-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_2915329-3091951

-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 Augustus_model.g38707.t1
Valid prediction for snap_scaffold_28-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_58461-T1
Valid prediction for GlimmerHMM_glimmerT_58433-T1
Valid prediction for GlimmerHMM_glimmerT_58451-T1
Valid prediction for snap_scaffold_28-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_58449-T1
Valid prediction for snap_scaffold_28-snap.725-T1
Valid prediction for snap_scaffold_28-snap.729-T1
Valid prediction for snap_scaffold_28-snap.744-T1
Couldn't classify 171031, 171255
Couldn't classify 171426, 171521
Sorry, prediction pasa_asmbl_37857.p1 fails validation.
(GGC)	 CG	171031-171255	GT	AGG
(GCG)	 AG	171426-171521	GG	AGG
Valid prediction for pasa_asmbl_37423.p1
Valid prediction for pasa_asmbl_37432.p1
Valid prediction for snap_scaffold_28-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_58437-T1
Valid prediction for snap_scaffold_28-snap.743-T1
Valid prediction for snap_scaffold_28-snap.756-T1
Valid prediction for snap_scaffold_28-snap.728-T1
Valid prediction for HiQ_model.g38697.t1
Valid prediction for pasa_asmbl_37427.p1
Valid prediction for snap_scaffold_28-snap.738-T1
Valid prediction for Augustus_model.g38720.t1
Valid prediction for GlimmerHMM_glimmerT_58434-T1
Valid prediction for snap_scaffold_28-snap.749-T1
Valid prediction for CodingQuarry_transcript_43598-T1
Valid prediction for Augustus_model.g38708.t1
Valid prediction for CodingQuarry_transcript_43597-T1
Valid prediction for Augustus_model.g38719.t1
Valid prediction for GlimmerHMM_glimmerT_58446-T1
Valid prediction for snap_scaffold_28-snap.766-T1
Couldn't classify 147852, 148079
Sorry, prediction pasa_asmbl_37430.p1 fails validation.
(CCT)	 CC	147852-148079	GT	AGG
(ATG)	 AG	148277-148396	GT	AGG
(TGG)	 AG	148489-148608	GT	AGG
(AAG)	 AG	148819-148914	GT	CGG
(ATC)	 AG	149032-149166	GG	AAG
-recovered pasa_asmbl_37430.p1, initial, 148277, 148396
-recovered pasa_asmbl_37430.p1, terminal, 149032, 149166
-recovered pasa_asmbl_37430.p1, internal, 148277, 148396
-recovered pasa_asmbl_37430.p1, internal, 148489, 148608
-recovered pasa_asmbl_37430.p1, internal, 148819, 148914
Valid prediction for snap_scaffold_28-snap.732-T1
Valid prediction for Augustus_model.g38696.t1
Valid prediction for snap_scaffold_28-snap.762-T1
Valid prediction for HiQ_model.g38701.t1
Valid prediction for GlimmerHMM_glimmerT_58458-T1
Valid prediction for snap_scaffold_28-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_58462-T1
Couldn't classify 12497, 12591
Sorry, prediction pasa_asmbl_37425.p1 fails validation.
