-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_685305-865300

-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 GeneMark_model.98083_t
Valid prediction for GeneMark_model.98057_t
Valid prediction for snap_scaffold_26-snap.145-T1
Valid prediction for GeneMark_model.98071_t
Valid prediction for snap_scaffold_26-snap.150-T1
Valid prediction for Augustus_model.g37550.t1
Valid prediction for GlimmerHMM_glimmerT_56352-T1
Valid prediction for GeneMark_model.98093_t
Valid prediction for GlimmerHMM_glimmerT_56349-T1
Valid prediction for snap_scaffold_26-snap.175-T1
Valid prediction for GeneMark_model.98077_t
Valid prediction for GeneMark_model.98078_t
Valid prediction for GlimmerHMM_glimmerT_56353-T1
Valid prediction for snap_scaffold_26-snap.154-T1
Valid prediction for snap_scaffold_26-snap.180-T1
Valid prediction for snap_scaffold_26-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_56339-T1
Valid prediction for snap_scaffold_26-snap.178-T1
Valid prediction for snap_scaffold_26-snap.166-T1
Valid prediction for GeneMark_model.98061_t
Valid prediction for GlimmerHMM_glimmerT_56341-T1
Valid prediction for snap_scaffold_26-snap.172-T1
Valid prediction for Augustus_model.g37553.t1
Valid prediction for GlimmerHMM_glimmerT_56347-T1
Valid prediction for GlimmerHMM_glimmerT_56342-T1
Valid prediction for GeneMark_model.98053_t
Valid prediction for GeneMark_model.98094_t
Couldn't classify 130651, 130813
Sorry, prediction pasa_asmbl_35229.p1 fails validation.
(ATG)	 TC	126590-126691	GT	AGG
(ATG)	 AG	128422-128506	GT	AGG
(GTA)	 AG	129309-129339	GT	AGG
(GGT)	 AG	130080-130126	GT	CAG
(TCA)	 AG	130200-130271	GT	CGG
(AGA)	 AG	130486-130543	GT	GAG
(GCA)	 AG	130651-130813	GT	AGG
-recovered pasa_asmbl_35229.p1, initial, 126590, 126691
-recovered pasa_asmbl_35229.p1, initial, 128422, 128506
-recovered pasa_asmbl_35229.p1, terminal, 130486, 130543
-recovered pasa_asmbl_35229.p1, internal, 128422, 128506
-recovered pasa_asmbl_35229.p1, internal, 129309, 129339
-recovered pasa_asmbl_35229.p1, internal, 130080, 130126
-recovered pasa_asmbl_35229.p1, internal, 130200, 130271
-recovered pasa_asmbl_35229.p1, internal, 130486, 130543
-recovered pasa_asmbl_35229.p1, internal, 130651, 130813
Valid prediction for snap_scaffold_26-snap.168-T1
Valid prediction for snap_scaffold_26-snap.158-T1
Valid prediction for GeneMark_model.98052_t
Valid prediction for Augustus_model.g37561.t1
Couldn't classify 18369, 18497
Couldn't classify 19632, 19712
Sorry, prediction CodingQuarry_transcript_40147-T1 fails validation.
(ATG)	 GA	16016-16087	GT	AGG
(GAA)	 AG	18369-18497	AG	AGA
(AGT)	 CT	19632-19712	CC	AAC
-recovered CodingQuarry_transcript_40147-T1, initial, 16016, 16087
Valid prediction for GeneMark_model.98049_t
Valid prediction for GeneMark_model.98096_t
Valid prediction for GeneMark_model.98073_t
Valid prediction for snap_scaffold_26-snap.148-T1
Valid prediction for GeneMark_model.98059_t
Valid prediction for GeneMark_model.98088_t
Valid prediction for GeneMark_model.98069_t
Valid prediction for GeneMark_model.98079_t
Valid prediction for snap_scaffold_26-snap.151-T1
Valid prediction for GeneMark_model.98090_t
Valid prediction for Augustus_model.g37551.t1
Valid prediction for Augustus_model.g37552.t1
Valid prediction for GeneMark_model.98065_t
Couldn't classify 48111, 48192
Sorry, prediction pasa_asmbl_35830.p2 fails validation.
(AGT)	 CC	48111-48192	GT	AGG
(GTG)	 AG	48411-48628	TG	GAT
-recovered pasa_asmbl_35830.p2, terminal, 48411, 48628
Valid prediction for CodingQuarry_transcript_40149-T1
Couldn't classify 132450, 132513
Couldn't classify 135598, 135758
Sorry, prediction pasa_asmbl_35843.p1 fails validation.
