-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_13562439-13817709

-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 snap_scaffold_18-snap.2886-T1
Valid prediction for pasa_asmbl_21047.p1
Valid prediction for snap_scaffold_18-snap.2922-T1
Valid prediction for snap_scaffold_18-snap.2888-T1
Valid prediction for snap_scaffold_18-snap.2919-T1
Couldn't classify 251126, 251670
Sorry, prediction GlimmerHMM_glimmerT_43425-T1 fails validation.
(ATG)	 AA	249207-249657	GT	AGG
(AAG)	 AG	250192-250330	GT	ACG
(CTC)	 AG	251126-251670	GT	GTG
-recovered GlimmerHMM_glimmerT_43425-T1, initial, 249207, 249657
-recovered GlimmerHMM_glimmerT_43425-T1, internal, 250192, 250330
-recovered GlimmerHMM_glimmerT_43425-T1, internal, 251126, 251670
Valid prediction for pasa_asmbl_21036.p1
Valid prediction for snap_scaffold_18-snap.2870-T1
Valid prediction for GlimmerHMM_glimmerT_43423-T1
Valid prediction for snap_scaffold_18-snap.2915-T1
Valid prediction for snap_scaffold_18-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_43397-T1
Valid prediction for GlimmerHMM_glimmerT_43396-T1
Valid prediction for CodingQuarry_transcript_23936-T1
Valid prediction for GlimmerHMM_glimmerT_43398-T1
Valid prediction for snap_scaffold_18-snap.2920-T1
Valid prediction for snap_scaffold_18-snap.2880-T1
Valid prediction for GlimmerHMM_glimmerT_43411-T1
Couldn't classify 77226, 77381
Sorry, prediction pasa_asmbl_21027.p1 fails validation.
(ATG)	 TC	76884-77060	GT	AGG
(GAA)	 AG	77226-77381	CG	CAC
-recovered pasa_asmbl_21027.p1, initial, 76884, 77060
Valid prediction for GlimmerHMM_glimmerT_43394-T1
Valid prediction for snap_scaffold_18-snap.2910-T1
Valid prediction for pasa_asmbl_21029.p1
Valid prediction for snap_scaffold_18-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_43416-T1
Valid prediction for snap_scaffold_18-snap.2905-T1
Valid prediction for GlimmerHMM_glimmerT_43419-T1
Couldn't classify 80606, 80641
Couldn't classify 81283, 81447
Sorry, prediction pasa_asmbl_21028.p1 fails validation.
(CCC)	 CA	80606-80641	GT	AGG
(ATC)	 AG	80907-81032	GT	AGG
(AGG)	 AG	81283-81447	GA	AGG
-recovered pasa_asmbl_21028.p1, internal, 80907, 81032
Valid prediction for snap_scaffold_18-snap.2890-T1
Valid prediction for GlimmerHMM_glimmerT_43410-T1
Valid prediction for GlimmerHMM_glimmerT_43406-T1
Valid prediction for snap_scaffold_18-snap.2862-T1
Valid prediction for snap_scaffold_18-snap.2869-T1
Valid prediction for snap_scaffold_18-snap.2892-T1
Valid prediction for GlimmerHMM_glimmerT_43408-T1
Valid prediction for snap_scaffold_18-snap.2902-T1
Valid prediction for snap_scaffold_18-snap.2896-T1
Valid prediction for snap_scaffold_18-snap.2878-T1
Valid prediction for pasa_asmbl_21043.p1
Couldn't classify 209205, 209537
Sorry, prediction pasa_asmbl_20196.p1 fails validation.
(TTG)	 TG	209205-209537	AC	GAA
Valid prediction for snap_scaffold_18-snap.2903-T1
Valid prediction for snap_scaffold_18-snap.2913-T1
Valid prediction for snap_scaffold_18-snap.2895-T1
Valid prediction for snap_scaffold_18-snap.2872-T1
Valid prediction for snap_scaffold_18-snap.2904-T1
Valid prediction for GlimmerHMM_glimmerT_43401-T1
Valid prediction for snap_scaffold_18-snap.2889-T1
Valid prediction for pasa_asmbl_21034.p1
Valid prediction for snap_scaffold_18-snap.2884-T1
Valid prediction for snap_scaffold_18-snap.2899-T1
Valid prediction for GlimmerHMM_glimmerT_43404-T1
Valid prediction for GlimmerHMM_glimmerT_43424-T1
Valid prediction for snap_scaffold_18-snap.2921-T1
Valid prediction for snap_scaffold_18-snap.2898-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43400-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_18-snap.2914-T1
Valid prediction for GlimmerHMM_glimmerT_43403-T1
Valid prediction for snap_scaffold_18-snap.2881-T1
Valid prediction for snap_scaffold_18-snap.2865-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_43402-T1
Couldn't classify 103016, 103129
Sorry, prediction pasa_asmbl_20190.p1 fails validation.
