-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_9550339-9722288

-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 GeneMark_model.71921_t
Valid prediction for GeneMark_model.71940_t
Valid prediction for snap_scaffold_17-snap.1919-T1
Valid prediction for snap_scaffold_17-snap.1925-T1
Couldn't classify 13338, 13632
Sorry, prediction pasa_asmbl_18238.p1 fails validation.
(TCG)	 TT	13338-13632	GT	AGG
(GTT)	 AG	15557-15761	GT	AGG
(GAC)	 AG	16076-16255	GT	CGG
(GAG)	 AG	16371-16488	GT	GGG
(GTG)	 AG	16841-17035	GT	AGG
(TCT)	 AG	17179-17310	GT	AGG
(CTG)	 AG	17443-17544	GT	AGG
(CAC)	 AG	17694-17834	GT	AGG
(CTG)	 AG	18281-18451	GT	GAG
-recovered pasa_asmbl_18238.p1, terminal, 18281, 18451
-recovered pasa_asmbl_18238.p1, internal, 15557, 15761
-recovered pasa_asmbl_18238.p1, internal, 16076, 16255
-recovered pasa_asmbl_18238.p1, internal, 16371, 16488
-recovered pasa_asmbl_18238.p1, internal, 16841, 17035
-recovered pasa_asmbl_18238.p1, internal, 17179, 17310
-recovered pasa_asmbl_18238.p1, internal, 17443, 17544
-recovered pasa_asmbl_18238.p1, internal, 17694, 17834
-recovered pasa_asmbl_18238.p1, internal, 18281, 18451
Valid prediction for snap_scaffold_17-snap.1924-T1
Couldn't classify 144649, 144675
Couldn't classify 146750, 146815
Sorry, prediction pasa_asmbl_18648.p2 fails validation.
(AAA)	 AA	144649-144675	GT	AAG
(GCT)	 AG	145530-145656	GT	GGG
(GTG)	 AG	145918-146063	GT	AAG
(CTG)	 AG	146316-146402	GT	AGG
(GGT)	 AG	146750-146815	GA	TGG
-recovered pasa_asmbl_18648.p2, internal, 145530, 145656
-recovered pasa_asmbl_18648.p2, internal, 145918, 146063
-recovered pasa_asmbl_18648.p2, internal, 146316, 146402
Valid prediction for GeneMark_model.71954_t
Valid prediction for GlimmerHMM_glimmerT_41803-T1
Valid prediction for GeneMark_model.71934_t
Valid prediction for GeneMark_model.71935_t
Valid prediction for snap_scaffold_17-snap.1913-T1
Valid prediction for Augustus_model.g28028.t1
Valid prediction for GlimmerHMM_glimmerT_41792-T1
Valid prediction for GeneMark_model.71944_t
Valid prediction for Augustus_model.g28025.t1
Valid prediction for GeneMark_model.71931_t
Valid prediction for Augustus_model.g28024.t1
Valid prediction for GeneMark_model.71942_t
Valid prediction for snap_scaffold_17-snap.1900-T1
Valid prediction for GeneMark_model.71912_t
Valid prediction for snap_scaffold_17-snap.1903-T1
Valid prediction for snap_scaffold_17-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_41800-T1
Valid prediction for Augustus_model.g28031.t1
Valid prediction for CodingQuarry_transcript_22087-T1
Valid prediction for Augustus_model.g28029.t1
Valid prediction for GeneMark_model.71915_t
Valid prediction for GeneMark_model.71950_t
Valid prediction for GeneMark_model.71923_t
Valid prediction for snap_scaffold_17-snap.1896-T1
Valid prediction for GeneMark_model.71949_t
Valid prediction for GeneMark_model.71914_t
Valid prediction for GeneMark_model.71957_t
Valid prediction for Augustus_model.g28020.t1
Valid prediction for GlimmerHMM_glimmerT_41802-T1
Valid prediction for GlimmerHMM_glimmerT_41791-T1
Valid prediction for snap_scaffold_17-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_41789-T1
Valid prediction for snap_scaffold_17-snap.1891-T1
Valid prediction for snap_scaffold_17-snap.1910-T1
Valid prediction for GeneMark_model.71939_t
Valid prediction for GeneMark_model.71925_t
Valid prediction for GeneMark_model.71930_t
Couldn't classify 147050, 147213
Sorry, prediction pasa_asmbl_18250.p1 fails validation.
