-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_1699419-1883596

-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_38679-T1
Valid prediction for GeneMark_model.66134_t
Valid prediction for HiQ_model.g25958.t1
Valid prediction for Augustus_model.g25945.t1
Valid prediction for GlimmerHMM_glimmerT_38666-T1
Valid prediction for GeneMark_model.66132_t
Valid prediction for GeneMark_model.66155_t
Valid prediction for GeneMark_model.66120_t
Valid prediction for GeneMark_model.66150_t
Valid prediction for snap_scaffold_16-snap.270-T1
Valid prediction for GeneMark_model.66124_t
Valid prediction for HiQ_model.g25951.t1
Valid prediction for GlimmerHMM_glimmerT_38678-T1
Valid prediction for snap_scaffold_16-snap.267-T1
Valid prediction for GeneMark_model.66142_t
Couldn't classify 92774, 93175
Sorry, prediction pasa_asmbl_16883.p2 fails validation.
(ATG)	 TC	92774-93175	TG	CCT
Valid prediction for GlimmerHMM_glimmerT_38671-T1
Valid prediction for GeneMark_model.66126_t
Valid prediction for GlimmerHMM_glimmerT_38676-T1
Valid prediction for snap_scaffold_16-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_38665-T1
Valid prediction for GlimmerHMM_glimmerT_38681-T1
Valid prediction for snap_scaffold_16-snap.280-T1
Valid prediction for GeneMark_model.66138_t
Valid prediction for snap_scaffold_16-snap.262-T1
Valid prediction for Augustus_model.g25949.t1
Valid prediction for GeneMark_model.66141_t
Valid prediction for snap_scaffold_16-snap.268-T1
Valid prediction for GlimmerHMM_glimmerT_38684-T1
Valid prediction for snap_scaffold_16-snap.259-T1
Valid prediction for GeneMark_model.66127_t
Valid prediction for GeneMark_model.66118_t
Valid prediction for GlimmerHMM_glimmerT_38674-T1
Valid prediction for GeneMark_model.66112_t
Valid prediction for Augustus_model.g25948.t1
Valid prediction for snap_scaffold_16-snap.250-T1
Valid prediction for GeneMark_model.66122_t
Valid prediction for snap_scaffold_16-snap.271-T1
Valid prediction for GeneMark_model.66117_t
Valid prediction for Augustus_model.g25956.t1
Valid prediction for Augustus_model.g25946.t1
Valid prediction for snap_scaffold_16-snap.277-T1
Valid prediction for GeneMark_model.66115_t
Valid prediction for GlimmerHMM_glimmerT_38669-T1
Valid prediction for snap_scaffold_16-snap.266-T1
Valid prediction for GlimmerHMM_glimmerT_38680-T1
Valid prediction for Augustus_model.g25943.t1
Valid prediction for snap_scaffold_16-snap.255-T1
Couldn't classify 93260, 93916
Sorry, prediction pasa_asmbl_16884.p2 fails validation.
(CGA)	 GA	93260-93916	GA	GAG
Valid prediction for snap_scaffold_16-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_38668-T1
Valid prediction for Augustus_model.g25944.t1
Valid prediction for GlimmerHMM_glimmerT_38686-T1
Valid prediction for snap_scaffold_16-snap.254-T1
Valid prediction for snap_scaffold_16-snap.256-T1
Valid prediction for GeneMark_model.66131_t
Valid prediction for GeneMark_model.66136_t
Valid prediction for GeneMark_model.66153_t
Valid prediction for GeneMark_model.66152_t
Couldn't classify 76047, 76100
Sorry, prediction pasa_asmbl_16875.p1 fails validation.
