-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_7714053-7923130

-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_3-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_6864-T1
Valid prediction for snap_scaffold_3-snap.1592-T1
Valid prediction for HiQ_model.g4478.t1
Valid prediction for snap_scaffold_3-snap.1579-T1
Valid prediction for snap_scaffold_3-snap.1584-T1
Valid prediction for GlimmerHMM_glimmerT_6890-T1
Couldn't classify 2362, 2678
Couldn't classify 2992, 3071
Sorry, prediction pasa_asmbl_40172.p1 fails validation.
(ACA)	 TA	2362-2678	GT	AAG
(GTA)	 AG	2759-2883	GT	GGG
(GTT)	 AG	2992-3071	GG	AAG
-recovered pasa_asmbl_40172.p1, internal, 2759, 2883
Valid prediction for GlimmerHMM_glimmerT_6886-T1
Valid prediction for snap_scaffold_3-snap.1594-T1
Valid prediction for snap_scaffold_3-snap.1588-T1
Valid prediction for Augustus_model.g4480.t1
Couldn't classify 3443, 3625
Sorry, prediction pasa_asmbl_40173.p1 fails validation.
(CGT)	 CC	3443-3625	GT	TGG
(GCT)	 AG	3737-3814	GT	AGG
(ATA)	 AG	3908-4053	GT	AGG
(GTG)	 AG	4198-4996	GT	AGG
-recovered pasa_asmbl_40173.p1, terminal, 4198, 4996
-recovered pasa_asmbl_40173.p1, internal, 3737, 3814
-recovered pasa_asmbl_40173.p1, internal, 3908, 4053
-recovered pasa_asmbl_40173.p1, internal, 4198, 4996
Valid prediction for GlimmerHMM_glimmerT_6872-T1
Valid prediction for snap_scaffold_3-snap.1603-T1
Valid prediction for Augustus_model.g4490.t1
Valid prediction for GlimmerHMM_glimmerT_6870-T1
Valid prediction for CodingQuarry_transcript_46215-T1
Valid prediction for snap_scaffold_3-snap.1599-T1
Valid prediction for snap_scaffold_3-snap.1604-T1
Valid prediction for snap_scaffold_3-snap.1582-T1
Valid prediction for Augustus_model.g4489.t1
Valid prediction for snap_scaffold_3-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_6885-T1
Valid prediction for snap_scaffold_3-snap.1590-T1
Valid prediction for snap_scaffold_3-snap.1600-T1
Valid prediction for Augustus_model.g4473.t1
Valid prediction for snap_scaffold_3-snap.1586-T1
Valid prediction for snap_scaffold_3-snap.1610-T1
Valid prediction for snap_scaffold_3-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_6869-T1
Valid prediction for GlimmerHMM_glimmerT_6878-T1
Valid prediction for snap_scaffold_3-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_6862-T1
Couldn't classify 11799, 11844
Sorry, prediction pasa_asmbl_40176.p1 fails validation.
(TGT)	 CC	11799-11844	GT	AGG
(TGT)	 AG	11933-12166	GT	GGG
(GTG)	 AG	12260-12496	GT	AGG
(GCC)	 AG	12596-12693	GT	AGG
(ATG)	 AG	12783-12970	GT	AGG
(ATA)	 AG	13054-13189	GT	CGG
(ATG)	 AG	13285-13458	CA	AAC
-recovered pasa_asmbl_40176.p1, initial, 12783, 12970
-recovered pasa_asmbl_40176.p1, terminal, 13285, 13458
-recovered pasa_asmbl_40176.p1, internal, 11933, 12166
-recovered pasa_asmbl_40176.p1, internal, 12260, 12496
-recovered pasa_asmbl_40176.p1, internal, 12596, 12693
-recovered pasa_asmbl_40176.p1, internal, 12783, 12970
-recovered pasa_asmbl_40176.p1, internal, 13054, 13189
Valid prediction for Augustus_model.g4487.t1
Valid prediction for snap_scaffold_3-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_6879-T1
Valid prediction for CodingQuarry_transcript_46219-T1
Valid prediction for pasa_asmbl_40179.p1
Valid prediction for GlimmerHMM_glimmerT_6861-T1
Valid prediction for snap_scaffold_3-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_6871-T1
Valid prediction for Augustus_model.g4481.t1
Valid prediction for snap_scaffold_3-snap.1575-T1
Valid prediction for HiQ_model.g4493.t1
Valid prediction for pasa_asmbl_40875.p1
Valid prediction for Augustus_model.g4479.t1
Valid prediction for GlimmerHMM_glimmerT_6882-T1
Valid prediction for snap_scaffold_3-snap.1601-T1
Valid prediction for snap_scaffold_3-snap.1596-T1
Couldn't classify 186647, 186800
Couldn't classify 187280, 187485
Sorry, prediction pasa_asmbl_40836.p1 fails validation.
