-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_13009071-13157112

-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_21111-T1
Valid prediction for GeneMark_model.35977_t
Valid prediction for Augustus_model.g14180.t1
Valid prediction for GlimmerHMM_glimmerT_21113-T1
Valid prediction for GlimmerHMM_glimmerT_21120-T1
Valid prediction for snap_scaffold_8-snap.2365-T1
Valid prediction for GeneMark_model.35986_t
Valid prediction for GlimmerHMM_glimmerT_21116-T1
Valid prediction for snap_scaffold_8-snap.2367-T1
Valid prediction for GeneMark_model.35976_t
Valid prediction for snap_scaffold_8-snap.2387-T1
Valid prediction for Augustus_model.g14177.t1
Valid prediction for GeneMark_model.35999_t
Valid prediction for GlimmerHMM_glimmerT_21115-T1
Valid prediction for GeneMark_model.35994_t
Couldn't classify 119367, 119762
Sorry, prediction pasa_asmbl_52341.p1 fails validation.
(GGT)	 GT	119367-119762	TG	GAT
Valid prediction for snap_scaffold_8-snap.2378-T1
Valid prediction for snap_scaffold_8-snap.2370-T1
Valid prediction for GeneMark_model.35992_t
Valid prediction for GeneMark_model.35993_t
Valid prediction for GeneMark_model.35988_t
Valid prediction for snap_scaffold_8-snap.2371-T1
Valid prediction for snap_scaffold_8-snap.2377-T1
Valid prediction for Augustus_model.g14176.t1
Valid prediction for GlimmerHMM_glimmerT_21107-T1
Valid prediction for GeneMark_model.35991_t
Valid prediction for Augustus_model.g14181.t1
Valid prediction for snap_scaffold_8-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_21110-T1
Valid prediction for GeneMark_model.35996_t
Valid prediction for snap_scaffold_8-snap.2381-T1
Valid prediction for GlimmerHMM_glimmerT_21104-T1
Valid prediction for GlimmerHMM_glimmerT_21108-T1
Valid prediction for snap_scaffold_8-snap.2383-T1
Valid prediction for Augustus_model.g14178.t1
Valid prediction for GeneMark_model.36002_t
Valid prediction for GeneMark_model.35979_t
Valid prediction for snap_scaffold_8-snap.2373-T1
Valid prediction for Augustus_model.g14179.t1
Valid prediction for GlimmerHMM_glimmerT_21119-T1
Valid prediction for GlimmerHMM_glimmerT_21123-T1
Valid prediction for snap_scaffold_8-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_21112-T1
Valid prediction for snap_scaffold_8-snap.2368-T1
Valid prediction for GeneMark_model.36000_t
Valid prediction for snap_scaffold_8-snap.2389-T1
Couldn't classify 112276, 112490
Couldn't classify 114595, 114616
Sorry, prediction pasa_asmbl_52658.p1 fails validation.
(CGT)	 GA	112276-112490	GT	CTG
(GCA)	 AG	113216-113287	GT	CTG
(GGA)	 AG	114595-114616	AA	TCA
-recovered pasa_asmbl_52658.p1, internal, 113216, 113287
Valid prediction for GeneMark_model.35982_t
Valid prediction for GeneMark_model.35984_t
Valid prediction for GeneMark_model.35975_t
Valid prediction for snap_scaffold_8-snap.2391-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 GeneMark_model.35981_t
Valid prediction for GlimmerHMM_glimmerT_21114-T1
Valid prediction for CodingQuarry_transcript_59729-T1
Valid prediction for GlimmerHMM_glimmerT_21118-T1
Valid prediction for GeneMark_model.36004_t
Valid prediction for GlimmerHMM_glimmerT_21105-T1
Valid prediction for snap_scaffold_8-snap.2372-T1
Valid prediction for GeneMark_model.35974_t
Valid prediction for GlimmerHMM_glimmerT_21106-T1
Valid prediction for GlimmerHMM_glimmerT_21121-T1
Valid prediction for snap_scaffold_8-snap.2363-T1
Valid prediction for snap_scaffold_8-snap.2369-T1
Valid prediction for GeneMark_model.35983_t
Valid prediction for GeneMark_model.35998_t
Couldn't classify 102, 371
Sorry, prediction Augustus_model.g14183.t1 fails validation.