(GGT)	 CA	103016-103129	GT	ATG
(GCT)	 AG	104629-104842	GT	GGG
(AGC)	 AG	105122-105235	GT	AGG
(GTT)	 AG	105732-105825	GT	AAG
(GCT)	 AG	106439-106577	GT	AGG
(GTG)	 AG	106846-107043	AC	AGA
-recovered pasa_asmbl_20190.p1, terminal, 106846, 107043
-recovered pasa_asmbl_20190.p1, internal, 104629, 104842
-recovered pasa_asmbl_20190.p1, internal, 105122, 105235
-recovered pasa_asmbl_20190.p1, internal, 105732, 105825
-recovered pasa_asmbl_20190.p1, internal, 106439, 106577
Valid prediction for snap_scaffold_18-snap.2887-T1
Valid prediction for snap_scaffold_18-snap.2912-T1
Valid prediction for GlimmerHMM_glimmerT_43421-T1
Valid prediction for GlimmerHMM_glimmerT_43417-T1
Valid prediction for snap_scaffold_18-snap.2883-T1
Valid prediction for snap_scaffold_18-snap.2900-T1
Couldn't classify 156125, 156152
Couldn't classify 156852, 157007
Sorry, prediction pasa_asmbl_20187.p1 fails validation.
(ATA)	 TT	156125-156152	GT	AGG
(CTT)	 AG	156504-156616	GT	AGG
(TCG)	 AG	156852-157007	GA	GAG
-recovered pasa_asmbl_20187.p1, internal, 156504, 156616
Couldn't classify 162521, 162586
Sorry, prediction pasa_asmbl_20180.p1 fails validation.
(GGC)	 CC	162521-162586	GT	AGG
(GGA)	 AG	163162-163267	GT	AGG
(CGA)	 AG	163876-163963	GT	AGG
(TCC)	 AG	164105-164189	GT	ATG
(ACT)	 AG	164559-164664	GT	AGG
(GAA)	 AG	164891-164966	GT	AGG
(GGC)	 AG	165152-165209	GT	AGG
(AGT)	 AG	165487-165595	GT	TGG
(CCA)	 AG	166129-166190	CT	GAC
-recovered pasa_asmbl_20180.p1, terminal, 166129, 166190
-recovered pasa_asmbl_20180.p1, internal, 163162, 163267
-recovered pasa_asmbl_20180.p1, internal, 163876, 163963
-recovered pasa_asmbl_20180.p1, internal, 164105, 164189
-recovered pasa_asmbl_20180.p1, internal, 164559, 164664
-recovered pasa_asmbl_20180.p1, internal, 164891, 164966
-recovered pasa_asmbl_20180.p1, internal, 165152, 165209
-recovered pasa_asmbl_20180.p1, internal, 165487, 165595
Valid prediction for snap_scaffold_18-snap.2918-T1
Valid prediction for snap_scaffold_18-snap.2882-T1
Valid prediction for snap_scaffold_18-snap.2877-T1
Couldn't classify 156987, 157098
Sorry, prediction pasa_asmbl_20237.p1 fails validation.
(GAA)	 GA	156987-157098	GT	AGG
(AGA)	 AG	157629-157773	GT	GGG
(GAG)	 AG	158174-158321	AC	AAA
-recovered pasa_asmbl_20237.p1, terminal, 158174, 158321
-recovered pasa_asmbl_20237.p1, internal, 157629, 157773
Valid prediction for GlimmerHMM_glimmerT_43413-T1
Valid prediction for snap_scaffold_18-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_43395-T1
Valid prediction for snap_scaffold_18-snap.2916-T1
Valid prediction for CodingQuarry_transcript_23935-T1
Valid prediction for snap_scaffold_18-snap.2863-T1
Valid prediction for snap_scaffold_18-snap.2897-T1
Valid prediction for snap_scaffold_18-snap.2911-T1
Valid prediction for snap_scaffold_18-snap.2909-T1
Valid prediction for snap_scaffold_18-snap.2894-T1
Valid prediction for pasa_asmbl_20177.p1
Valid prediction for snap_scaffold_18-snap.2879-T1
Valid prediction for pasa_asmbl_20189.p1
Valid prediction for CodingQuarry_transcript_23934-T1
Valid prediction for snap_scaffold_18-snap.2871-T1
Valid prediction for GlimmerHMM_glimmerT_43412-T1
Valid prediction for snap_scaffold_18-snap.2875-T1
Valid prediction for snap_scaffold_18-snap.2923-T1
Couldn't classify 156852, 157030
Couldn't classify 157052, 157098
Sorry, prediction CodingQuarry_transcript_23933-T1 fails validation.