(TCA)	 CC	12497-12591	GT	AGG
(GGC)	 AG	13477-13615	GT	AGG
(GAA)	 AG	13952-14089	GG	AAG
-recovered pasa_asmbl_37425.p1, terminal, 13952, 14089
-recovered pasa_asmbl_37425.p1, internal, 13477, 13615
Valid prediction for GlimmerHMM_glimmerT_58448-T1
Valid prediction for Augustus_model.g38706.t1
Valid prediction for GlimmerHMM_glimmerT_58456-T1
Valid prediction for CodingQuarry_transcript_43588-T1
Valid prediction for GlimmerHMM_glimmerT_58465-T1
Valid prediction for Augustus_model.g38718.t1
Valid prediction for snap_scaffold_28-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_58450-T1
Valid prediction for snap_scaffold_28-snap.768-T1
Valid prediction for snap_scaffold_28-snap.737-T1
Valid prediction for CodingQuarry_transcript_43590-T1
Valid prediction for Augustus_model.g38709.t1
Valid prediction for snap_scaffold_28-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_58455-T1
Valid prediction for GlimmerHMM_glimmerT_58453-T1
Valid prediction for GlimmerHMM_glimmerT_58439-T1
Valid prediction for snap_scaffold_28-snap.759-T1
Valid prediction for snap_scaffold_28-snap.765-T1
Valid prediction for snap_scaffold_28-snap.740-T1
Valid prediction for Augustus_model.g38712.t1
Valid prediction for snap_scaffold_28-snap.747-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58464-T1
Valid prediction for HiQ_model.g38698.t1
Valid prediction for snap_scaffold_28-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_58432-T1
Valid prediction for CodingQuarry_transcript_43595-T1
Couldn't classify 172486, 172495
Sorry, prediction pasa_asmbl_37435.p1 fails validation.
(ACA)	 CC	172486-172495	GT	GGG
(GGT)	 AG	172710-172969	GT	AGG
(ATT)	 AG	173091-173175	GT	AGG
(AAC)	 AG	173298-173359	AA	AGA
-recovered pasa_asmbl_37435.p1, terminal, 173298, 173359
-recovered pasa_asmbl_37435.p1, internal, 172710, 172969
-recovered pasa_asmbl_37435.p1, internal, 173091, 173175
Valid prediction for snap_scaffold_28-snap.752-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_28-snap.767-T1
Valid prediction for snap_scaffold_28-snap.739-T1
Valid prediction for snap_scaffold_28-snap.736-T1
Valid prediction for pasa_asmbl_38115.p1
Valid prediction for snap_scaffold_28-snap.764-T1
Valid prediction for Augustus_model.g38715.t1
Valid prediction for Augustus_model.g38716.t1
Valid prediction for GlimmerHMM_glimmerT_58435-T1
Valid prediction for GlimmerHMM_glimmerT_58457-T1
Valid prediction for HiQ_model.g38702.t1
Valid prediction for GlimmerHMM_glimmerT_58436-T1
Valid prediction for Augustus_model.g38705.t1
Valid prediction for snap_scaffold_28-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_58454-T1
Couldn't classify 48749, 48865
Couldn't classify 50298, 50387
Sorry, prediction pasa_asmbl_38554.p1 fails validation.
(GGA)	 AG	48749-48865	GT	AGG
(GAC)	 AG	48982-49123	GT	TGG
(GCT)	 AG	49734-49840	GT	CGG
(AGT)	 AG	50298-50387	CA	CAC
-recovered pasa_asmbl_38554.p1, internal, 48749, 48865
-recovered pasa_asmbl_38554.p1, internal, 48982, 49123
-recovered pasa_asmbl_38554.p1, internal, 49734, 49840
Couldn't classify 153996, 154083
Sorry, prediction pasa_asmbl_38114.p1 fails validation.
(GCT)	 TG	153996-154083	GT	AGG
(GTG)	 AG	154824-154990	GT	AGG
(AGC)	 AG	155140-155268	GT	AGG
(GAA)	 AG	155426-155542	GT	AGG
(CTG)	 AG	155685-155832	GT	TGG
(CTC)	 AG	156259-156434	GT	CGG
(GGA)	 AG	156636-156765	GT	CGG
(GCC)	 AG	156936-157006	GT	AGG
(GTG)	 AG	157146-157300	GT	AGG
(GCG)	 AG	157583-157667	AG	GAA
-recovered pasa_asmbl_38114.p1, terminal, 157583, 157667
-recovered pasa_asmbl_38114.p1, internal, 154824, 154990
-recovered pasa_asmbl_38114.p1, internal, 155140, 155268
-recovered pasa_asmbl_38114.p1, internal, 155426, 155542
-recovered pasa_asmbl_38114.p1, internal, 155685, 155832
-recovered pasa_asmbl_38114.p1, internal, 156259, 156434
-recovered pasa_asmbl_38114.p1, internal, 156636, 156765
-recovered pasa_asmbl_38114.p1, internal, 156936, 157006
-recovered pasa_asmbl_38114.p1, internal, 157146, 157300
Valid prediction for snap_scaffold_28-snap.748-T1
Valid prediction for snap_scaffold_28-snap.745-T1
Couldn't classify 84587, 84704
Sorry, prediction pasa_asmbl_38542.p1 fails validation.