(AGG)	 CC	132450-132513	GT	AGG
(ACG)	 AG	132792-132892	GT	AGG
(GAC)	 AG	133244-133385	GT	AGG
(GAG)	 AG	135598-135758	GT	GGG
-recovered pasa_asmbl_35843.p1, internal, 132792, 132892
-recovered pasa_asmbl_35843.p1, internal, 133244, 133385
-recovered pasa_asmbl_35843.p1, internal, 135598, 135758
Valid prediction for GeneMark_model.98086_t
Valid prediction for Augustus_model.g37560.t1
Valid prediction for GlimmerHMM_glimmerT_56337-T1
Couldn't classify 47223, 47765
Sorry, prediction pasa_asmbl_35222.p1 fails validation.
(GAG)	 TG	47223-47765	AC	GAA
Valid prediction for snap_scaffold_26-snap.152-T1
Valid prediction for snap_scaffold_26-snap.147-T1
Valid prediction for CodingQuarry_transcript_40148-T1
Valid prediction for Augustus_model.g37555.t1
Valid prediction for GlimmerHMM_glimmerT_56343-T1
Valid prediction for snap_scaffold_26-snap.144-T1
Valid prediction for GeneMark_model.98063_t
Valid prediction for GeneMark_model.98081_t
Valid prediction for GlimmerHMM_glimmerT_56348-T1
Couldn't classify 46380, 46664
Sorry, prediction pasa_asmbl_35221.p1 fails validation.
(ATG)	 CC	44854-44907	GT	AGG
(CTG)	 AG	46006-46107	GT	AGG
(GTC)	 AG	46380-46664	CG	GTC
-recovered pasa_asmbl_35221.p1, initial, 44854, 44907
-recovered pasa_asmbl_35221.p1, internal, 46006, 46107
Valid prediction for snap_scaffold_26-snap.155-T1
Couldn't classify 23219, 23284
Sorry, prediction pasa_asmbl_35875.p1 fails validation.
(GTG)	 GG	23219-23284	GT	AGG
(GGG)	 AG	23620-24216	TG	GAT
-recovered pasa_asmbl_35875.p1, terminal, 23620, 24216
Valid prediction for snap_scaffold_26-snap.164-T1
Valid prediction for pasa_asmbl_35879.p1
Valid prediction for snap_scaffold_26-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_56356-T1
Valid prediction for Augustus_model.g37557.t1
Valid prediction for GeneMark_model.98055_t
Valid prediction for GlimmerHMM_glimmerT_56355-T1
Couldn't classify 15203, 15353
Couldn't classify 15558, 15751
Sorry, prediction pasa_asmbl_35219.p1 fails validation.
(GAG)	 AG	15203-15353	GT	AGG
(GTA)	 AG	15558-15751	CC	GCC
-recovered pasa_asmbl_35219.p1, internal, 15203, 15353
Valid prediction for GlimmerHMM_glimmerT_56344-T1
Valid prediction for Augustus_model.g37554.t1
Valid prediction for Augustus_model.g37549.t1
Valid prediction for GeneMark_model.98075_t
Valid prediction for HiQ_model.g37558.t1
Valid prediction for GeneMark_model.98060_t
Valid prediction for GeneMark_model.98068_t
Valid prediction for snap_scaffold_26-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_56338-T1
Valid prediction for snap_scaffold_26-snap.181-T1
Couldn't classify 92104, 92290
Sorry, prediction pasa_asmbl_35226.p1 fails validation.
(ATG)	 AG	88208-88255	GT	AGG
(TTC)	 AG	90589-90775	GT	AGG
(GAG)	 AG	91123-91199	GT	AGG
(ACC)	 AG	91707-91750	GT	AGG
(GAA)	 AG	92104-92290	GT	CTG
-recovered pasa_asmbl_35226.p1, initial, 88208, 88255
add_exon() Sorry, pasa_asmbl_35226.p1 90589-90775-terminal-3 is invalid.
