-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_8687734-8851404

-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.60145_t
Valid prediction for GeneMark_model.60167_t
Valid prediction for GlimmerHMM_glimmerT_35129-T1
Valid prediction for GeneMark_model.60134_t
Valid prediction for GeneMark_model.60170_t
Valid prediction for snap_scaffold_14-snap.1846-T1
Valid prediction for GeneMark_model.60177_t
Valid prediction for snap_scaffold_14-snap.1838-T1
Valid prediction for Augustus_model.g23627.t1
Valid prediction for GlimmerHMM_glimmerT_35119-T1
Couldn't classify 46312, 46427
Sorry, prediction pasa_asmbl_12250.p2 fails validation.
(CTG)	 AG	46312-46427	GT	AGG
(GGC)	 AG	46542-46685	GT	TGG
(GTT)	 AG	46841-46961	CC	AAC
-recovered pasa_asmbl_12250.p2, terminal, 46841, 46961
-recovered pasa_asmbl_12250.p2, internal, 46312, 46427
-recovered pasa_asmbl_12250.p2, internal, 46542, 46685
Couldn't classify 35984, 36107
Couldn't classify 42354, 42365
Sorry, prediction pasa_asmbl_12249.p1 fails validation.
(CTT)	 AC	35984-36107	GT	TAG
(ATG)	 AG	36203-36326	GT	AGG
(GTT)	 AG	36569-36665	GT	GAG
(CAA)	 AG	36792-36899	GT	AGG
(TTG)	 AG	37418-37550	GT	TGG
(GCA)	 AG	38103-38191	GT	CTG
(CTG)	 AG	40052-40210	GT	CGG
(GAT)	 AG	42104-42178	GT	AGG
(GTC)	 AG	42354-42365	GA	AGG
add_exon() Sorry, pasa_asmbl_12249.p1 36203-36326-initial-1 is invalid.
-recovered pasa_asmbl_12249.p1, initial, 36203, 36326
-recovered pasa_asmbl_12249.p1, internal, 36203, 36326
-recovered pasa_asmbl_12249.p1, internal, 36569, 36665
-recovered pasa_asmbl_12249.p1, internal, 36792, 36899
-recovered pasa_asmbl_12249.p1, internal, 37418, 37550
-recovered pasa_asmbl_12249.p1, internal, 38103, 38191
-recovered pasa_asmbl_12249.p1, internal, 40052, 40210
-recovered pasa_asmbl_12249.p1, internal, 42104, 42178
Valid prediction for snap_scaffold_14-snap.1835-T1
Valid prediction for snap_scaffold_14-snap.1829-T1
Valid prediction for GeneMark_model.60163_t
Valid prediction for GeneMark_model.60157_t
Valid prediction for GeneMark_model.60149_t
Couldn't classify 35765, 35866
Sorry, prediction pasa_asmbl_12248.p1 fails validation.
(ATG)	 AA	29970-30062	GT	CCG
(GTT)	 AG	30916-31042	GT	TGG
(GCA)	 AG	32235-32373	GT	CTG
(GGA)	 AG	32590-32692	GT	AGG
(AAA)	 AG	33458-33547	GT	CGG
(CCT)	 AG	33699-33763	GT	GGG
(GCG)	 AG	33864-33909	GT	AGG
(AAC)	 AG	35765-35866	CT	GGC
-recovered pasa_asmbl_12248.p1, initial, 29970, 30062
-recovered pasa_asmbl_12248.p1, internal, 30916, 31042
-recovered pasa_asmbl_12248.p1, internal, 32235, 32373
-recovered pasa_asmbl_12248.p1, internal, 32590, 32692
-recovered pasa_asmbl_12248.p1, internal, 33458, 33547
-recovered pasa_asmbl_12248.p1, internal, 33699, 33763
-recovered pasa_asmbl_12248.p1, internal, 33864, 33909
Valid prediction for GeneMark_model.60138_t
Valid prediction for pasa_asmbl_12244.p1
Valid prediction for GeneMark_model.60143_t
Valid prediction for GeneMark_model.60165_t
Valid prediction for GeneMark_model.60161_t
Valid prediction for snap_scaffold_14-snap.1818-T1
Valid prediction for Augustus_model.g23630.t1
Valid prediction for snap_scaffold_14-snap.1832-T1
Valid prediction for snap_scaffold_14-snap.1841-T1
Valid prediction for pasa_asmbl_12246.p1
Valid prediction for GlimmerHMM_glimmerT_35111-T1
Valid prediction for snap_scaffold_14-snap.1836-T1
Valid prediction for GeneMark_model.60152_t
Valid prediction for GeneMark_model.60183_t
Valid prediction for GeneMark_model.60179_t
Valid prediction for GlimmerHMM_glimmerT_35128-T1
Valid prediction for GeneMark_model.60171_t
Valid prediction for GeneMark_model.60147_t
Valid prediction for snap_scaffold_14-snap.1849-T1
Valid prediction for snap_scaffold_14-snap.1844-T1
Valid prediction for Augustus_model.g23626.t1
Valid prediction for snap_scaffold_14-snap.1833-T1
Valid prediction for GeneMark_model.60175_t
Valid prediction for snap_scaffold_14-snap.1826-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_15728-T1
Valid prediction for Augustus_model.g23633.t1
Valid prediction for GlimmerHMM_glimmerT_35115-T1
Valid prediction for CodingQuarry_transcript_15733-T1
Valid prediction for GeneMark_model.60186_t
Valid prediction for snap_scaffold_14-snap.1843-T1
Valid prediction for Augustus_model.g23622.t1
Valid prediction for snap_scaffold_14-snap.1817-T1
Valid prediction for Augustus_model.g23631.t1
Valid prediction for snap_scaffold_14-snap.1820-T1
Valid prediction for snap_scaffold_14-snap.1814-T1
Valid prediction for GeneMark_model.60168_t
Valid prediction for CodingQuarry_transcript_15731-T1
