-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_17931300-18108940

-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 CodingQuarry_transcript_59803-T1
Valid prediction for Augustus_model.g14606.t1
Valid prediction for snap_scaffold_8-snap.3329-T1
Valid prediction for GeneMark_model.37113_t
Valid prediction for GeneMark_model.37106_t
Valid prediction for GeneMark_model.37127_t
Valid prediction for Augustus_model.g14612.t1
Valid prediction for GlimmerHMM_glimmerT_21783-T1
Valid prediction for pasa_asmbl_52523.p1
Valid prediction for Augustus_model.g14605.t1
Valid prediction for GeneMark_model.37102_t
Valid prediction for Augustus_model.g14610.t1
Valid prediction for GeneMark_model.37094_t
Valid prediction for snap_scaffold_8-snap.3335-T1
Valid prediction for snap_scaffold_8-snap.3302-T1
Valid prediction for snap_scaffold_8-snap.3310-T1
Valid prediction for GlimmerHMM_glimmerT_21792-T1
Valid prediction for Augustus_model.g14607.t1
Valid prediction for CodingQuarry_transcript_59801-T1
Valid prediction for GlimmerHMM_glimmerT_21801-T1
Valid prediction for Augustus_model.g14603.t1
Valid prediction for snap_scaffold_8-snap.3326-T1
Valid prediction for GlimmerHMM_glimmerT_21796-T1
Valid prediction for Augustus_model.g14615.t1
Valid prediction for pasa_asmbl_52515.p1
Valid prediction for GeneMark_model.37118_t
Valid prediction for GeneMark_model.37098_t
Valid prediction for snap_scaffold_8-snap.3336-T1
Valid prediction for GeneMark_model.37130_t
Valid prediction for GeneMark_model.37103_t
Valid prediction for GeneMark_model.37099_t
Couldn't classify 166521, 166640
Sorry, prediction pasa_asmbl_52521.p1 fails validation.
(ATG)	 AT	164095-164324	GT	AGG
(GCC)	 AG	164492-164594	GT	AAG
(GGG)	 AG	166521-166640	AG	TAA
-recovered pasa_asmbl_52521.p1, initial, 164095, 164324
-recovered pasa_asmbl_52521.p1, internal, 164492, 164594
Valid prediction for GlimmerHMM_glimmerT_21806-T1
Valid prediction for GlimmerHMM_glimmerT_21798-T1
Valid prediction for snap_scaffold_8-snap.3327-T1
Valid prediction for GeneMark_model.37125_t
Valid prediction for GlimmerHMM_glimmerT_21800-T1
Valid prediction for GeneMark_model.37122_t
Valid prediction for GeneMark_model.37100_t
Valid prediction for GlimmerHMM_glimmerT_21795-T1
Valid prediction for GlimmerHMM_glimmerT_21793-T1
Valid prediction for GeneMark_model.37092_t
Valid prediction for GeneMark_model.37123_t
Valid prediction for GeneMark_model.37129_t
Valid prediction for Augustus_model.g14602.t1
Valid prediction for GeneMark_model.37110_t
Valid prediction for GeneMark_model.37116_t
Valid prediction for HiQ_model.g14597.t1
Valid prediction for snap_scaffold_8-snap.3314-T1
Valid prediction for GeneMark_model.37085_t
Valid prediction for GeneMark_model.37124_t
Valid prediction for HiQ_model.g14609.t1
Valid prediction for GlimmerHMM_glimmerT_21791-T1
Valid prediction for GeneMark_model.37117_t
Valid prediction for snap_scaffold_8-snap.3317-T1
Valid prediction for GeneMark_model.37087_t
Valid prediction for snap_scaffold_8-snap.3306-T1
Valid prediction for GlimmerHMM_glimmerT_21794-T1
Valid prediction for Augustus_model.g14608.t1
Valid prediction for snap_scaffold_8-snap.3332-T1
