-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_8482460-8691389

-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_35082-T1
Valid prediction for snap_scaffold_14-snap.1793-T1
Valid prediction for snap_scaffold_14-snap.1797-T1
Valid prediction for snap_scaffold_14-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_35102-T1
Valid prediction for pasa_asmbl_12236.p1
Valid prediction for GlimmerHMM_glimmerT_35101-T1
Valid prediction for snap_scaffold_14-snap.1812-T1
Couldn't classify 45096, 45282
Sorry, prediction pasa_asmbl_12230.p1 fails validation.
(TTC)	 TG	45096-45282	GT	AGG
(GTA)	 AG	46013-46166	GT	AGG
(TAT)	 AG	46379-46562	GT	AGG
(ACA)	 AG	46751-46863	GT	AGG
(GTG)	 AG	47003-47183	CT	GAC
-recovered pasa_asmbl_12230.p1, terminal, 47003, 47183
-recovered pasa_asmbl_12230.p1, internal, 46013, 46166
-recovered pasa_asmbl_12230.p1, internal, 46379, 46562
-recovered pasa_asmbl_12230.p1, internal, 46751, 46863
Valid prediction for snap_scaffold_14-snap.1781-T1
Valid prediction for snap_scaffold_14-snap.1805-T1
Valid prediction for Augustus_model.g23610.t1
Valid prediction for snap_scaffold_14-snap.1770-T1
Couldn't classify 162763, 163317
Sorry, prediction pasa_asmbl_12240.p1 fails validation.
(CGG)	 GA	162763-163317	TA	GAT
Valid prediction for CodingQuarry_transcript_15726-T1
Valid prediction for GlimmerHMM_glimmerT_35087-T1
Valid prediction for Augustus_model.g23598.t1
Couldn't classify 16552, 16553
Sorry, prediction pasa_asmbl_12228.p1 fails validation.
(ATG)	 AG	16552-16553	GT	ATG
(GGC)	 AG	16953-17102	GT	AGG
(CTC)	 AG	17273-17443	GT	AAG
(GTC)	 AG	17817-17919	GT	AGG
(GAC)	 AG	18008-18161	GT	AGG
(GCC)	 AG	18392-18533	GT	AGG
(GTC)	 AG	18700-18805	CA	AAC
-recovered pasa_asmbl_12228.p1, terminal, 18700, 18805
-recovered pasa_asmbl_12228.p1, internal, 16552, 16553
-recovered pasa_asmbl_12228.p1, internal, 16953, 17102
-recovered pasa_asmbl_12228.p1, internal, 17273, 17443
-recovered pasa_asmbl_12228.p1, internal, 17817, 17919
-recovered pasa_asmbl_12228.p1, internal, 18008, 18161
-recovered pasa_asmbl_12228.p1, internal, 18392, 18533
Valid prediction for GlimmerHMM_glimmerT_35084-T1
Valid prediction for snap_scaffold_14-snap.1767-T1
Valid prediction for GeneMark_model.60114_t
Valid prediction for Augustus_model.g23599.t1
Valid prediction for snap_scaffold_14-snap.1809-T1
Valid prediction for snap_scaffold_14-snap.1789-T1
Valid prediction for HiQ_model.g23609.t1
Valid prediction for snap_scaffold_14-snap.1771-T1
Valid prediction for Augustus_model.g23617.t1
Valid prediction for snap_scaffold_14-snap.1769-T1
Valid prediction for Augustus_model.g23611.t1
Valid prediction for HiQ_model.g23606.t1
Valid prediction for CodingQuarry_transcript_15722-T1
Valid prediction for Augustus_model.g23614.t1
Valid prediction for GeneMark_model.60104_t
Valid prediction for Augustus_model.g23602.t1
Valid prediction for GeneMark_model.60112_t
Couldn't classify 166242, 166970
Sorry, prediction pasa_asmbl_12242.p1 fails validation.