(ATG)	 TC	79461-79487	GT	AGG
(TTC)	 AG	80380-80479	GT	CGG
(GGG)	 AG	80614-80700	GT	AGG
(AGA)	 AG	82831-82954	GT	TGG
(CTT)	 AG	83673-83807	GT	GGG
(TTT)	 AG	84587-84704	GT	GGG
-recovered pasa_asmbl_38542.p1, initial, 79461, 79487
-recovered pasa_asmbl_38542.p1, internal, 80380, 80479
-recovered pasa_asmbl_38542.p1, internal, 80614, 80700
-recovered pasa_asmbl_38542.p1, internal, 82831, 82954
-recovered pasa_asmbl_38542.p1, internal, 83673, 83807
-recovered pasa_asmbl_38542.p1, internal, 84587, 84704
Valid prediction for snap_scaffold_28-snap.731-T1
Valid prediction for pasa_asmbl_38113.p1
Valid prediction for GlimmerHMM_glimmerT_58441-T1
Valid prediction for snap_scaffold_28-snap.727-T1
Valid prediction for Augustus_model.g38711.t1
Valid prediction for CodingQuarry_transcript_43591-T1
Valid prediction for Augustus_model.g38713.t1
Valid prediction for CodingQuarry_transcript_43593-T1
Valid prediction for GlimmerHMM_glimmerT_58440-T1
Valid prediction for CodingQuarry_transcript_43589-T1
Valid prediction for snap_scaffold_28-snap.730-T1
Valid prediction for Augustus_model.g38717.t1
Valid prediction for GlimmerHMM_glimmerT_58452-T1
Couldn't classify 140772, 140819
Sorry, prediction pasa_asmbl_38559.p1 fails validation.
(TAC)	 TC	140772-140819	GT	AGG
(GTG)	 AG	140895-141127	GT	AGG
(GTT)	 AG	141251-141362	GT	AGG
(GTG)	 AG	141489-141595	GT	AGG
(GGT)	 AG	141765-141953	GT	AGG
(ACT)	 AG	142273-142397	GT	GGG
(GTG)	 AG	142582-142698	GT	AGG
(TGA)	 AG	143024-143196	GT	AGG
(ACG)	 AG	143310-143424	GT	AGG
(GTG)	 AG	143623-143760	GT	CTG
(TCC)	 AG	143948-144042	GT	AGG
(GTG)	 AG	144255-144328	GT	AAG
(ACT)	 AG	144597-144694	GT	ATG
(TCC)	 AG	144832-144908	AC	GAA
add_exon() Sorry, pasa_asmbl_38559.p1 140895-141127-terminal-2 is invalid.
-recovered pasa_asmbl_38559.p1, terminal, 140895, 141127
-recovered pasa_asmbl_38559.p1, terminal, 144832, 144908
-recovered pasa_asmbl_38559.p1, internal, 140895, 141127
-recovered pasa_asmbl_38559.p1, internal, 141251, 141362
-recovered pasa_asmbl_38559.p1, internal, 141489, 141595
-recovered pasa_asmbl_38559.p1, internal, 141765, 141953
-recovered pasa_asmbl_38559.p1, internal, 142273, 142397
-recovered pasa_asmbl_38559.p1, internal, 142582, 142698
-recovered pasa_asmbl_38559.p1, internal, 143024, 143196
-recovered pasa_asmbl_38559.p1, internal, 143310, 143424
-recovered pasa_asmbl_38559.p1, internal, 143623, 143760
-recovered pasa_asmbl_38559.p1, internal, 143948, 144042
-recovered pasa_asmbl_38559.p1, internal, 144255, 144328
-recovered pasa_asmbl_38559.p1, internal, 144597, 144694
Valid prediction for snap_scaffold_28-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_58442-T1
Valid prediction for CodingQuarry_transcript_43592-T1
Valid prediction for GlimmerHMM_glimmerT_58460-T1
Valid prediction for GlimmerHMM_glimmerT_58438-T1
Valid prediction for GlimmerHMM_glimmerT_58443-T1
Valid prediction for snap_scaffold_28-snap.742-T1
Valid prediction for snap_scaffold_28-snap.763-T1
Valid prediction for snap_scaffold_28-snap.755-T1
Valid prediction for snap_scaffold_28-snap.769-T1
Couldn't classify 137537, 137887
Couldn't classify 138798, 138837
Sorry, prediction pasa_asmbl_38119.p1 fails validation.