Valid prediction for GlimmerHMM_glimmerT_21782-T1
Valid prediction for GlimmerHMM_glimmerT_21799-T1
Valid prediction for snap_scaffold_8-snap.3322-T1
Valid prediction for snap_scaffold_8-snap.3305-T1
Valid prediction for snap_scaffold_8-snap.3312-T1
Valid prediction for GeneMark_model.37109_t
Valid prediction for GeneMark_model.37084_t
Valid prediction for GeneMark_model.37089_t
Valid prediction for snap_scaffold_8-snap.3334-T1
Valid prediction for Augustus_model.g14614.t1
Valid prediction for GlimmerHMM_glimmerT_21804-T1
Valid prediction for CodingQuarry_transcript_59802-T1
Valid prediction for GeneMark_model.37115_t
Valid prediction for GeneMark_model.37097_t
Valid prediction for Augustus_model.g14613.t1
Valid prediction for GlimmerHMM_glimmerT_21802-T1
Valid prediction for GeneMark_model.37120_t
Valid prediction for snap_scaffold_8-snap.3319-T1
Valid prediction for Augustus_model.g14604.t1
Valid prediction for CodingQuarry_transcript_59805-T1
Valid prediction for snap_scaffold_8-snap.3325-T1
Valid prediction for GlimmerHMM_glimmerT_21805-T1
Valid prediction for pasa_asmbl_52519.p1
Valid prediction for snap_scaffold_8-snap.3323-T1
Valid prediction for pasa_asmbl_52513.p1
Valid prediction for GeneMark_model.37108_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: -)Couldn't classify 121050, 121757
Couldn't classify 122341, 122493
Sorry, prediction pasa_asmbl_53510.p1 fails validation.
(TCA)	 CC	121050-121757	GT	TGG
(GTA)	 AG	122341-122493	AA	AGA
Valid prediction for pasa_asmbl_53511.p1
Couldn't classify 153803, 153967
Sorry, prediction pasa_asmbl_53503.p1 fails validation.
(CAG)	 CT	153803-153967	GT	AGG
(ATC)	 AG	154778-154933	GT	CAG
(CTG)	 AG	155399-155543	GT	TGG
(GTA)	 AG	155657-155838	GT	TGG
(GTA)	 AG	156005-156133	GT	TGG
(TAC)	 AG	156210-156395	GT	AGG
(CCT)	 AG	156707-156951	GT	AGG
(GTA)	 AG	157088-157230	GT	AGG
(ATG)	 AG	157338-157568	GT	CGG
(ACA)	 AG	157727-157969	GT	TTG
(TGC)	 AG	158056-158204	GT	AGG
(AAT)	 AG	158292-158480	GT	ATG
(GGC)	 AG	158594-158794	GG	AGG
add_exon() Sorry, pasa_asmbl_53503.p1 157338-157568-initial-1 is invalid.
-recovered pasa_asmbl_53503.p1, initial, 157338, 157568
-recovered pasa_asmbl_53503.p1, terminal, 158594, 158794
-recovered pasa_asmbl_53503.p1, internal, 154778, 154933
-recovered pasa_asmbl_53503.p1, internal, 155399, 155543
-recovered pasa_asmbl_53503.p1, internal, 155657, 155838
-recovered pasa_asmbl_53503.p1, internal, 156005, 156133
-recovered pasa_asmbl_53503.p1, internal, 156210, 156395
-recovered pasa_asmbl_53503.p1, internal, 156707, 156951
-recovered pasa_asmbl_53503.p1, internal, 157088, 157230
-recovered pasa_asmbl_53503.p1, internal, 157338, 157568
-recovered pasa_asmbl_53503.p1, internal, 157727, 157969
-recovered pasa_asmbl_53503.p1, internal, 158056, 158204
-recovered pasa_asmbl_53503.p1, internal, 158292, 158480
Valid prediction for GlimmerHMM_glimmerT_21784-T1
Valid prediction for snap_scaffold_8-snap.3318-T1
Valid prediction for snap_scaffold_8-snap.3304-T1
Valid prediction for GeneMark_model.37107_t
Valid prediction for GlimmerHMM_glimmerT_21785-T1
Couldn't classify 128517, 128558
Sorry, prediction GeneMark_model.37091_t fails validation.