(AAA)	 TC	166242-166970	CA	GGC
Valid prediction for Augustus_model.g23605.t1
Valid prediction for GeneMark_model.60124_t
Valid prediction for Augustus_model.g23600.t1
Valid prediction for HiQ_model.g23595.t1
Valid prediction for GeneMark_model.60095_t
Valid prediction for GeneMark_model.60131_t
Valid prediction for GeneMark_model.60122_t
Valid prediction for GlimmerHMM_glimmerT_35099-T1
Valid prediction for GlimmerHMM_glimmerT_35108-T1
Valid prediction for snap_scaffold_14-snap.1773-T1
Valid prediction for snap_scaffold_14-snap.1808-T1
Valid prediction for Augustus_model.g23613.t1
Valid prediction for Augustus_model.g23596.t1
Valid prediction for GeneMark_model.60106_t
Valid prediction for pasa_asmbl_12237.p1
Valid prediction for GeneMark_model.60130_t
Valid prediction for GlimmerHMM_glimmerT_35089-T1
Valid prediction for GeneMark_model.60125_t
Valid prediction for snap_scaffold_14-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_35096-T1
Valid prediction for snap_scaffold_14-snap.1776-T1
Valid prediction for snap_scaffold_14-snap.1796-T1
Couldn't classify 165193, 165342
Sorry, prediction pasa_asmbl_12239.p1 fails validation.
(ATG)	 GA	161845-162477	GT	AGG
(GTG)	 AG	165193-165342	GA	ATG
-recovered pasa_asmbl_12239.p1, initial, 161845, 162477
Valid prediction for GeneMark_model.60103_t
Valid prediction for GeneMark_model.60110_t
Valid prediction for GlimmerHMM_glimmerT_35088-T1
Valid prediction for snap_scaffold_14-snap.1803-T1
Valid prediction for CodingQuarry_transcript_15723-T1
Valid prediction for GlimmerHMM_glimmerT_35092-T1
Valid prediction for snap_scaffold_14-snap.1783-T1
Valid prediction for snap_scaffold_14-snap.1790-T1
Valid prediction for GeneMark_model.60097_t
Valid prediction for GlimmerHMM_glimmerT_35091-T1
Valid prediction for snap_scaffold_14-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_35090-T1
Valid prediction for snap_scaffold_14-snap.1782-T1
Valid prediction for GeneMark_model.60128_t
Valid prediction for GlimmerHMM_glimmerT_35095-T1
Valid prediction for Augustus_model.g23604.t1
Valid prediction for GeneMark_model.60117_t
Valid prediction for snap_scaffold_14-snap.1787-T1
Couldn't classify 161845, 162759
Sorry, prediction pasa_asmbl_12238.p1 fails validation.
(ATG)	 GA	161845-162759	AG	GGA
Valid prediction for Augustus_model.g23601.t1
Valid prediction for snap_scaffold_14-snap.1801-T1
Valid prediction for snap_scaffold_14-snap.1778-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 HiQ_model.g23607.t1
Valid prediction for snap_scaffold_14-snap.1779-T1
Valid prediction for GeneMark_model.60099_t
Valid prediction for snap_scaffold_14-snap.1802-T1
Couldn't classify 26452, 26525
Sorry, prediction pasa_asmbl_13316.p1 fails validation.
(GTC)	 TA	26452-26525	GT	AGG
(CCT)	 AG	26969-27145	GT	AGG
(CTT)	 AG	27433-27556	GT	AGG
(AAA)	 AG	28658-28783	GT	AGG
(GGT)	 AG	28885-28944	AG	GAA
-recovered pasa_asmbl_13316.p1, terminal, 28885, 28944
-recovered pasa_asmbl_13316.p1, internal, 26969, 27145
-recovered pasa_asmbl_13316.p1, internal, 27433, 27556
-recovered pasa_asmbl_13316.p1, internal, 28658, 28783
Valid prediction for GeneMark_model.60109_t
Valid prediction for snap_scaffold_14-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_35103-T1
Valid prediction for HiQ_model.g23615.t1
Valid prediction for snap_scaffold_14-snap.1777-T1
Valid prediction for snap_scaffold_14-snap.1774-T1
Valid prediction for snap_scaffold_14-snap.1810-T1
Valid prediction for Augustus_model.g23594.t1
Valid prediction for Augustus_model.g23618.t1
Valid prediction for Augustus_model.g23603.t1
Valid prediction for Augustus_model.g23619.t1
Valid prediction for GlimmerHMM_glimmerT_35105-T1
Valid prediction for snap_scaffold_14-snap.1784-T1
Valid prediction for CodingQuarry_transcript_15725-T1
Valid prediction for HiQ_model.g23608.t1
Valid prediction for GlimmerHMM_glimmerT_35100-T1
Valid prediction for GlimmerHMM_glimmerT_35104-T1
Valid prediction for GlimmerHMM_glimmerT_35086-T1
Valid prediction for GeneMark_model.60096_t
Valid prediction for GeneMark_model.60101_t
Valid prediction for GeneMark_model.60121_t
Valid prediction for GlimmerHMM_glimmerT_35107-T1
Valid prediction for snap_scaffold_14-snap.1799-T1
Valid prediction for snap_scaffold_14-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_35083-T1
Valid prediction for snap_scaffold_14-snap.1788-T1
Valid prediction for CodingQuarry_transcript_15721-T1
Valid prediction for snap_scaffold_14-snap.1772-T1
Valid prediction for snap_scaffold_14-snap.1813-T1
Valid prediction for snap_scaffold_14-snap.1800-T1
Valid prediction for HiQ_model.g23616.t1
Valid prediction for GlimmerHMM_glimmerT_35106-T1
Valid prediction for GlimmerHMM_glimmerT_35093-T1
Valid prediction for pasa_asmbl_13307.p1
Valid prediction for pasa_asmbl_13310.p1
