-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_9309279-9556550

-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_56136-T1
Valid prediction for Augustus_model.g37423.t1
Valid prediction for snap_scaffold_25-snap.2091-T1
Couldn't classify 119751, 119814
Couldn't classify 124967, 125159
Sorry, prediction pasa_asmbl_33802.p1 fails validation.
(ACC)	 CA	119751-119814	GT	TAG
(ATC)	 AG	122726-122757	GT	TGG
(CAT)	 AG	122885-122995	GT	AGG
(AGA)	 AG	124747-124871	GT	TGG
(GGA)	 AG	124967-125159	TC	AGT
-recovered pasa_asmbl_33802.p1, internal, 122726, 122757
-recovered pasa_asmbl_33802.p1, internal, 122885, 122995
-recovered pasa_asmbl_33802.p1, internal, 124747, 124871
Valid prediction for Augustus_model.g37444.t1
Valid prediction for Augustus_model.g37445.t1
Couldn't classify 210467, 210594
Sorry, prediction pasa_asmbl_33813.p1 fails validation.
(ATG)	 CA	206955-207012	GT	TGG
(CTG)	 AG	207110-207185	GT	TGG
(GTA)	 AG	209333-209514	GT	AGG
(AGG)	 AG	210467-210594	GT	ATG
-recovered pasa_asmbl_33813.p1, initial, 206955, 207012
-recovered pasa_asmbl_33813.p1, internal, 207110, 207185
-recovered pasa_asmbl_33813.p1, internal, 209333, 209514
-recovered pasa_asmbl_33813.p1, internal, 210467, 210594
Valid prediction for Augustus_model.g37433.t1
Valid prediction for GlimmerHMM_glimmerT_56149-T1
Valid prediction for snap_scaffold_25-snap.2094-T1
Valid prediction for snap_scaffold_25-snap.2086-T1
Couldn't classify 25157, 26039
Sorry, prediction pasa_asmbl_33799.p1 fails validation.
(TCC)	 AC	25157-26039	GT	AGG
(GCT)	 AG	26484-26590	GT	GAG
(TCT)	 AG	26759-26933	GT	CCG
(TGC)	 AG	27018-27132	GT	CGG
(ATG)	 AG	27217-27372	GT	AGG
(CGA)	 AG	27821-27953	GT	AGG
(TCC)	 AG	28077-28273	GT	TGG
(GAA)	 AG	28469-28533	GT	AGG
(GCT)	 AG	28673-28840	GT	AGG
(GAA)	 AG	28950-28978	AT	GAA
add_exon() Sorry, pasa_asmbl_33799.p1 27217-27372-initial-1 is invalid.
-recovered pasa_asmbl_33799.p1, initial, 27217, 27372
-recovered pasa_asmbl_33799.p1, terminal, 27217, 27372
-recovered pasa_asmbl_33799.p1, terminal, 28950, 28978
-recovered pasa_asmbl_33799.p1, internal, 26484, 26590
-recovered pasa_asmbl_33799.p1, internal, 26759, 26933
-recovered pasa_asmbl_33799.p1, internal, 27018, 27132
-recovered pasa_asmbl_33799.p1, internal, 27217, 27372
-recovered pasa_asmbl_33799.p1, internal, 27821, 27953
-recovered pasa_asmbl_33799.p1, internal, 28077, 28273
-recovered pasa_asmbl_33799.p1, internal, 28469, 28533
-recovered pasa_asmbl_33799.p1, internal, 28673, 28840
Valid prediction for Augustus_model.g37446.t1
Valid prediction for Augustus_model.g37422.t1
Valid prediction for snap_scaffold_25-snap.2066-T1
Couldn't classify 136417, 136522
Sorry, prediction pasa_asmbl_33807.p1 fails validation.
(CGT)	 GG	136417-136522	GT	AGG
(ATG)	 AG	138994-139075	GT	AGG
(AGA)	 AG	140504-140639	GT	AGG
(GTG)	 AG	140732-140936	GT	TTG
(GTA)	 AG	141071-141171	GT	AGG
(GAG)	 AG	141467-141604	TG	AGT
add_exon() Sorry, pasa_asmbl_33807.p1 138994-139075-initial-1 is invalid.