(TTC)	 AG	147050-147213	GT	AAG
(ATT)	 AG	147500-147603	GT	TGG
(TGA)	 AG	147696-147821	GT	AGG
(GGG)	 AG	147939-148072	GT	AGG
(ACC)	 AG	148229-148437	GT	CCG
(GAA)	 AG	148774-148900	GT	AGG
(GGC)	 AG	149031-149141	GT	AGG
(GGG)	 AG	149267-149410	GT	AGG
(ATC)	 AG	149612-149726	GT	ACG
(GTG)	 AG	149865-149895	GT	GGG
(GAA)	 AG	150005-150068	GT	AGG
(AGT)	 AG	150180-150264	GT	GGG
(ATC)	 AG	150493-150686	GA	AGG
-recovered pasa_asmbl_18250.p1, terminal, 150493, 150686
-recovered pasa_asmbl_18250.p1, internal, 147050, 147213
-recovered pasa_asmbl_18250.p1, internal, 147500, 147603
-recovered pasa_asmbl_18250.p1, internal, 147696, 147821
-recovered pasa_asmbl_18250.p1, internal, 147939, 148072
-recovered pasa_asmbl_18250.p1, internal, 148229, 148437
-recovered pasa_asmbl_18250.p1, internal, 148774, 148900
-recovered pasa_asmbl_18250.p1, internal, 149031, 149141
-recovered pasa_asmbl_18250.p1, internal, 149267, 149410
-recovered pasa_asmbl_18250.p1, internal, 149612, 149726
-recovered pasa_asmbl_18250.p1, internal, 149865, 149895
-recovered pasa_asmbl_18250.p1, internal, 150005, 150068
-recovered pasa_asmbl_18250.p1, internal, 150180, 150264
Valid prediction for CodingQuarry_transcript_22083-T1
Valid prediction for snap_scaffold_17-snap.1894-T1
Valid prediction for GeneMark_model.71910_t
Valid prediction for GeneMark_model.71926_t
Valid prediction for snap_scaffold_17-snap.1922-T1
Valid prediction for CodingQuarry_transcript_22082-T1
Valid prediction for GeneMark_model.71919_t
Valid prediction for pasa_asmbl_18245.p1
Valid prediction for GeneMark_model.71937_t
Valid prediction for snap_scaffold_17-snap.1904-T1
Valid prediction for CodingQuarry_transcript_22081-T1
Valid prediction for GlimmerHMM_glimmerT_41795-T1
Valid prediction for GeneMark_model.71946_t
Valid prediction for snap_scaffold_17-snap.1920-T1
Valid prediction for snap_scaffold_17-snap.1908-T1
Valid prediction for snap_scaffold_17-snap.1929-T1
Valid prediction for GeneMark_model.71947_t
Valid prediction for HiQ_model.g28021.t1
Valid prediction for snap_scaffold_17-snap.1906-T1
Valid prediction for GeneMark_model.71927_t
Valid prediction for snap_scaffold_17-snap.1898-T1
Valid prediction for HiQ_model.g28030.t1
Valid prediction for snap_scaffold_17-snap.1914-T1
Valid prediction for GeneMark_model.71907_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: -)Valid prediction for snap_scaffold_17-snap.1928-T1
Valid prediction for GeneMark_model.71924_t
Valid prediction for snap_scaffold_17-snap.1907-T1
Valid prediction for snap_scaffold_17-snap.1901-T1
Valid prediction for GlimmerHMM_glimmerT_41801-T1
Valid prediction for Augustus_model.g28022.t1
Valid prediction for GeneMark_model.71936_t
Valid prediction for snap_scaffold_17-snap.1917-T1
Couldn't classify 105548, 105580
Sorry, prediction pasa_asmbl_19232.p1 fails validation.
(CGC)	 CG	105548-105580	GT	AGG
(GAG)	 AG	105682-105781	GT	CGG
(GGA)	 AG	106098-106177	GT	AGG
(ATC)	 AG	106261-106512	GT	AGG
(GTG)	 AG	106681-106935	GG	GAG
-recovered pasa_asmbl_19232.p1, terminal, 106681, 106935
-recovered pasa_asmbl_19232.p1, internal, 105682, 105781
-recovered pasa_asmbl_19232.p1, internal, 106098, 106177
-recovered pasa_asmbl_19232.p1, internal, 106261, 106512
Valid prediction for GeneMark_model.71955_t
Valid prediction for CodingQuarry_transcript_22080-T1
Valid prediction for GeneMark_model.71951_t
Valid prediction for snap_scaffold_17-snap.1892-T1
Valid prediction for GeneMark_model.71918_t
Valid prediction for GeneMark_model.71932_t
Valid prediction for GeneMark_model.71958_t
Valid prediction for GeneMark_model.71906_t
Valid prediction for GeneMark_model.71948_t
Valid prediction for Augustus_model.g28027.t1
Valid prediction for GlimmerHMM_glimmerT_41799-T1
Valid prediction for GeneMark_model.71913_t
Valid prediction for GlimmerHMM_glimmerT_41790-T1
Valid prediction for GeneMark_model.71928_t
Valid prediction for CodingQuarry_transcript_22086-T1
Valid prediction for snap_scaffold_17-snap.1916-T1
Valid prediction for GeneMark_model.71929_t
Valid prediction for GeneMark_model.71941_t
Valid prediction for HiQ_model.g28023.t1
Valid prediction for snap_scaffold_17-snap.1911-T1
Valid prediction for snap_scaffold_17-snap.1923-T1
Couldn't classify 98515, 98632
Couldn't classify 101514, 101600
Sorry, prediction pasa_asmbl_19234.p1 fails validation.