Valid prediction for GlimmerHMM_glimmerT_35098-T1
Valid prediction for snap_scaffold_14-snap.1794-T1
Valid prediction for snap_scaffold_14-snap.1768-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.1780-T1
Valid prediction for snap_scaffold_14-snap.1766-T1
Valid prediction for GeneMark_model.60116_t
Valid prediction for GlimmerHMM_glimmerT_35094-T1
Valid prediction for GlimmerHMM_glimmerT_35109-T1
Valid prediction for GeneMark_model.60107_t
Valid prediction for GeneMark_model.60132_t
Valid prediction for GeneMark_model.60094_t
Valid prediction for GeneMark_model.60129_t
Valid prediction for GlimmerHMM_glimmerT_35110-T1
Valid prediction for CodingQuarry_transcript_15727-T1
Valid prediction for Augustus_model.g23597.t1
Valid prediction for CodingQuarry_transcript_15724-T1
Valid prediction for snap_scaffold_14-snap.1775-T1
Valid prediction for snap_scaffold_14-snap.1792-T1
Valid prediction for GeneMark_model.60111_t
Valid prediction for GeneMark_model.60127_t
Valid prediction for GlimmerHMM_glimmerT_35081-T1
Valid prediction for GeneMark_model.60133_t
Valid prediction for GeneMark_model.60115_t
Valid prediction for GeneMark_model.60119_t
Valid prediction for snap_scaffold_14-snap.1798-T1
Valid prediction for GeneMark_model.60118_t
Valid prediction for GeneMark_model.60120_t
Valid prediction for snap_scaffold_14-snap.1806-T1
Valid prediction for Augustus_model.g23612.t1
Valid prediction for snap_scaffold_14-snap.1786-T1
Valid prediction for pasa_asmbl_13314.p1
Valid prediction for GeneMark_model.60098_t
Valid prediction for GeneMark_model.60093_t
Valid prediction for GeneMark_model.60123_t
Valid prediction for GeneMark_model.60108_t
Valid prediction for snap_scaffold_14-snap.1807-T1
Valid prediction for GeneMark_model.60102_t
Valid prediction for GlimmerHMM_glimmerT_35085-T1
Couldn't classify 22739, 22967
Couldn't classify 26272, 26322
Sorry, prediction pasa_asmbl_13317.p1 fails validation.
(GGT)	 AC	22739-22967	GT	ACG
(CCT)	 AG	25674-26026	GT	CGG
(ATA)	 AG	26272-26322	GG	ATG
-recovered pasa_asmbl_13317.p1, internal, 25674, 26026
Valid prediction for GlimmerHMM_glimmerT_35097-T1
Valid prediction for GeneMark_model.60105_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25669, rend_intergenic: 23772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47183, rend_intergenic: 37013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53305, rend_intergenic: 49802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70871, rend_intergenic: 54279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78491, rend_intergenic: 73945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93885, rend_intergenic: 85473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104523, rend_intergenic: 101525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109768, rend_intergenic: 104664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125541, rend_intergenic: 120526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148423, rend_intergenic: 137569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150320, rend_intergenic: 148896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155321, rend_intergenic: 151087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184970, rend_intergenic: 180399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206086, rend_intergenic: 200105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208930
-exon list size: 630


building trellis

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87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 25669, rend_intergenic: 23772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47183, rend_intergenic: 37013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53305, rend_intergenic: 49802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70871, rend_intergenic: 54279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78491, rend_intergenic: 73945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93885, rend_intergenic: 85473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104523, rend_intergenic: 101525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109768, rend_intergenic: 104664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125541, rend_intergenic: 120526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148423, rend_intergenic: 137569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150320, rend_intergenic: 148896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155321, rend_intergenic: 151087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184970, rend_intergenic: 180399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206086, rend_intergenic: 200105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14242
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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