-recovered pasa_asmbl_33807.p1, initial, 138994, 139075
add_exon() Sorry, pasa_asmbl_33807.p1 138994-139075-terminal-3 is invalid.
-recovered pasa_asmbl_33807.p1, terminal, 138994, 139075
-recovered pasa_asmbl_33807.p1, terminal, 141467, 141604
-recovered pasa_asmbl_33807.p1, internal, 138994, 139075
-recovered pasa_asmbl_33807.p1, internal, 140504, 140639
-recovered pasa_asmbl_33807.p1, internal, 140732, 140936
-recovered pasa_asmbl_33807.p1, internal, 141071, 141171
Valid prediction for GeneMark_model.97787_t
Valid prediction for Augustus_model.g37427.t1
Valid prediction for GlimmerHMM_glimmerT_56134-T1
Valid prediction for snap_scaffold_25-snap.2090-T1
Valid prediction for Augustus_model.g37421.t1
Valid prediction for Augustus_model.g37447.t1
Valid prediction for Augustus_model.g37425.t1
Valid prediction for GeneMark_model.97782_t
Valid prediction for GeneMark_model.97797_t
Valid prediction for snap_scaffold_25-snap.2078-T1
Valid prediction for HiQ_model.g37448.t1
Valid prediction for GlimmerHMM_glimmerT_56146-T1
Valid prediction for CodingQuarry_transcript_38748-T1
Valid prediction for GeneMark_model.97800_t
Valid prediction for GlimmerHMM_glimmerT_56117-T1
Valid prediction for GlimmerHMM_glimmerT_56147-T1
Valid prediction for GeneMark_model.97801_t
Valid prediction for GlimmerHMM_glimmerT_56144-T1
Valid prediction for GeneMark_model.97781_t
Valid prediction for Augustus_model.g37439.t1
Valid prediction for snap_scaffold_25-snap.2083-T1
Valid prediction for GeneMark_model.97783_t
Valid prediction for GeneMark_model.97803_t
Valid prediction for GeneMark_model.97785_t
Valid prediction for snap_scaffold_25-snap.2061-T1
Valid prediction for snap_scaffold_25-snap.2069-T1
Valid prediction for Augustus_model.g37440.t1
Valid prediction for Augustus_model.g37438.t1
Valid prediction for GeneMark_model.97796_t
Valid prediction for GlimmerHMM_glimmerT_56122-T1
Valid prediction for GlimmerHMM_glimmerT_56118-T1
Valid prediction for snap_scaffold_25-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_56126-T1
Couldn't classify 229908, 229956
Sorry, prediction pasa_asmbl_33816.p1 fails validation.