(ACC)	 GG	137537-137887	GT	AGG
(GAG)	 AG	138031-138179	GT	AGG
(TGG)	 AG	138340-138432	GT	CGG
(GGT)	 AG	138798-138837	AG	CGA
-recovered pasa_asmbl_38119.p1, internal, 138031, 138179
-recovered pasa_asmbl_38119.p1, internal, 138340, 138432
Valid prediction for HiQ_model.g38700.t1
Valid prediction for Augustus_model.g38714.t1
Valid prediction for GlimmerHMM_glimmerT_58447-T1
Valid prediction for snap_scaffold_28-snap.758-T1
Valid prediction for snap_scaffold_28-snap.757-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58445-T1
Valid prediction for snap_scaffold_28-snap.733-T1
Valid prediction for HiQ_model.g38703.t1
Valid prediction for pasa_asmbl_38116.p1
Valid prediction for GlimmerHMM_glimmerT_58459-T1
Valid prediction for snap_scaffold_28-snap.751-T1
Valid prediction for Augustus_model.g38704.t1
Valid prediction for GlimmerHMM_glimmerT_58444-T1
Valid prediction for Augustus_model.g38710.t1
Couldn't classify 140480, 140503
Sorry, prediction pasa_asmbl_38118.p2 fails validation.
(ATG)	 CC	139329-139533	GT	AGG
(GGG)	 AG	140097-140195	GT	TGG
(GCG)	 AG	140302-140372	GT	TGG
(TCG)	 AG	140480-140503	AC	ACA
-recovered pasa_asmbl_38118.p2, initial, 139329, 139533
-recovered pasa_asmbl_38118.p2, internal, 140097, 140195
-recovered pasa_asmbl_38118.p2, internal, 140302, 140372
Valid prediction for GlimmerHMM_glimmerT_58463-T1
Valid prediction for snap_scaffold_28-snap.735-T1
Valid prediction for HiQ_model.g38699.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6499, rend_intergenic: 5706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7469, rend_intergenic: 6630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40065, rend_intergenic: 33286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44392, rend_intergenic: 40902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49648, rend_intergenic: 45178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58445, rend_intergenic: 50215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61177, rend_intergenic: 60138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81664, rend_intergenic: 79191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84627, rend_intergenic: 82012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 85413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107548, rend_intergenic: 103972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115942, rend_intergenic: 110522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136896, rend_intergenic: 124639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139144, rend_intergenic: 137099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149552, rend_intergenic: 145106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161562, rend_intergenic: 157874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173359, rend_intergenic: 164574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176623
-exon list size: 527


building trellis

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66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 6499, rend_intergenic: 5706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7469, rend_intergenic: 6630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40065, rend_intergenic: 33286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44392, rend_intergenic: 40902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49648, rend_intergenic: 45178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58445, rend_intergenic: 50215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61177, rend_intergenic: 60138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81664, rend_intergenic: 79191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84627, rend_intergenic: 82012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 85413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107548, rend_intergenic: 103972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115942, rend_intergenic: 110522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136896, rend_intergenic: 124639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139144, rend_intergenic: 137099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149552, rend_intergenic: 145106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161562, rend_intergenic: 157874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173359, rend_intergenic: 164574  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