-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_6311250-6562272

-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_11-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_27837-T1
Valid prediction for GlimmerHMM_glimmerT_27814-T1
Valid prediction for snap_scaffold_11-snap.1508-T1
Valid prediction for snap_scaffold_11-snap.1548-T1
Valid prediction for snap_scaffold_11-snap.1547-T1
Valid prediction for GeneMark_model.48086_t
Valid prediction for snap_scaffold_11-snap.1545-T1
Valid prediction for Augustus_model.g18567.t1
Valid prediction for GlimmerHMM_glimmerT_27835-T1
Valid prediction for GeneMark_model.48085_t
Valid prediction for snap_scaffold_11-snap.1514-T1
Valid prediction for snap_scaffold_11-snap.1543-T1
Valid prediction for snap_scaffold_11-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_27842-T1
Valid prediction for GeneMark_model.48078_t
Valid prediction for GlimmerHMM_glimmerT_27826-T1
Valid prediction for snap_scaffold_11-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_27825-T1
Valid prediction for GlimmerHMM_glimmerT_27817-T1
Valid prediction for snap_scaffold_11-snap.1517-T1
Valid prediction for snap_scaffold_11-snap.1540-T1
Valid prediction for snap_scaffold_11-snap.1521-T1
Valid prediction for snap_scaffold_11-snap.1513-T1
Valid prediction for Augustus_model.g18564.t1
Valid prediction for GeneMark_model.48090_t
Valid prediction for GlimmerHMM_glimmerT_27836-T1
Valid prediction for pasa_asmbl_5593.p1
Valid prediction for GlimmerHMM_glimmerT_27824-T1
Valid prediction for snap_scaffold_11-snap.1533-T1
Valid prediction for snap_scaffold_11-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_27831-T1
Valid prediction for HiQ_model.g18551.t1
Valid prediction for GlimmerHMM_glimmerT_27828-T1
Valid prediction for HiQ_model.g18560.t1
Valid prediction for snap_scaffold_11-snap.1522-T1
Valid prediction for snap_scaffold_11-snap.1524-T1
Valid prediction for snap_scaffold_11-snap.1520-T1
Valid prediction for Augustus_model.g18561.t1
Valid prediction for snap_scaffold_11-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_27841-T1
Valid prediction for GlimmerHMM_glimmerT_27815-T1
Valid prediction for Augustus_model.g18557.t1
Valid prediction for GeneMark_model.48096_t
Valid prediction for GeneMark_model.48089_t
Couldn't classify 4188, 4896
Sorry, prediction pasa_asmbl_5591.p1 fails validation.
(GAT)	 GT	4188-4896	GC	AGG
(GGG)	 AG	4999-5166	GT	AGG
(AGC)	 AG	5435-5518	GT	CGG
(GCA)	 AG	5629-5712	GT	AGG
(GTG)	 AG	5835-5916	GT	AGG
(AGG)	 AG	6069-6957	GA	GAG
-recovered pasa_asmbl_5591.p1, terminal, 6069, 6957
-recovered pasa_asmbl_5591.p1, internal, 4999, 5166
-recovered pasa_asmbl_5591.p1, internal, 5435, 5518
-recovered pasa_asmbl_5591.p1, internal, 5629, 5712
-recovered pasa_asmbl_5591.p1, internal, 5835, 5916
Valid prediction for snap_scaffold_11-snap.1544-T1
Valid prediction for snap_scaffold_11-snap.1537-T1
Valid prediction for snap_scaffold_11-snap.1531-T1
Valid prediction for Augustus_model.g18562.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.g18563.t1
Valid prediction for GeneMark_model.48079_t
Valid prediction for CodingQuarry_transcript_8062-T1
Valid prediction for GeneMark_model.48084_t
Valid prediction for GlimmerHMM_glimmerT_27829-T1
Valid prediction for snap_scaffold_11-snap.1546-T1
Valid prediction for GeneMark_model.48080_t
Valid prediction for Augustus_model.g18559.t1
Valid prediction for GlimmerHMM_glimmerT_27833-T1
Valid prediction for GlimmerHMM_glimmerT_27830-T1
Valid prediction for GlimmerHMM_glimmerT_27813-T1
Valid prediction for Augustus_model.g18566.t1
Valid prediction for snap_scaffold_11-snap.1539-T1
Valid prediction for snap_scaffold_11-snap.1532-T1
Valid prediction for snap_scaffold_11-snap.1519-T1
Valid prediction for snap_scaffold_11-snap.1526-T1
Valid prediction for GeneMark_model.48087_t
Valid prediction for GeneMark_model.48082_t
Valid prediction for GeneMark_model.48081_t
Valid prediction for snap_scaffold_11-snap.1525-T1
Valid prediction for GeneMark_model.48094_t
Valid prediction for snap_scaffold_11-snap.1542-T1
Valid prediction for GeneMark_model.48092_t
Valid prediction for snap_scaffold_11-snap.1515-T1
Couldn't classify 34035, 34101
Sorry, prediction pasa_asmbl_6693.p1 fails validation.