(ATG)	 CT	156560-156616	GT	AGG
(TCG)	 AG	156852-157030	AC	GAA
(TCA)	 GA	157052-157098	GT	AGG
(AGA)	 AG	157629-157773	GT	GGG
(GAG)	 AG	158174-158306	GT	AGG
(GAT)	 AG	158477-158600	GT	AGG
(AGA)	 AG	158697-158769	GT	AGG
(AAC)	 AG	159222-159336	GT	AGG
(AAC)	 AG	159553-159661	GT	AGG
(CAA)	 AG	159792-159847	CC	AGC
-recovered CodingQuarry_transcript_23933-T1, initial, 156560, 156616
add_exon() Sorry, CodingQuarry_transcript_23933-T1 159553-159661-terminal-3 is invalid.
-recovered CodingQuarry_transcript_23933-T1, terminal, 159553, 159661
-recovered CodingQuarry_transcript_23933-T1, terminal, 159792, 159847
-recovered CodingQuarry_transcript_23933-T1, internal, 157629, 157773
-recovered CodingQuarry_transcript_23933-T1, internal, 158174, 158306
-recovered CodingQuarry_transcript_23933-T1, internal, 158477, 158600
-recovered CodingQuarry_transcript_23933-T1, internal, 158697, 158769
-recovered CodingQuarry_transcript_23933-T1, internal, 159222, 159336
-recovered CodingQuarry_transcript_23933-T1, internal, 159553, 159661
Valid prediction for GlimmerHMM_glimmerT_43405-T1
Couldn't classify 44740, 45038
Sorry, prediction pasa_asmbl_20198.p1 fails validation.
(ATG)	 CA	42187-42331	GT	AGG
(AAC)	 AG	44740-45038	GG	GGG
-recovered pasa_asmbl_20198.p1, initial, 42187, 42331
Valid prediction for GlimmerHMM_glimmerT_43407-T1
Valid prediction for snap_scaffold_18-snap.2873-T1
Valid prediction for snap_scaffold_18-snap.2908-T1
Valid prediction for snap_scaffold_18-snap.2893-T1
Valid prediction for snap_scaffold_18-snap.2867-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2885-T1
Valid prediction for GlimmerHMM_glimmerT_43414-T1
Valid prediction for CodingQuarry_transcript_23932-T1
Valid prediction for GlimmerHMM_glimmerT_43409-T1
Valid prediction for snap_scaffold_18-snap.2906-T1
Valid prediction for CodingQuarry_transcript_23931-T1
Valid prediction for GlimmerHMM_glimmerT_43399-T1
Valid prediction for GlimmerHMM_glimmerT_43418-T1
Valid prediction for snap_scaffold_18-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_43415-T1
Valid prediction for snap_scaffold_18-snap.2866-T1
Valid prediction for GlimmerHMM_glimmerT_43422-T1
Valid prediction for snap_scaffold_18-snap.2907-T1
Valid prediction for snap_scaffold_18-snap.2917-T1
Valid prediction for snap_scaffold_18-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_43420-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16989, rend_intergenic: 1748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33096, rend_intergenic: 27180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44706, rend_intergenic: 33102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45953, rend_intergenic: 44900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65118, rend_intergenic: 50035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70932, rend_intergenic: 65157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73722, rend_intergenic: 71162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86159, rend_intergenic: 76219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93950, rend_intergenic: 86560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115036, rend_intergenic: 101835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129628, rend_intergenic: 125915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131447, rend_intergenic: 129943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138636, rend_intergenic: 132031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147116, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170143, rend_intergenic: 150045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188129, rend_intergenic: 185902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211848, rend_intergenic: 188380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222777, rend_intergenic: 214390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231636, rend_intergenic: 223787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242061, rend_intergenic: 237240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 120672, rend_intergenic: 120669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 255271
-exon list size: 514


building trellis

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86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
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    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 16989, rend_intergenic: 1748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33096, rend_intergenic: 27180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44706, rend_intergenic: 33102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45953, rend_intergenic: 44900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65118, rend_intergenic: 50035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70932, rend_intergenic: 65157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73722, rend_intergenic: 71162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86159, rend_intergenic: 76219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93950, rend_intergenic: 86560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115036, rend_intergenic: 101835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129628, rend_intergenic: 125915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131447, rend_intergenic: 129943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138636, rend_intergenic: 132031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147116, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170143, rend_intergenic: 150045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188129, rend_intergenic: 185902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211848, rend_intergenic: 188380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222777, rend_intergenic: 214390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231636, rend_intergenic: 223787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242061, rend_intergenic: 237240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 120672, rend_intergenic: 120669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support