(AGG)	 CC	98515-98632	GT	CCG
(GAA)	 AG	99876-99927	GT	AGG
(GAA)	 AG	100309-100417	GT	AGG
(TTG)	 AG	100509-100598	GT	CGG
(CAC)	 AG	100677-100751	GT	GGG
(AGT)	 AG	100893-100960	GT	ACG
(GTT)	 AG	101110-101212	GT	AGG
(GGA)	 AG	101514-101600	AG	CCA
-recovered pasa_asmbl_19234.p1, internal, 99876, 99927
-recovered pasa_asmbl_19234.p1, internal, 100309, 100417
-recovered pasa_asmbl_19234.p1, internal, 100509, 100598
-recovered pasa_asmbl_19234.p1, internal, 100677, 100751
-recovered pasa_asmbl_19234.p1, internal, 100893, 100960
-recovered pasa_asmbl_19234.p1, internal, 101110, 101212
Valid prediction for GeneMark_model.71922_t
Valid prediction for GeneMark_model.71916_t
Valid prediction for CodingQuarry_transcript_22085-T1
Valid prediction for GeneMark_model.71909_t
Valid prediction for snap_scaffold_17-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_41794-T1
Valid prediction for GeneMark_model.71953_t
Valid prediction for pasa_asmbl_19227.p2
Valid prediction for snap_scaffold_17-snap.1927-T1
Valid prediction for GeneMark_model.71938_t
Couldn't classify 101899, 101958
Couldn't classify 105375, 105442
Sorry, prediction pasa_asmbl_19233.p1 fails validation.
(TCC)	 TC	101899-101958	GT	AGG
(GGG)	 AG	102175-102347	GT	ATG
(CCG)	 AG	102481-102623	GT	CTG
(TGA)	 AG	102845-102951	GT	AGG
(AAC)	 AG	103543-103628	GT	TGG
(TGC)	 AG	104051-104322	GT	AGG
(ATG)	 AG	104802-104864	GT	AGG
(GCC)	 AG	105375-105442	AC	CCA
add_exon() Sorry, pasa_asmbl_19233.p1 104802-104864-initial-1 is invalid.
-recovered pasa_asmbl_19233.p1, initial, 104802, 104864
-recovered pasa_asmbl_19233.p1, internal, 102175, 102347
-recovered pasa_asmbl_19233.p1, internal, 102481, 102623
-recovered pasa_asmbl_19233.p1, internal, 102845, 102951
-recovered pasa_asmbl_19233.p1, internal, 103543, 103628
-recovered pasa_asmbl_19233.p1, internal, 104051, 104322
-recovered pasa_asmbl_19233.p1, internal, 104802, 104864
Valid prediction for GlimmerHMM_glimmerT_41793-T1
Valid prediction for HiQ_model.g28019.t1
Valid prediction for GlimmerHMM_glimmerT_41797-T1
Valid prediction for GeneMark_model.71920_t
Valid prediction for pasa_asmbl_19226.p1
Valid prediction for GeneMark_model.71952_t
Valid prediction for snap_scaffold_17-snap.1921-T1
Valid prediction for Augustus_model.g28033.t1
Valid prediction for snap_scaffold_17-snap.1899-T1
Valid prediction for Augustus_model.g28026.t1
Valid prediction for GeneMark_model.71911_t
Valid prediction for GeneMark_model.71945_t
Valid prediction for snap_scaffold_17-snap.1918-T1
Valid prediction for GlimmerHMM_glimmerT_41798-T1
Valid prediction for pasa_asmbl_19228.p1
Valid prediction for snap_scaffold_17-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_41796-T1
Valid prediction for Augustus_model.g28032.t1
Valid prediction for snap_scaffold_17-snap.1897-T1
Valid prediction for snap_scaffold_17-snap.1915-T1
Valid prediction for snap_scaffold_17-snap.1895-T1
Valid prediction for GeneMark_model.71933_t
Valid prediction for GlimmerHMM_glimmerT_41804-T1
Valid prediction for GeneMark_model.71956_t
Valid prediction for snap_scaffold_17-snap.1912-T1
Valid prediction for GeneMark_model.71943_t
Valid prediction for snap_scaffold_17-snap.1905-T1
Valid prediction for GeneMark_model.71908_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25082, rend_intergenic: 24452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38560, rend_intergenic: 27141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52938, rend_intergenic: 50679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62813, rend_intergenic: 57602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75196, rend_intergenic: 66667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88795, rend_intergenic: 81096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103105, rend_intergenic: 96937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118915, rend_intergenic: 103869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122572, rend_intergenic: 120638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128443, rend_intergenic: 123736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133950, rend_intergenic: 131460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150686, rend_intergenic: 147046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169591, rend_intergenic: 159542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171950
-exon list size: 654


building trellis

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69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 25082, rend_intergenic: 24452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38560, rend_intergenic: 27141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52938, rend_intergenic: 50679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62813, rend_intergenic: 57602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75196, rend_intergenic: 66667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88795, rend_intergenic: 81096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103105, rend_intergenic: 96937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118915, rend_intergenic: 103869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122572, rend_intergenic: 120638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128443, rend_intergenic: 123736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133950, rend_intergenic: 131460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150686, rend_intergenic: 147046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169591, rend_intergenic: 159542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support