(GTG)	 GG	186647-186800	GT	CGG
(ACC)	 AG	187280-187485	GA	GGG
Valid prediction for GlimmerHMM_glimmerT_6873-T1
Valid prediction for CodingQuarry_transcript_46216-T1
Couldn't classify 188702, 188721
Sorry, prediction pasa_asmbl_40182.p1 fails validation.
(CCT)	 CT	188702-188721	GT	AGG
(TGA)	 AG	188799-188877	GT	AGG
(GAT)	 AG	189035-189241	TC	GAT
-recovered pasa_asmbl_40182.p1, terminal, 189035, 189241
-recovered pasa_asmbl_40182.p1, internal, 188799, 188877
Valid prediction for snap_scaffold_3-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_6887-T1
Valid prediction for snap_scaffold_3-snap.1608-T1
Valid prediction for Augustus_model.g4475.t1
Valid prediction for snap_scaffold_3-snap.1613-T1
Valid prediction for GlimmerHMM_glimmerT_6866-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_3-snap.1576-T1
Valid prediction for Augustus_model.g4477.t1
Valid prediction for GlimmerHMM_glimmerT_6876-T1
Valid prediction for GlimmerHMM_glimmerT_6888-T1
Valid prediction for GlimmerHMM_glimmerT_6874-T1
Valid prediction for snap_scaffold_3-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_6865-T1
Valid prediction for snap_scaffold_3-snap.1607-T1
Valid prediction for snap_scaffold_3-snap.1587-T1
Valid prediction for snap_scaffold_3-snap.1611-T1
Valid prediction for snap_scaffold_3-snap.1614-T1
Valid prediction for GlimmerHMM_glimmerT_6863-T1
Valid prediction for GlimmerHMM_glimmerT_6868-T1
Couldn't classify 63840, 63923
Couldn't classify 67264, 67319
Sorry, prediction pasa_asmbl_38993.p1 fails validation.
(ACG)	 AC	63840-63923	GT	AGG
(AGT)	 AG	65474-65677	GT	CGG
(ATG)	 AG	66789-66864	GT	AGG
(GGA)	 AG	67264-67319	CG	GAC
-recovered pasa_asmbl_38993.p1, initial, 66789, 66864
-recovered pasa_asmbl_38993.p1, internal, 65474, 65677
-recovered pasa_asmbl_38993.p1, internal, 66789, 66864
Valid prediction for GlimmerHMM_glimmerT_6881-T1
Valid prediction for HiQ_model.g4491.t1
Couldn't classify 634, 749
Sorry, prediction pasa_asmbl_38999.p1 fails validation.
(CAG)	 AT	634-749	GT	AGG
(GTA)	 AG	2584-2736	GT	GGG
(GTT)	 AG	3403-3595	GT	AGG
(GCG)	 AG	3800-3901	GT	CTG
(ATC)	 AG	4132-4299	TG	AGT
-recovered pasa_asmbl_38999.p1, terminal, 4132, 4299
-recovered pasa_asmbl_38999.p1, internal, 2584, 2736
-recovered pasa_asmbl_38999.p1, internal, 3403, 3595
-recovered pasa_asmbl_38999.p1, internal, 3800, 3901
Valid prediction for Augustus_model.g4484.t1
Valid prediction for snap_scaffold_3-snap.1605-T1
Valid prediction for CodingQuarry_transcript_46214-T1
Valid prediction for CodingQuarry_transcript_46217-T1
Valid prediction for snap_scaffold_3-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_6875-T1
Valid prediction for GlimmerHMM_glimmerT_6891-T1
Valid prediction for snap_scaffold_3-snap.1602-T1
Valid prediction for HiQ_model.g4474.t1
Valid prediction for Augustus_model.g4482.t1
Valid prediction for snap_scaffold_3-snap.1593-T1
Valid prediction for snap_scaffold_3-snap.1609-T1
Valid prediction for Augustus_model.g4485.t1
Couldn't classify 60117, 60446
Sorry, prediction pasa_asmbl_39766.p1 fails validation.
(ATG)	 GC	60117-60446	AC	ACA
Valid prediction for HiQ_model.g4494.t1
Valid prediction for GlimmerHMM_glimmerT_6884-T1
Valid prediction for pasa_asmbl_38995.p1
Valid prediction for HiQ_model.g4492.t1
Valid prediction for pasa_asmbl_38994.p1
Valid prediction for snap_scaffold_3-snap.1583-T1
Valid prediction for CodingQuarry_transcript_46218-T1
Valid prediction for snap_scaffold_3-snap.1581-T1
Couldn't classify 190868, 191295
Couldn't classify 191401, 191587
Sorry, prediction pasa_asmbl_38988.p1 fails validation.