(AGG)	 GA	229908-229956	GT	TGG
(ACA)	 AG	231295-232655	AT	AAA
-recovered pasa_asmbl_33816.p1, terminal, 231295, 232655
Valid prediction for snap_scaffold_25-snap.2080-T1
Valid prediction for pasa_asmbl_33815.p1
Valid prediction for snap_scaffold_25-snap.2095-T1
Valid prediction for GlimmerHMM_glimmerT_56133-T1
Valid prediction for GlimmerHMM_glimmerT_56137-T1
Valid prediction for snap_scaffold_25-snap.2085-T1
Valid prediction for GeneMark_model.97802_t
Valid prediction for GeneMark_model.97794_t
Valid prediction for GlimmerHMM_glimmerT_56145-T1
Valid prediction for GlimmerHMM_glimmerT_56121-T1
Valid prediction for snap_scaffold_25-snap.2071-T1
Valid prediction for snap_scaffold_25-snap.2093-T1
Valid prediction for Augustus_model.g37424.t1
Valid prediction for snap_scaffold_25-snap.2062-T1
Valid prediction for snap_scaffold_25-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_56128-T1
Valid prediction for snap_scaffold_25-snap.2064-T1
Valid prediction for snap_scaffold_25-snap.2070-T1
Valid prediction for Augustus_model.g37436.t1
Valid prediction for GlimmerHMM_glimmerT_56124-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_25-snap.2076-T1
Valid prediction for snap_scaffold_25-snap.2089-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56130-T1
Valid prediction for snap_scaffold_25-snap.2096-T1
Valid prediction for Augustus_model.g37437.t1
Valid prediction for GeneMark_model.97776_t
Valid prediction for Augustus_model.g37431.t1
Valid prediction for GeneMark_model.97799_t
Valid prediction for GlimmerHMM_glimmerT_56119-T1
Valid prediction for GlimmerHMM_glimmerT_56127-T1
Valid prediction for GlimmerHMM_glimmerT_56125-T1
Valid prediction for GlimmerHMM_glimmerT_56140-T1
Valid prediction for GlimmerHMM_glimmerT_56123-T1
Valid prediction for GlimmerHMM_glimmerT_56135-T1
Valid prediction for GlimmerHMM_glimmerT_56132-T1
Valid prediction for GeneMark_model.97791_t
Valid prediction for snap_scaffold_25-snap.2087-T1
Valid prediction for GeneMark_model.97784_t
Valid prediction for snap_scaffold_25-snap.2075-T1
Valid prediction for GeneMark_model.97790_t
Valid prediction for snap_scaffold_25-snap.2072-T1
Valid prediction for GeneMark_model.97780_t
Couldn't classify 132576, 132745
Sorry, prediction pasa_asmbl_34472.p1 fails validation.
(ATG)	 TA	131743-131881	GT	AGG
(ATG)	 AG	132026-132133	GT	AGG
(GGT)	 AG	132576-132745	GT	TGG
-recovered pasa_asmbl_34472.p1, initial, 131743, 131881
add_exon() Sorry, pasa_asmbl_34472.p1 132026-132133-initial-1 is invalid.
-recovered pasa_asmbl_34472.p1, initial, 132026, 132133
-recovered pasa_asmbl_34472.p1, internal, 132026, 132133
-recovered pasa_asmbl_34472.p1, internal, 132576, 132745
Valid prediction for snap_scaffold_25-snap.2063-T1
Valid prediction for snap_scaffold_25-snap.2088-T1
Valid prediction for GeneMark_model.97786_t
Valid prediction for snap_scaffold_25-snap.2073-T1
Valid prediction for Augustus_model.g37432.t1
Valid prediction for GlimmerHMM_glimmerT_56138-T1
Valid prediction for Augustus_model.g37428.t1
Valid prediction for GlimmerHMM_glimmerT_56120-T1
Valid prediction for snap_scaffold_25-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_56129-T1
Valid prediction for snap_scaffold_25-snap.2074-T1
Couldn't classify 54598, 54717
Sorry, prediction pasa_asmbl_34474.p1 fails validation.
(ATG)	 GA	50802-50834	GT	GTG
(GGC)	 AG	50927-51027	GT	AGG
(ACC)	 AG	52026-52169	GT	GGG
(GAG)	 AG	52267-52390	GT	AGG
(GTA)	 AG	53078-53136	GT	AGG
(GGG)	 AG	53279-53420	GT	AGG
(CTG)	 AG	54598-54717	AT	TCA
-recovered pasa_asmbl_34474.p1, initial, 50802, 50834
-recovered pasa_asmbl_34474.p1, internal, 50927, 51027
-recovered pasa_asmbl_34474.p1, internal, 52026, 52169
-recovered pasa_asmbl_34474.p1, internal, 52267, 52390
-recovered pasa_asmbl_34474.p1, internal, 53078, 53136
-recovered pasa_asmbl_34474.p1, internal, 53279, 53420
Valid prediction for snap_scaffold_25-snap.2077-T1
Valid prediction for GlimmerHMM_glimmerT_56148-T1
Couldn't classify 137619, 137765
Couldn't classify 140181, 140326
Sorry, prediction pasa_asmbl_34599.p1 fails validation.