-recovered pasa_asmbl_35226.p1, terminal, 90589, 90775
-recovered pasa_asmbl_35226.p1, internal, 88208, 88255
-recovered pasa_asmbl_35226.p1, internal, 90589, 90775
-recovered pasa_asmbl_35226.p1, internal, 91123, 91199
-recovered pasa_asmbl_35226.p1, internal, 91707, 91750
-recovered pasa_asmbl_35226.p1, internal, 92104, 92290
Valid prediction for snap_scaffold_26-snap.162-T1
Valid prediction for GeneMark_model.98098_t

-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 GeneMark_model.98066_t
Valid prediction for snap_scaffold_26-snap.157-T1
Valid prediction for snap_scaffold_26-snap.160-T1
Valid prediction for snap_scaffold_26-snap.163-T1
Valid prediction for GeneMark_model.98082_t
Valid prediction for snap_scaffold_26-snap.184-T1
Valid prediction for GeneMark_model.98092_t
Valid prediction for GeneMark_model.98067_t
Valid prediction for GlimmerHMM_glimmerT_56346-T1
Valid prediction for GlimmerHMM_glimmerT_56345-T1
Valid prediction for GeneMark_model.98058_t
Valid prediction for snap_scaffold_26-snap.167-T1
Valid prediction for snap_scaffold_26-snap.171-T1
Valid prediction for GeneMark_model.98070_t
Valid prediction for GeneMark_model.98091_t
Valid prediction for Augustus_model.g37556.t1
Valid prediction for GeneMark_model.98080_t
Valid prediction for GeneMark_model.98072_t
Valid prediction for snap_scaffold_26-snap.182-T1
Valid prediction for GeneMark_model.98097_t
Valid prediction for GeneMark_model.98084_t
Valid prediction for GeneMark_model.98085_t
Valid prediction for GeneMark_model.98095_t
Valid prediction for snap_scaffold_26-snap.183-T1
Valid prediction for GeneMark_model.98076_t
Valid prediction for GlimmerHMM_glimmerT_56351-T1
Valid prediction for GeneMark_model.98089_t
Valid prediction for GeneMark_model.98056_t
Valid prediction for GeneMark_model.98048_t
Valid prediction for snap_scaffold_26-snap.177-T1
Valid prediction for GeneMark_model.98062_t
Valid prediction for snap_scaffold_26-snap.170-T1
Valid prediction for GeneMark_model.98074_t
Valid prediction for snap_scaffold_26-snap.149-T1
Valid prediction for Augustus_model.g37548.t1
Valid prediction for Augustus_model.g37559.t1
Couldn't classify 107814, 108038
Couldn't classify 108772, 108921
Sorry, prediction pasa_asmbl_35123.p1 fails validation.
(GTT)	 GA	107814-108038	GT	AGG
(GAT)	 AG	108772-108921	GG	CAG
Valid prediction for snap_scaffold_26-snap.173-T1
Valid prediction for GeneMark_model.98064_t
Valid prediction for GlimmerHMM_glimmerT_56340-T1
Valid prediction for GeneMark_model.98087_t
Valid prediction for snap_scaffold_26-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_56350-T1
Valid prediction for snap_scaffold_26-snap.159-T1
Valid prediction for snap_scaffold_26-snap.146-T1
Valid prediction for GeneMark_model.98051_t
Valid prediction for GlimmerHMM_glimmerT_56336-T1
Valid prediction for snap_scaffold_26-snap.165-T1
Valid prediction for GeneMark_model.98050_t
Valid prediction for snap_scaffold_26-snap.156-T1
Valid prediction for GeneMark_model.98099_t
Valid prediction for GlimmerHMM_glimmerT_56354-T1
Valid prediction for snap_scaffold_26-snap.153-T1
Valid prediction for snap_scaffold_26-snap.174-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21456, rend_intergenic: 16293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23863, rend_intergenic: 21564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35002, rend_intergenic: 31348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38607, rend_intergenic: 37816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39207, rend_intergenic: 38628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52224, rend_intergenic: 46304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57283, rend_intergenic: 53319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63814, rend_intergenic: 61474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71301, rend_intergenic: 68314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87727, rend_intergenic: 83502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94147, rend_intergenic: 89988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107898, rend_intergenic: 99219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118223, rend_intergenic: 110120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126657, rend_intergenic: 118241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137223, rend_intergenic: 128434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145554, rend_intergenic: 143006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178963, rend_intergenic: 160915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179996
-exon list size: 705


building trellis

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76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 21456, rend_intergenic: 16293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23863, rend_intergenic: 21564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35002, rend_intergenic: 31348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38607, rend_intergenic: 37816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39207, rend_intergenic: 38628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52224, rend_intergenic: 46304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57283, rend_intergenic: 53319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63814, rend_intergenic: 61474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71301, rend_intergenic: 68314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87727, rend_intergenic: 83502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94147, rend_intergenic: 89988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107898, rend_intergenic: 99219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118223, rend_intergenic: 110120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126657, rend_intergenic: 118241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137223, rend_intergenic: 128434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145554, rend_intergenic: 143006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178963, rend_intergenic: 160915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support