(CTG)	 AC	34035-34101	GT	AAG
(ATC)	 AG	34426-34573	GT	AGG
(GAA)	 AG	34781-34952	GT	AGG
(AGA)	 AG	35215-35319	GT	AGG
(CGA)	 AG	35430-35480	GT	GGG
(AAA)	 AG	35601-35790	GT	AGG
(AGA)	 AG	35898-35908	CC	GAC
-recovered pasa_asmbl_6693.p1, terminal, 35898, 35908
-recovered pasa_asmbl_6693.p1, internal, 34426, 34573
-recovered pasa_asmbl_6693.p1, internal, 34781, 34952
-recovered pasa_asmbl_6693.p1, internal, 35215, 35319
-recovered pasa_asmbl_6693.p1, internal, 35430, 35480
-recovered pasa_asmbl_6693.p1, internal, 35601, 35790
Valid prediction for pasa_asmbl_6694.p1
Valid prediction for GeneMark_model.48095_t
Valid prediction for Augustus_model.g18552.t1
Valid prediction for snap_scaffold_11-snap.1507-T1
Valid prediction for GlimmerHMM_glimmerT_27819-T1
Valid prediction for GeneMark_model.48093_t
Valid prediction for GlimmerHMM_glimmerT_27832-T1
Valid prediction for GlimmerHMM_glimmerT_27834-T1
Valid prediction for Augustus_model.g18555.t1
Valid prediction for pasa_asmbl_6682.p1
Valid prediction for GlimmerHMM_glimmerT_27821-T1
Valid prediction for snap_scaffold_11-snap.1527-T1
Valid prediction for GeneMark_model.48083_t
Valid prediction for GlimmerHMM_glimmerT_27840-T1
Couldn't classify 48597, 48626
Sorry, prediction pasa_asmbl_6691.p1 fails validation.
(ATG)	 GG	46792-46890	GT	AGG
(GAG)	 AG	46981-47099	GT	GTG
(GCT)	 AG	47533-47663	GT	CGG
(GTG)	 AG	47781-47921	GT	AGG
(TGG)	 AG	48194-48378	GT	TCG
(GAG)	 AG	48597-48626	TA	GAT
-recovered pasa_asmbl_6691.p1, initial, 46792, 46890
-recovered pasa_asmbl_6691.p1, internal, 46981, 47099
-recovered pasa_asmbl_6691.p1, internal, 47533, 47663
-recovered pasa_asmbl_6691.p1, internal, 47781, 47921
-recovered pasa_asmbl_6691.p1, internal, 48194, 48378
Couldn't classify 150377, 150433
Couldn't classify 151639, 151821
Sorry, prediction pasa_asmbl_6688.p1 fails validation.
(CTG)	 CC	150377-150433	GT	AGG
(GAG)	 AG	150742-150929	GT	AGG
(GAT)	 AG	151289-151439	GT	AGG
(GCT)	 AG	151639-151821	GT	AGG
add_exon() Sorry, pasa_asmbl_6688.p1 150742-150929-terminal-2 is invalid.