(GGA)	 AA	76047-76100	GT	AGG
(GCG)	 AG	76970-77068	GT	AGG
(GAG)	 AG	77225-77336	GT	AGG
(AGG)	 AG	77475-77593	GT	ATG
(AGC)	 AG	77726-77796	GT	CAG
(GAT)	 AG	77950-78038	GT	ATG
(CGG)	 AG	78238-78273	GT	TGG
(TTC)	 AG	78393-78475	GT	AGG
(ATG)	 AG	78709-78874	GT	CGG
(GCA)	 AG	79474-79685	GT	AGG
(ACT)	 AG	80167-80210	GT	AGG
(GAA)	 AG	81599-81703	GT	AGG
(GTT)	 AG	81800-81866	GT	AGG
(GGA)	 AG	82053-82216	GT	GAG
(GGA)	 AG	82587-82749	GC	AGG
(ATC)	 AG	82848-82927	GT	TAG
(CTT)	 AG	83014-83101	GT	AGG
(CAA)	 AG	83242-83394	GT	AGG
(ACT)	 AG	83663-83906	GT	CTG
(TGG)	 AG	84237-84323	GT	AGG
(CTG)	 AG	84440-84488	GT	AAG
(GGA)	 AG	84857-85004	GT	AGG
(GTG)	 AG	85262-85372	GT	AGG
(GAG)	 AG	85497-85621	GT	AGG
(GCG)	 AG	85721-85933	GT	AGG
(GTC)	 AG	86158-86296	CA	GAC
-recovered pasa_asmbl_16875.p1, initial, 78709, 78874
-recovered pasa_asmbl_16875.p1, terminal, 86158, 86296
-recovered pasa_asmbl_16875.p1, internal, 76970, 77068
-recovered pasa_asmbl_16875.p1, internal, 77225, 77336
-recovered pasa_asmbl_16875.p1, internal, 77475, 77593
-recovered pasa_asmbl_16875.p1, internal, 77726, 77796
-recovered pasa_asmbl_16875.p1, internal, 77950, 78038
-recovered pasa_asmbl_16875.p1, internal, 78238, 78273
-recovered pasa_asmbl_16875.p1, internal, 78393, 78475
-recovered pasa_asmbl_16875.p1, internal, 78709, 78874
-recovered pasa_asmbl_16875.p1, internal, 79474, 79685
-recovered pasa_asmbl_16875.p1, internal, 80167, 80210
-recovered pasa_asmbl_16875.p1, internal, 81599, 81703
-recovered pasa_asmbl_16875.p1, internal, 81800, 81866
-recovered pasa_asmbl_16875.p1, internal, 82053, 82216
-recovered pasa_asmbl_16875.p1, internal, 82587, 82749
-recovered pasa_asmbl_16875.p1, internal, 82848, 82927
-recovered pasa_asmbl_16875.p1, internal, 83014, 83101
-recovered pasa_asmbl_16875.p1, internal, 83242, 83394
-recovered pasa_asmbl_16875.p1, internal, 83663, 83906
-recovered pasa_asmbl_16875.p1, internal, 84237, 84323
-recovered pasa_asmbl_16875.p1, internal, 84440, 84488
-recovered pasa_asmbl_16875.p1, internal, 84857, 85004
-recovered pasa_asmbl_16875.p1, internal, 85262, 85372
-recovered pasa_asmbl_16875.p1, internal, 85497, 85621
-recovered pasa_asmbl_16875.p1, internal, 85721, 85933
Valid prediction for GeneMark_model.66139_t
Couldn't classify 106373, 106508
Sorry, prediction pasa_asmbl_16887.p1 fails validation.
(ATG)	 CG	104442-104605	GT	AGG
(TCG)	 AG	104764-104809	GT	AGG
(AAA)	 AG	104898-104987	GT	AGG
(TTG)	 AG	105106-105215	GT	AGG
(AAA)	 AG	105338-105424	GT	AGG
(TCA)	 AG	105544-105628	GT	CAG
(GCC)	 AG	105860-105964	GT	CGG
(TGT)	 AG	106141-106268	GT	AAG
(GTA)	 AG	106373-106508	GT	AGG
-recovered pasa_asmbl_16887.p1, initial, 104442, 104605
-recovered pasa_asmbl_16887.p1, internal, 104764, 104809
-recovered pasa_asmbl_16887.p1, internal, 104898, 104987
-recovered pasa_asmbl_16887.p1, internal, 105106, 105215
-recovered pasa_asmbl_16887.p1, internal, 105338, 105424
-recovered pasa_asmbl_16887.p1, internal, 105544, 105628
-recovered pasa_asmbl_16887.p1, internal, 105860, 105964
-recovered pasa_asmbl_16887.p1, internal, 106141, 106268
-recovered pasa_asmbl_16887.p1, internal, 106373, 106508
Couldn't classify 178680, 178775
Sorry, prediction pasa_asmbl_16891.p1 fails validation.