(TGT)	 TG	137619-137765	GT	AGG
(GTG)	 AG	139867-139972	GT	TGG
(TTG)	 AG	140181-140326	CC	GCC
-recovered pasa_asmbl_34599.p1, internal, 139867, 139972
Valid prediction for HiQ_model.g37443.t1
Valid prediction for GeneMark_model.97777_t
Couldn't classify 149826, 150036
Sorry, prediction pasa_asmbl_34471.p1 fails validation.
(GTG)	 AG	149826-150036	GT	AGG
(ACA)	 AG	150185-150318	GT	AGG
(GGC)	 AG	151617-151809	GT	CTG
(CTA)	 AG	152579-152792	GT	AGG
(GAT)	 AG	154184-154267	GT	AGG
(GTG)	 AG	154554-154680	AC	GAA
add_exon() Sorry, pasa_asmbl_34471.p1 152579-152792-terminal-3 is invalid.
-recovered pasa_asmbl_34471.p1, terminal, 152579, 152792
-recovered pasa_asmbl_34471.p1, terminal, 154554, 154680
-recovered pasa_asmbl_34471.p1, internal, 149826, 150036
-recovered pasa_asmbl_34471.p1, internal, 150185, 150318
-recovered pasa_asmbl_34471.p1, internal, 151617, 151809
-recovered pasa_asmbl_34471.p1, internal, 152579, 152792
-recovered pasa_asmbl_34471.p1, internal, 154184, 154267
Valid prediction for GlimmerHMM_glimmerT_56143-T1
Valid prediction for Augustus_model.g37426.t1
Valid prediction for GlimmerHMM_glimmerT_56142-T1
Valid prediction for GeneMark_model.97779_t
Valid prediction for GeneMark_model.97795_t
Valid prediction for Augustus_model.g37442.t1
Valid prediction for Augustus_model.g37429.t1
Valid prediction for GeneMark_model.97793_t
Valid prediction for Augustus_model.g37430.t1
Valid prediction for GeneMark_model.97788_t
Couldn't classify 160438, 161551
Couldn't classify 161782, 161852
Sorry, prediction pasa_asmbl_34469.p1 fails validation.
(GGA)	 AT	160438-161551	GT	CGG
(ATA)	 AG	161782-161852	CA	CCC
Valid prediction for GlimmerHMM_glimmerT_56141-T1
Valid prediction for Augustus_model.g37435.t1
Valid prediction for GlimmerHMM_glimmerT_56139-T1
Valid prediction for snap_scaffold_25-snap.2082-T1
Valid prediction for snap_scaffold_25-snap.2065-T1
Valid prediction for GeneMark_model.97798_t
Valid prediction for CodingQuarry_transcript_38746-T1
Valid prediction for snap_scaffold_25-snap.2081-T1
Valid prediction for snap_scaffold_25-snap.2079-T1
Valid prediction for GeneMark_model.97775_t
Valid prediction for snap_scaffold_25-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_56131-T1
Valid prediction for snap_scaffold_25-snap.2067-T1
Valid prediction for Augustus_model.g37434.t1
Valid prediction for Augustus_model.g37441.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10141, rend_intergenic: 8189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26644, rend_intergenic: 16707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247272
-exon list size: 460


building trellis

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18.8    
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28.6    
28.8    
29.0    
29.2    
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29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
31.0    
31.2    
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31.6    
31.8    
32.0    
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32.5    
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32.9    
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33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.1    
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35.9    
36.1    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
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39.6    
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40.0    
40.3    
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40.9    
41.1    
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41.6    
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42.0    
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42.6    
42.9    
43.1    
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43.5    
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43.9    
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44.6    
44.8    
45.0    
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47.8    
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61.3    
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82.7    
82.9    
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83.3    
83.5    
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84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
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85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
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88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10141, rend_intergenic: 8189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26644, rend_intergenic: 16707  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