-recovered pasa_asmbl_6688.p1, terminal, 150742, 150929
-recovered pasa_asmbl_6688.p1, internal, 150742, 150929
-recovered pasa_asmbl_6688.p1, internal, 151289, 151439
-recovered pasa_asmbl_6688.p1, internal, 151639, 151821
Valid prediction for Augustus_model.g18554.t1
Valid prediction for snap_scaffold_11-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_27820-T1
Valid prediction for snap_scaffold_11-snap.1516-T1
Valid prediction for snap_scaffold_11-snap.1538-T1
Valid prediction for GeneMark_model.48091_t
Couldn't classify 190184, 190732
Sorry, prediction pasa_asmbl_6680.p1 fails validation.
(TTA)	 AT	190184-190732	GC	AGG
Valid prediction for GlimmerHMM_glimmerT_27818-T1
Valid prediction for GlimmerHMM_glimmerT_27823-T1
Valid prediction for snap_scaffold_11-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_27838-T1
Valid prediction for GlimmerHMM_glimmerT_27839-T1
Valid prediction for snap_scaffold_11-snap.1510-T1
Valid prediction for GeneMark_model.48088_t
Couldn't classify 42530, 43050
Couldn't classify 46358, 46397
Sorry, prediction pasa_asmbl_6692.p1 fails validation.
(ATC)	 CA	42530-43050	GT	AGG
(TGT)	 AG	43647-43783	GT	AGG
(GGG)	 AG	43866-44052	GT	AGG
(TCA)	 AG	44149-44341	GT	AGG
(ATC)	 AG	44445-44540	GT	AGG
(CTA)	 AG	44678-44863	GT	ACG
(GTG)	 AG	45122-45274	GT	AGG
(GCC)	 AG	45657-45789	GT	CGG
(TGT)	 AG	45889-46012	GT	AGG
(AAT)	 AG	46358-46397	GT	AGG
add_exon() Sorry, pasa_asmbl_6692.p1 45889-46012-terminal-3 is invalid.
-recovered pasa_asmbl_6692.p1, terminal, 45889, 46012
-recovered pasa_asmbl_6692.p1, internal, 43647, 43783
-recovered pasa_asmbl_6692.p1, internal, 43866, 44052
-recovered pasa_asmbl_6692.p1, internal, 44149, 44341
-recovered pasa_asmbl_6692.p1, internal, 44445, 44540
-recovered pasa_asmbl_6692.p1, internal, 44678, 44863
-recovered pasa_asmbl_6692.p1, internal, 45122, 45274
-recovered pasa_asmbl_6692.p1, internal, 45657, 45789
-recovered pasa_asmbl_6692.p1, internal, 45889, 46012
-recovered pasa_asmbl_6692.p1, internal, 46358, 46397
Valid prediction for HiQ_model.g18558.t1
Couldn't classify 50971, 51152
Sorry, prediction pasa_asmbl_6690.p1 fails validation.
(GCT)	 CT	50971-51152	GT	AGG
(AAC)	 AG	51254-51419	AC	AGA
-recovered pasa_asmbl_6690.p1, terminal, 51254, 51419
Valid prediction for snap_scaffold_11-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_27816-T1
Valid prediction for snap_scaffold_11-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_27827-T1
Valid prediction for GlimmerHMM_glimmerT_27822-T1
Valid prediction for Augustus_model.g18556.t1
Valid prediction for Augustus_model.g18565.t1
Valid prediction for CodingQuarry_transcript_8065-T1
Valid prediction for snap_scaffold_11-snap.1536-T1
Couldn't classify 116436, 117344
Sorry, prediction pasa_asmbl_5592.p1 fails validation.
(TGG)	 GC	116436-117344	GG	GTG
Valid prediction for snap_scaffold_11-snap.1541-T1
Valid prediction for snap_scaffold_11-snap.1523-T1
Valid prediction for Augustus_model.g18553.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6957, rend_intergenic: 4323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135005, rend_intergenic: 125775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166299, rend_intergenic: 141309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191661, rend_intergenic: 188173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237116, rend_intergenic: 234584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237804, rend_intergenic: 237321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251023
-exon list size: 719


building trellis

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86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 6957, rend_intergenic: 4323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135005, rend_intergenic: 125775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166299, rend_intergenic: 141309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191661, rend_intergenic: 188173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237116, rend_intergenic: 234584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237804, rend_intergenic: 237321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support