(ATG)	 TG	124180-124205	GT	AGG
(TGG)	 AG	124239-124466	GT	AGG
(AGG)	 AG	124564-124617	GT	GAG
(GTA)	 AG	124675-124714	GT	AGG
(GTA)	 AG	125546-125680	GT	CGG
(TTG)	 AG	125781-125827	GT	ACG
(GGC)	 AG	125955-125964	GT	CTG
(CGT)	 AG	126074-126251	GT	AGG
(CCT)	 AG	126989-127116	GT	CAG
(AAG)	 AG	127463-127486	GT	AGG
(CTC)	 AG	127583-127606	GT	AGG
(CCC)	 AG	127649-127659	GT	GGG
(ATT)	 AG	127686-127692	GT	CTG
(GTG)	 AG	127924-127949	GT	GAG
(GGT)	 AG	128174-128262	GT	AGG
(AGA)	 AG	128460-128469	GT	ACG
(AGA)	 AG	128517-128558	GC	GAG
-recovered GeneMark_model.37091_t, initial, 124180, 124205
-recovered GeneMark_model.37091_t, internal, 124239, 124466
-recovered GeneMark_model.37091_t, internal, 124564, 124617
-recovered GeneMark_model.37091_t, internal, 124675, 124714
-recovered GeneMark_model.37091_t, internal, 125546, 125680
-recovered GeneMark_model.37091_t, internal, 125781, 125827
-recovered GeneMark_model.37091_t, internal, 125955, 125964
-recovered GeneMark_model.37091_t, internal, 126074, 126251
-recovered GeneMark_model.37091_t, internal, 126989, 127116
-recovered GeneMark_model.37091_t, internal, 127463, 127486
-recovered GeneMark_model.37091_t, internal, 127583, 127606
-recovered GeneMark_model.37091_t, internal, 127649, 127659
-recovered GeneMark_model.37091_t, internal, 127686, 127692
-recovered GeneMark_model.37091_t, internal, 127924, 127949
-recovered GeneMark_model.37091_t, internal, 128174, 128262
-recovered GeneMark_model.37091_t, internal, 128460, 128469
-recovered GeneMark_model.37091_t, internal, 128517, 128558
Valid prediction for GlimmerHMM_glimmerT_21789-T1
Valid prediction for GeneMark_model.37096_t
Valid prediction for snap_scaffold_8-snap.3320-T1
Valid prediction for GeneMark_model.37126_t
Valid prediction for GlimmerHMM_glimmerT_21787-T1
Valid prediction for Augustus_model.g14601.t1
Valid prediction for snap_scaffold_8-snap.3307-T1
Valid prediction for Augustus_model.g14599.t1
Valid prediction for HiQ_model.g14598.t1
Valid prediction for snap_scaffold_8-snap.3316-T1
Valid prediction for GlimmerHMM_glimmerT_21803-T1
Valid prediction for snap_scaffold_8-snap.3333-T1
Valid prediction for GeneMark_model.37105_t
Valid prediction for snap_scaffold_8-snap.3321-T1
Valid prediction for snap_scaffold_8-snap.3330-T1
Valid prediction for snap_scaffold_8-snap.3328-T1
Valid prediction for GeneMark_model.37101_t
Valid prediction for GeneMark_model.37088_t
Valid prediction for GeneMark_model.37086_t
Couldn't classify 128719, 128736
Sorry, prediction GeneMark_model.37090_t fails validation.