(TCT)	 AG	102-371	GT	AGG
(AAG)	 AG	1376-1600	GT	GGG
(AGG)	 AG	1783-1860	GT	GGG
(GTG)	 AG	2083-2231	GT	AGG
(ATA)	 AG	2359-2476	GT	TGG
(AGG)	 AG	2612-2660	GT	ACG
(TAG)	 AG	4011-4070	GT	AGG
(GGC)	 AG	5995-6158	GT	AGG
(CTT)	 AG	6401-6533	GT	AGG
(ATA)	 AG	7015-7139	GT	AGG
(AGC)	 AG	7361-7466	GT	TGG
(GGA)	 AG	8524-8690	GT	GGG
(AGA)	 AG	10559-10724	GT	AGG
(GAT)	 AG	11091-11197	GT	AGG
(AGG)	 AG	11293-11322	GT	GGG
(ACC)	 AG	11599-11738	GT	AGG
(GGA)	 AG	12384-12434	GT	AAG
(GTG)	 AG	13202-13361	GT	CGG
(ATG)	 AG	13559-13663	GT	TGG
(GCT)	 AG	13809-13997	GT	GGG
(GGG)	 AG	14758-14894	TC	GAT
-recovered Augustus_model.g14183.t1, initial, 13559, 13663
add_exon() Sorry, Augustus_model.g14183.t1 11091-11197-terminal-2 is invalid.
-recovered Augustus_model.g14183.t1, terminal, 11091, 11197
-recovered Augustus_model.g14183.t1, terminal, 14758, 14894
-recovered Augustus_model.g14183.t1, internal, 102, 371
-recovered Augustus_model.g14183.t1, internal, 1376, 1600
-recovered Augustus_model.g14183.t1, internal, 1783, 1860
-recovered Augustus_model.g14183.t1, internal, 2083, 2231
-recovered Augustus_model.g14183.t1, internal, 2359, 2476
-recovered Augustus_model.g14183.t1, internal, 2612, 2660
-recovered Augustus_model.g14183.t1, internal, 4011, 4070
-recovered Augustus_model.g14183.t1, internal, 5995, 6158
-recovered Augustus_model.g14183.t1, internal, 6401, 6533
-recovered Augustus_model.g14183.t1, internal, 7015, 7139
-recovered Augustus_model.g14183.t1, internal, 7361, 7466
-recovered Augustus_model.g14183.t1, internal, 8524, 8690
-recovered Augustus_model.g14183.t1, internal, 10559, 10724
-recovered Augustus_model.g14183.t1, internal, 11091, 11197
-recovered Augustus_model.g14183.t1, internal, 11293, 11322
-recovered Augustus_model.g14183.t1, internal, 11599, 11738
-recovered Augustus_model.g14183.t1, internal, 12384, 12434
-recovered Augustus_model.g14183.t1, internal, 13202, 13361
-recovered Augustus_model.g14183.t1, internal, 13559, 13663
-recovered Augustus_model.g14183.t1, internal, 13809, 13997
Valid prediction for snap_scaffold_8-snap.2382-T1
Valid prediction for CodingQuarry_transcript_59733-T1
Valid prediction for CodingQuarry_transcript_59732-T1
Valid prediction for GeneMark_model.36003_t
Valid prediction for GeneMark_model.35997_t
Valid prediction for CodingQuarry_transcript_59731-T1
Valid prediction for GeneMark_model.35980_t
Valid prediction for snap_scaffold_8-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_21122-T1
Valid prediction for snap_scaffold_8-snap.2366-T1
Valid prediction for snap_scaffold_8-snap.2384-T1
Valid prediction for snap_scaffold_8-snap.2375-T1
Valid prediction for CodingQuarry_transcript_59730-T1
Valid prediction for HiQ_model.g14182.t1
Valid prediction for snap_scaffold_8-snap.2390-T1
Valid prediction for snap_scaffold_8-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_21124-T1
Valid prediction for snap_scaffold_8-snap.2385-T1
Valid prediction for snap_scaffold_8-snap.2362-T1
Valid prediction for GeneMark_model.35989_t
Valid prediction for GeneMark_model.35985_t
Valid prediction for GlimmerHMM_glimmerT_21103-T1
Valid prediction for GlimmerHMM_glimmerT_21109-T1
Valid prediction for GlimmerHMM_glimmerT_21102-T1
Valid prediction for GlimmerHMM_glimmerT_21117-T1
Valid prediction for GeneMark_model.35987_t
Valid prediction for GeneMark_model.36001_t
Valid prediction for snap_scaffold_8-snap.2380-T1
Valid prediction for snap_scaffold_8-snap.2386-T1
Valid prediction for pasa_asmbl_53274.p1
Couldn't classify 1378, 1600
Couldn't classify 13809, 13996
Sorry, prediction pasa_asmbl_53280.p1 fails validation.