(ATG)	 AA	173704-173711	GT	GGG
(TGA)	 AG	175009-175030	GT	AGG
(AGG)	 AG	176524-176593	GT	TGG
(ACG)	 AG	177271-177443	GC	AGG
(GCC)	 AG	177693-177833	GT	AGG
(AGG)	 AG	178040-178204	GT	AAG
(ATC)	 AG	178680-178775	GC	CCG
-recovered pasa_asmbl_16891.p1, initial, 173704, 173711
-recovered pasa_asmbl_16891.p1, internal, 175009, 175030
-recovered pasa_asmbl_16891.p1, internal, 176524, 176593
-recovered pasa_asmbl_16891.p1, internal, 177271, 177443
-recovered pasa_asmbl_16891.p1, internal, 177693, 177833
-recovered pasa_asmbl_16891.p1, internal, 178040, 178204
-recovered pasa_asmbl_16891.p1, internal, 178680, 178775
Valid prediction for GeneMark_model.66145_t
Valid prediction for GlimmerHMM_glimmerT_38687-T1
Valid prediction for snap_scaffold_16-snap.274-T1
Valid prediction for pasa_asmbl_16877.p1
Valid prediction for snap_scaffold_16-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_38685-T1
Valid prediction for GlimmerHMM_glimmerT_38672-T1
Valid prediction for GeneMark_model.66151_t
Valid prediction for snap_scaffold_16-snap.257-T1
Valid prediction for GeneMark_model.66147_t
Valid prediction for snap_scaffold_16-snap.264-T1
Valid prediction for Augustus_model.g25953.t1
Valid prediction for HiQ_model.g25955.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 94804, 94892
Sorry, prediction pasa_asmbl_16123.p1 fails validation.
(GGT)	 AT	94804-94892	GT	AGG
(ACA)	 AG	95303-95388	GT	TGG
(ACG)	 AG	95515-95586	GT	GGG
(GGG)	 AG	95705-95859	GT	ATG
(GAG)	 AG	96043-96159	GT	AGG
(ATT)	 AG	96339-96448	GT	ATG
(GTA)	 AG	96647-96761	GA	GAG
-recovered pasa_asmbl_16123.p1, terminal, 96647, 96761
-recovered pasa_asmbl_16123.p1, internal, 95303, 95388
-recovered pasa_asmbl_16123.p1, internal, 95515, 95586
-recovered pasa_asmbl_16123.p1, internal, 95705, 95859
-recovered pasa_asmbl_16123.p1, internal, 96043, 96159
-recovered pasa_asmbl_16123.p1, internal, 96339, 96448
Valid prediction for GeneMark_model.66135_t
Valid prediction for snap_scaffold_16-snap.273-T1
Valid prediction for GeneMark_model.66116_t
Valid prediction for GeneMark_model.66137_t
Valid prediction for GlimmerHMM_glimmerT_38675-T1
Valid prediction for snap_scaffold_16-snap.263-T1
Valid prediction for snap_scaffold_16-snap.279-T1
Valid prediction for GeneMark_model.66148_t
Valid prediction for GlimmerHMM_glimmerT_38673-T1
Valid prediction for snap_scaffold_16-snap.275-T1
Valid prediction for Augustus_model.g25950.t1
Couldn't classify 86327, 86424
Sorry, prediction pasa_asmbl_16125.p1 fails validation.
