffold_1-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_94-T1
Valid prediction for snap_scaffold_1-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_105-T1
Valid prediction for GlimmerHMM_glimmerT_113-T1
Valid prediction for snap_scaffold_1-snap.162-T1
Valid prediction for snap_scaffold_1-snap.142-T1
Valid prediction for Augustus_model.g97.t1
Valid prediction for snap_scaffold_1-snap.166-T1
Valid prediction for Augustus_model.g98.t1
Valid prediction for GlimmerHMM_glimmerT_115-T1
Valid prediction for pasa_asmbl_1432.p1
Couldn't classify 233578, 233670
Sorry, prediction pasa_asmbl_1439.p1 fails validation.
(GGG)	 AA	233578-233670	GT	AGG
(TGG)	 AG	233914-233985	GT	TGG
(GAA)	 AG	234151-234268	GT	AGG
(GCG)	 AG	234381-234450	GT	AGG
(CGA)	 AG	234614-234861	GT	CGG
(AGG)	 AG	235101-235307	GT	TGG
(GGA)	 AG	236313-236365	TG	GAT
-recovered pasa_asmbl_1439.p1, terminal, 236313, 236365
-recovered pasa_asmbl_1439.p1, internal, 233914, 233985
-recovered pasa_asmbl_1439.p1, internal, 234151, 234268
-recovered pasa_asmbl_1439.p1, internal, 234381, 234450
-recovered pasa_asmbl_1439.p1, internal, 234614, 234861
-recovered pasa_asmbl_1439.p1, internal, 235101, 235307
Valid prediction for snap_scaffold_1-snap.160-T1
Valid prediction for snap_scaffold_1-snap.132-T1
Valid prediction for snap_scaffold_1-snap.171-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.g100.t1
Valid prediction for GlimmerHMM_glimmerT_114-T1
Valid prediction for HiQ_model.g96.t1
Valid prediction for snap_scaffold_1-snap.163-T1
Valid prediction for GlimmerHMM_glimmerT_102-T1
Valid prediction for GlimmerHMM_glimmerT_120-T1
Valid prediction for Augustus_model.g87.t1
Valid prediction for GlimmerHMM_glimmerT_106-T1
Valid prediction for GlimmerHMM_glimmerT_111-T1
Valid prediction for snap_scaffold_1-snap.135-T1
Valid prediction for snap_scaffold_1-snap.147-T1
Valid prediction for snap_scaffold_1-snap.145-T1
Valid prediction for snap_scaffold_1-snap.154-T1
Valid prediction for snap_scaffold_1-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_100-T1
Valid prediction for snap_scaffold_1-snap.129-T1
Valid prediction for snap_scaffold_1-snap.148-T1
Valid prediction for CodingQuarry_transcript_2506-T1
Valid prediction for Augustus_model.g93.t1
Valid prediction for Augustus_model.g90.t1
Valid prediction for GlimmerHMM_glimmerT_95-T1
Valid prediction for snap_scaffold_1-snap.136-T1
Valid prediction for snap_scaffold_1-snap.173-T1
Couldn't classify 106728, 106751
Couldn't classify 109488, 109565
Sorry, prediction pasa_asmbl_1286.p1 fails validation.
(GGA)	 AA	106728-106751	GT	TGG
(ATG)	 AG	109053-109256	GT	AGG
(ATT)	 AG	109488-109565	GG	GGG
-recovered pasa_asmbl_1286.p1, initial, 109053, 109256
-recovered pasa_asmbl_1286.p1, internal, 109053, 109256
Valid prediction for GlimmerHMM_glimmerT_101-T1
Valid prediction for GlimmerHMM_glimmerT_117-T1
Valid prediction for snap_scaffold_1-snap.131-T1
Valid prediction for CodingQuarry_transcript_2507-T1
Valid prediction for GlimmerHMM_glimmerT_121-T1
Valid prediction for snap_scaffold_1-snap.138-T1
Valid prediction for snap_scaffold_1-snap.127-T1
Valid prediction for pasa_asmbl_26.p1
Valid prediction for snap_scaffold_1-snap.155-T1
Couldn't classify 44871, 44981
Sorry, prediction pasa_asmbl_36.p1 fails validation.