(GCT)	 AA	1378-1600	GT	GGG
(AGG)	 AG	1783-1860	GT	GGG
(GTG)	 AG	2083-2231	GT	AGG
(ATA)	 AG	2359-2476	GT	TGG
(AGG)	 AG	2612-2660	GT	ACG
(TAG)	 AG	4011-4070	GT	AGG
(AGA)	 AG	4315-4317	GT	GAG
(GGC)	 AG	5995-6158	GT	AGG
(CTT)	 AG	6401-6533	GT	AGG
(CAA)	 AG	6815-6817	GT	AAG
(ATA)	 AG	7015-7139	GT	AGG
(AGC)	 AG	7361-7466	GT	TGG
(GGA)	 AG	8524-8690	GT	GGG
(AGA)	 AG	10559-10724	GT	AGG
(GAT)	 AG	11091-11197	GT	AGG
(AGG)	 AG	11293-11322	GT	GGG
(ACC)	 AG	11599-11738	GT	AGG
(GGA)	 AG	12384-12434	GT	AAG
(GTG)	 AG	13202-13361	GT	CGG
(ATG)	 AG	13559-13663	GT	TGG
(GCT)	 AG	13809-13996	GG	TGG
-recovered pasa_asmbl_53280.p1, initial, 13559, 13663
add_exon() Sorry, pasa_asmbl_53280.p1 11091-11197-terminal-2 is invalid.
-recovered pasa_asmbl_53280.p1, terminal, 11091, 11197
-recovered pasa_asmbl_53280.p1, internal, 1783, 1860
-recovered pasa_asmbl_53280.p1, internal, 2083, 2231
-recovered pasa_asmbl_53280.p1, internal, 2359, 2476
-recovered pasa_asmbl_53280.p1, internal, 2612, 2660
-recovered pasa_asmbl_53280.p1, internal, 4011, 4070
-recovered pasa_asmbl_53280.p1, internal, 4315, 4317
-recovered pasa_asmbl_53280.p1, internal, 5995, 6158
-recovered pasa_asmbl_53280.p1, internal, 6401, 6533
-recovered pasa_asmbl_53280.p1, internal, 6815, 6817
-recovered pasa_asmbl_53280.p1, internal, 7015, 7139
-recovered pasa_asmbl_53280.p1, internal, 7361, 7466
-recovered pasa_asmbl_53280.p1, internal, 8524, 8690
-recovered pasa_asmbl_53280.p1, internal, 10559, 10724
-recovered pasa_asmbl_53280.p1, internal, 11091, 11197
-recovered pasa_asmbl_53280.p1, internal, 11293, 11322
-recovered pasa_asmbl_53280.p1, internal, 11599, 11738
-recovered pasa_asmbl_53280.p1, internal, 12384, 12434
-recovered pasa_asmbl_53280.p1, internal, 13202, 13361
-recovered pasa_asmbl_53280.p1, internal, 13559, 13663
Valid prediction for GeneMark_model.35995_t
Valid prediction for GeneMark_model.35978_t
Valid prediction for snap_scaffold_8-snap.2379-T1
Valid prediction for GeneMark_model.35990_t
Valid prediction for Augustus_model.g14175.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18361, rend_intergenic: 8406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27468, rend_intergenic: 27309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50993, rend_intergenic: 48915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60623, rend_intergenic: 59032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71539, rend_intergenic: 67921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104543, rend_intergenic: 101457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105642, rend_intergenic: 104698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119762, rend_intergenic: 107412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125946, rend_intergenic: 124838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129812, rend_intergenic: 125968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131960, rend_intergenic: 131015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133244, rend_intergenic: 132438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147957, rend_intergenic: 135351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148042
-exon list size: 482


building trellis

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28.3    
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29.1    
29.3    
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31.6    
31.8    
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32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.5    
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33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
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36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
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38.2    
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38.8    
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40.1    
40.3    
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40.9    
41.1    
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42.8    
43.0    
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93.4    
93.6    
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97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 18361, rend_intergenic: 8406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27468, rend_intergenic: 27309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50993, rend_intergenic: 48915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60623, rend_intergenic: 59032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71539, rend_intergenic: 67921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104543, rend_intergenic: 101457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105642, rend_intergenic: 104698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119762, rend_intergenic: 107412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125946, rend_intergenic: 124838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129812, rend_intergenic: 125968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131960, rend_intergenic: 131015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133244, rend_intergenic: 132438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147957, rend_intergenic: 135351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support