(ATG)	 GC	80011-80276	GT	AGG
(CGC)	 AG	80358-80457	GT	AGG
(GTT)	 AG	81479-81604	GT	AGG
(GGG)	 AG	81815-81976	GT	AGG
(GTG)	 AG	82345-82509	GT	AGG
(GCA)	 AG	82612-82753	GT	AGG
(GTG)	 AG	82950-83071	GC	AGG
(GGG)	 AG	83369-83475	GT	AGG
(TCT)	 AG	83663-83777	GT	AGG
(GAA)	 AG	83958-84035	GT	AGG
(GGG)	 AG	84807-84945	GT	TGG
(ACA)	 AG	85230-85337	GT	CGG
(AGC)	 AG	86327-86424	GG	GCG
-recovered pasa_asmbl_16125.p1, initial, 80011, 80276
-recovered pasa_asmbl_16125.p1, internal, 80358, 80457
-recovered pasa_asmbl_16125.p1, internal, 81479, 81604
-recovered pasa_asmbl_16125.p1, internal, 81815, 81976
-recovered pasa_asmbl_16125.p1, internal, 82345, 82509
-recovered pasa_asmbl_16125.p1, internal, 82612, 82753
-recovered pasa_asmbl_16125.p1, internal, 82950, 83071
-recovered pasa_asmbl_16125.p1, internal, 83369, 83475
-recovered pasa_asmbl_16125.p1, internal, 83663, 83777
-recovered pasa_asmbl_16125.p1, internal, 83958, 84035
-recovered pasa_asmbl_16125.p1, internal, 84807, 84945
-recovered pasa_asmbl_16125.p1, internal, 85230, 85337
Valid prediction for snap_scaffold_16-snap.260-T1
Valid prediction for Augustus_model.g25952.t1
Valid prediction for GeneMark_model.66143_t
Valid prediction for Augustus_model.g25957.t1
Valid prediction for GeneMark_model.66133_t
Valid prediction for snap_scaffold_16-snap.269-T1
Valid prediction for Augustus_model.g25947.t1
Valid prediction for GeneMark_model.66123_t
Valid prediction for GeneMark_model.66128_t
Valid prediction for GeneMark_model.66144_t
Valid prediction for CodingQuarry_transcript_19865-T1
Valid prediction for GeneMark_model.66125_t
Valid prediction for snap_scaffold_16-snap.258-T1
Valid prediction for snap_scaffold_16-snap.251-T1
Valid prediction for snap_scaffold_16-snap.265-T1
Valid prediction for GeneMark_model.66140_t
Valid prediction for GeneMark_model.66130_t
Valid prediction for snap_scaffold_16-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_38682-T1
Valid prediction for GeneMark_model.66119_t
Valid prediction for GeneMark_model.66146_t
Valid prediction for snap_scaffold_16-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_38677-T1
Valid prediction for GlimmerHMM_glimmerT_38670-T1
Valid prediction for snap_scaffold_16-snap.261-T1
Valid prediction for HiQ_model.g25954.t1
Couldn't classify 85230, 85230
Sorry, prediction CodingQuarry_transcript_19864-T1 fails validation.
(ATG)	 AG	84002-84035	GT	AGG
(GGG)	 AG	84807-84945	GT	TGG
(ACA)	 AG	85230-85230	CA	GAC
-recovered CodingQuarry_transcript_19864-T1, initial, 84002, 84035
-recovered CodingQuarry_transcript_19864-T1, internal, 84002, 84035
-recovered CodingQuarry_transcript_19864-T1, internal, 84807, 84945
Valid prediction for GeneMark_model.66149_t
Valid prediction for snap_scaffold_16-snap.276-T1
Valid prediction for GeneMark_model.66113_t
Valid prediction for GlimmerHMM_glimmerT_38667-T1
Valid prediction for GeneMark_model.66114_t
Valid prediction for GeneMark_model.66154_t
Valid prediction for GlimmerHMM_glimmerT_38683-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6016, rend_intergenic: 5263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9111, rend_intergenic: 6877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119495, rend_intergenic: 118500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122684, rend_intergenic: 119981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132806, rend_intergenic: 132477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137415, rend_intergenic: 132919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149404, rend_intergenic: 148564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163730, rend_intergenic: 149423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184178
-exon list size: 573


building trellis

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69.6    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 6016, rend_intergenic: 5263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9111, rend_intergenic: 6877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119495, rend_intergenic: 118500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122684, rend_intergenic: 119981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132806, rend_intergenic: 132477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137415, rend_intergenic: 132919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149404, rend_intergenic: 148564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163730, rend_intergenic: 149423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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