(AGG)	 CC	44871-44981	GT	AGG
(GAG)	 AG	45301-45443	GT	AAG
(GGT)	 AG	45762-45946	GT	AGG
(GGT)	 AG	46268-46365	GT	CTG
(GCT)	 AG	46516-46656	GT	AGG
(GTA)	 AG	46835-47116	GT	AGG
(GTG)	 AG	47246-47397	GT	AGG
(ACG)	 AG	47722-47924	GT	CAG
(GCC)	 AG	48049-48162	GT	CGG
(CTC)	 AG	48420-48491	GT	GGG
(GCT)	 AG	48708-48797	GT	TGG
(GAC)	 AG	49072-49187	GT	AGG
(AAA)	 AG	49350-49394	GT	AAG
add_exon() Sorry, pasa_asmbl_36.p1 45762-45946-terminal-2 is invalid.
-recovered pasa_asmbl_36.p1, terminal, 45762, 45946
-recovered pasa_asmbl_36.p1, terminal, 49350, 49394
-recovered pasa_asmbl_36.p1, internal, 45301, 45443
-recovered pasa_asmbl_36.p1, internal, 45762, 45946
-recovered pasa_asmbl_36.p1, internal, 46268, 46365
-recovered pasa_asmbl_36.p1, internal, 46516, 46656
-recovered pasa_asmbl_36.p1, internal, 46835, 47116
-recovered pasa_asmbl_36.p1, internal, 47246, 47397
-recovered pasa_asmbl_36.p1, internal, 47722, 47924
-recovered pasa_asmbl_36.p1, internal, 48049, 48162
-recovered pasa_asmbl_36.p1, internal, 48420, 48491
-recovered pasa_asmbl_36.p1, internal, 48708, 48797
-recovered pasa_asmbl_36.p1, internal, 49072, 49187
-recovered pasa_asmbl_36.p1, internal, 49350, 49394
Valid prediction for Augustus_model.g77.t1
Couldn't classify 82217, 82253
Sorry, prediction pasa_asmbl_30.p1 fails validation.
(CTG)	 AA	82217-82253	GT	CAG
(CCT)	 AG	82991-83233	GC	AGG
(GTT)	 AG	83385-83473	GG	GAG
-recovered pasa_asmbl_30.p1, terminal, 83385, 83473
-recovered pasa_asmbl_30.p1, internal, 82991, 83233
Valid prediction for CodingQuarry_transcript_2510-T1
Couldn't classify 76157, 76195
Couldn't classify 79324, 79377
Sorry, prediction pasa_asmbl_31.p1 fails validation.
(GGA)	 AG	76157-76195	GT	AGG
(CTG)	 AG	76345-76457	GT	AGG
(TGA)	 AG	77431-77500	GT	TGG
(CCC)	 AG	77588-77665	GT	AGG
(ATC)	 AG	78332-78472	GT	AAG
(ATC)	 AG	79324-79377	GT	GGG
-recovered pasa_asmbl_31.p1, internal, 76157, 76195
-recovered pasa_asmbl_31.p1, internal, 76345, 76457
-recovered pasa_asmbl_31.p1, internal, 77431, 77500
-recovered pasa_asmbl_31.p1, internal, 77588, 77665
-recovered pasa_asmbl_31.p1, internal, 78332, 78472
-recovered pasa_asmbl_31.p1, internal, 79324, 79377
Valid prediction for GlimmerHMM_glimmerT_108-T1
Valid prediction for Augustus_model.g91.t1
Valid prediction for GlimmerHMM_glimmerT_119-T1
Valid prediction for snap_scaffold_1-snap.168-T1
Valid prediction for Augustus_model.g101.t1
Valid prediction for GlimmerHMM_glimmerT_103-T1
Valid prediction for snap_scaffold_1-snap.169-T1
Valid prediction for snap_scaffold_1-snap.150-T1
Valid prediction for snap_scaffold_1-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_112-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8778, rend_intergenic: 4823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37943, rend_intergenic: 34702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80162, rend_intergenic: 70367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88038, rend_intergenic: 82625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134024, rend_intergenic: 131348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143068, rend_intergenic: 137731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190452, rend_intergenic: 184473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223118, rend_intergenic: 216752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253289, rend_intergenic: 243708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258215, rend_intergenic: 253292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265904
-exon list size: 433


building trellis

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80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 8778, rend_intergenic: 4823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37943, rend_intergenic: 34702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80162, rend_intergenic: 70367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88038, rend_intergenic: 82625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134024, rend_intergenic: 131348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143068, rend_intergenic: 137731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190452, rend_intergenic: 184473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223118, rend_intergenic: 216752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253289, rend_intergenic: 243708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258215, rend_intergenic: 253292  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