(AGA)	 AG	128719-128736	GT	ATG
(GAG)	 AG	128856-128954	GT	GAG
(GGG)	 AG	129039-129085	GT	GAG
(ACA)	 AG	129111-129132	GT	GAG
(AAG)	 AG	129154-129237	GT	GAG
(GGA)	 AG	129263-129281	GA	GAG
-recovered GeneMark_model.37090_t, terminal, 129263, 129281
-recovered GeneMark_model.37090_t, internal, 128719, 128736
-recovered GeneMark_model.37090_t, internal, 128856, 128954
-recovered GeneMark_model.37090_t, internal, 129039, 129085
-recovered GeneMark_model.37090_t, internal, 129111, 129132
-recovered GeneMark_model.37090_t, internal, 129154, 129237
Valid prediction for GeneMark_model.37112_t
Valid prediction for GlimmerHMM_glimmerT_21790-T1
Valid prediction for GlimmerHMM_glimmerT_21788-T1
Valid prediction for snap_scaffold_8-snap.3308-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.3313-T1
Valid prediction for snap_scaffold_8-snap.3311-T1
Valid prediction for GeneMark_model.37104_t
Valid prediction for snap_scaffold_8-snap.3309-T1
Valid prediction for snap_scaffold_8-snap.3331-T1
Valid prediction for snap_scaffold_8-snap.3303-T1
Couldn't classify 125546, 125700
Couldn't classify 128136, 128261
Sorry, prediction pasa_asmbl_53509.p1 fails validation.
(GTA)	 AG	125546-125700	GT	AGG
(GCT)	 AG	126106-126251	GT	AGG
(GTG)	 AG	127924-128021	GT	GGG
(ATA)	 AG	128136-128261	GG	CAG
-recovered pasa_asmbl_53509.p1, internal, 125546, 125700
-recovered pasa_asmbl_53509.p1, internal, 126106, 126251
-recovered pasa_asmbl_53509.p1, internal, 127924, 128021
Valid prediction for GeneMark_model.37114_t
Valid prediction for GlimmerHMM_glimmerT_21786-T1
Couldn't classify 133997, 134132
Sorry, prediction pasa_asmbl_53508.p2 fails validation.
(GGA)	 CA	133997-134132	GT	AGG
(ATG)	 AG	134912-135023	GT	AGG
(AGA)	 AG	136701-136818	GA	AGG
add_exon() Sorry, pasa_asmbl_53508.p2 134912-135023-initial-1 is invalid.
-recovered pasa_asmbl_53508.p2, initial, 134912, 135023
-recovered pasa_asmbl_53508.p2, terminal, 136701, 136818
-recovered pasa_asmbl_53508.p2, internal, 134912, 135023
Valid prediction for GeneMark_model.37128_t
Valid prediction for GeneMark_model.37093_t
Valid prediction for GeneMark_model.37119_t
Valid prediction for GlimmerHMM_glimmerT_21797-T1
Valid prediction for GeneMark_model.37121_t
Valid prediction for Augustus_model.g14600.t1
Valid prediction for GeneMark_model.37111_t
Valid prediction for GeneMark_model.37095_t
Valid prediction for snap_scaffold_8-snap.3315-T1
Valid prediction for HiQ_model.g14611.t1
Valid prediction for snap_scaffold_8-snap.3324-T1
Valid prediction for CodingQuarry_transcript_59804-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42743, rend_intergenic: 32306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44686, rend_intergenic: 43490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51626, rend_intergenic: 45142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56379, rend_intergenic: 52472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81001, rend_intergenic: 76471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88870, rend_intergenic: 82737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102391, rend_intergenic: 95798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106042, rend_intergenic: 102773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133456, rend_intergenic: 126478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141209, rend_intergenic: 133811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177641
-exon list size: 575


building trellis

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79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
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 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 42743, rend_intergenic: 32306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44686, rend_intergenic: 43490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51626, rend_intergenic: 45142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56379, rend_intergenic: 52472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81001, rend_intergenic: 76471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88870, rend_intergenic: 82737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102391, rend_intergenic: 95798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106042, rend_intergenic: 102773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133456, rend_intergenic: 126478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141209, rend_intergenic: 133811  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

-building DP trellis

-building trellis in range 1 - 10917
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support