(TGC)	 GC	190868-191295	GT	AAG
(AGA)	 AG	191401-191587	AC	GCA
Valid prediction for snap_scaffold_3-snap.1595-T1
Valid prediction for GlimmerHMM_glimmerT_6883-T1
Valid prediction for HiQ_model.g4483.t1
Valid prediction for GlimmerHMM_glimmerT_6889-T1
Couldn't classify 94615, 94767
Sorry, prediction pasa_asmbl_38989.p1 fails validation.
(GAG)	 GG	94615-94767	GT	CGG
(ATC)	 AG	94925-94987	GT	TGG
(ACG)	 AG	95292-95411	GT	AGG
(GAG)	 AG	95737-95824	GT	AGG
(ATG)	 AG	95944-96072	GT	TGG
(AGC)	 AG	96255-96397	GT	AGG
(AAT)	 AG	96851-96965	GT	TGG
(AGG)	 AG	97214-97283	GT	AGG
(CTC)	 AG	97769-97913	GT	CAG
(TGT)	 AG	98677-98899	GT	GGG
(ATG)	 AG	99524-99612	GT	AGG
(AGC)	 AG	100905-100946	GT	GGG
(CAA)	 AG	101090-101247	GT	AGG
(ACG)	 AG	101694-101758	GT	TGG
(GTT)	 AG	101991-102124	GT	AGG
(CTG)	 AG	102318-102749	TG	GAT
-recovered pasa_asmbl_38989.p1, initial, 95944, 96072
add_exon() Sorry, pasa_asmbl_38989.p1 99524-99612-initial-1 is invalid.
-recovered pasa_asmbl_38989.p1, initial, 99524, 99612
-recovered pasa_asmbl_38989.p1, terminal, 102318, 102749
-recovered pasa_asmbl_38989.p1, internal, 94925, 94987
-recovered pasa_asmbl_38989.p1, internal, 95292, 95411
-recovered pasa_asmbl_38989.p1, internal, 95737, 95824
-recovered pasa_asmbl_38989.p1, internal, 95944, 96072
-recovered pasa_asmbl_38989.p1, internal, 96255, 96397
-recovered pasa_asmbl_38989.p1, internal, 96851, 96965
-recovered pasa_asmbl_38989.p1, internal, 97214, 97283
-recovered pasa_asmbl_38989.p1, internal, 97769, 97913
-recovered pasa_asmbl_38989.p1, internal, 98677, 98899
-recovered pasa_asmbl_38989.p1, internal, 99524, 99612
-recovered pasa_asmbl_38989.p1, internal, 100905, 100946
-recovered pasa_asmbl_38989.p1, internal, 101090, 101247
-recovered pasa_asmbl_38989.p1, internal, 101694, 101758
-recovered pasa_asmbl_38989.p1, internal, 101991, 102124
Valid prediction for Augustus_model.g4486.t1
Valid prediction for CodingQuarry_transcript_46213-T1
Valid prediction for GlimmerHMM_glimmerT_6880-T1
Valid prediction for pasa_asmbl_38985.p1
Valid prediction for snap_scaffold_3-snap.1612-T1
Valid prediction for Augustus_model.g4488.t1
Valid prediction for Augustus_model.g4476.t1
Valid prediction for GlimmerHMM_glimmerT_6867-T1
Valid prediction for GlimmerHMM_glimmerT_6877-T1
Valid prediction for snap_scaffold_3-snap.1585-T1
Valid prediction for snap_scaffold_3-snap.1577-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14003, rend_intergenic: 11195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57696, rend_intergenic: 52121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65744, rend_intergenic: 58374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71548, rend_intergenic: 68047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76995, rend_intergenic: 75580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78179, rend_intergenic: 77956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116872, rend_intergenic: 115311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124147, rend_intergenic: 117961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135670, rend_intergenic: 133343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145363, rend_intergenic: 141420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156524, rend_intergenic: 145758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157004, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166643, rend_intergenic: 160955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172674, rend_intergenic: 168590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209078
-exon list size: 407


building trellis

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98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14003, rend_intergenic: 11195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57696, rend_intergenic: 52121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65744, rend_intergenic: 58374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71548, rend_intergenic: 68047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76995, rend_intergenic: 75580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78179, rend_intergenic: 77956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116872, rend_intergenic: 115311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124147, rend_intergenic: 117961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135670, rend_intergenic: 133343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145363, rend_intergenic: 141420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156524, rend_intergenic: 145758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157004, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166643, rend_intergenic: 160955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172674, rend_intergenic: 168590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support