Valid prediction for GeneMark_model.60158_t
Valid prediction for snap_scaffold_14-snap.1823-T1
Valid prediction for GlimmerHMM_glimmerT_35126-T1
Valid prediction for GlimmerHMM_glimmerT_35124-T1
Valid prediction for GlimmerHMM_glimmerT_35122-T1
Valid prediction for Augustus_model.g23623.t1
Valid prediction for snap_scaffold_14-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_35113-T1
Valid prediction for HiQ_model.g23620.t1
Valid prediction for snap_scaffold_14-snap.1825-T1
Valid prediction for snap_scaffold_14-snap.1845-T1
Valid prediction for GeneMark_model.60159_t
Valid prediction for GeneMark_model.60139_t
Valid prediction for GlimmerHMM_glimmerT_35125-T1
Valid prediction for GeneMark_model.60141_t
Valid prediction for CodingQuarry_transcript_15732-T1
Valid prediction for GeneMark_model.60155_t
Valid prediction for snap_scaffold_14-snap.1827-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.60180_t
Valid prediction for GeneMark_model.60146_t
Valid prediction for snap_scaffold_14-snap.1840-T1
Valid prediction for pasa_asmbl_13324.p1
Valid prediction for snap_scaffold_14-snap.1848-T1
Valid prediction for HiQ_model.g23624.t1
Valid prediction for snap_scaffold_14-snap.1828-T1
Valid prediction for GeneMark_model.60174_t
Valid prediction for GlimmerHMM_glimmerT_35116-T1
Valid prediction for GeneMark_model.60182_t
Valid prediction for snap_scaffold_14-snap.1822-T1
Valid prediction for GeneMark_model.60172_t
Valid prediction for Augustus_model.g23632.t1
Valid prediction for snap_scaffold_14-snap.1824-T1
Valid prediction for GeneMark_model.60162_t
Valid prediction for GeneMark_model.60144_t
Valid prediction for GlimmerHMM_glimmerT_35112-T1
Valid prediction for CodingQuarry_transcript_15730-T1
Valid prediction for snap_scaffold_14-snap.1842-T1
Valid prediction for GeneMark_model.60148_t
Valid prediction for pasa_asmbl_13318.p1
Valid prediction for GeneMark_model.60173_t
Couldn't classify 90773, 91259
Couldn't classify 91397, 91587
Sorry, prediction pasa_asmbl_13328.p1 fails validation.
(CCC)	 TC	90773-91259	GT	AGG
(ACC)	 AG	91397-91587	AT	AGA
Valid prediction for snap_scaffold_14-snap.1837-T1
Valid prediction for GeneMark_model.60185_t
Valid prediction for HiQ_model.g23621.t1
Valid prediction for snap_scaffold_14-snap.1830-T1
Valid prediction for Augustus_model.g23628.t1
Valid prediction for GeneMark_model.60176_t
Valid prediction for GlimmerHMM_glimmerT_35127-T1
Valid prediction for GeneMark_model.60135_t
Valid prediction for GlimmerHMM_glimmerT_35120-T1
Valid prediction for GlimmerHMM_glimmerT_35121-T1
Valid prediction for GlimmerHMM_glimmerT_35118-T1
Valid prediction for snap_scaffold_14-snap.1847-T1
Valid prediction for snap_scaffold_14-snap.1831-T1
Valid prediction for GeneMark_model.60164_t
Valid prediction for CodingQuarry_transcript_15735-T1
Valid prediction for GeneMark_model.60151_t
Valid prediction for GeneMark_model.60136_t
Valid prediction for snap_scaffold_14-snap.1813-T1
Valid prediction for GeneMark_model.60187_t
Valid prediction for snap_scaffold_14-snap.1821-T1
Valid prediction for GeneMark_model.60166_t
Valid prediction for GlimmerHMM_glimmerT_35117-T1
Valid prediction for GeneMark_model.60160_t
Valid prediction for GeneMark_model.60150_t
Valid prediction for GeneMark_model.60169_t
Valid prediction for GeneMark_model.60156_t
Valid prediction for Augustus_model.g23629.t1
Valid prediction for GeneMark_model.60178_t
Valid prediction for GlimmerHMM_glimmerT_35130-T1
Valid prediction for snap_scaffold_14-snap.1839-T1
Valid prediction for GeneMark_model.60137_t
Valid prediction for CodingQuarry_transcript_15729-T1
Valid prediction for snap_scaffold_14-snap.1819-T1
Valid prediction for GeneMark_model.60140_t
Valid prediction for GeneMark_model.60154_t
Valid prediction for snap_scaffold_14-snap.1834-T1
Valid prediction for GeneMark_model.60181_t
Valid prediction for GeneMark_model.60184_t
Valid prediction for GeneMark_model.60142_t
Valid prediction for GeneMark_model.60153_t
Valid prediction for Augustus_model.g23625.t1
Valid prediction for snap_scaffold_14-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_35114-T1
Couldn't classify 91951, 92395
Sorry, prediction pasa_asmbl_13325.p1 fails validation.
(CTC)	 CC	91951-92395	GT	AGG
(CGA)	 AG	92717-92946	GT	AGG
(GGG)	 AG	93040-93166	GT	CGG
(GCA)	 AG	93252-93445	GT	GAG
(GCT)	 AG	94386-94662	GT	AGG
(TCC)	 AG	94765-95210	GA	GAG
-recovered pasa_asmbl_13325.p1, terminal, 94765, 95210
-recovered pasa_asmbl_13325.p1, internal, 92717, 92946
-recovered pasa_asmbl_13325.p1, internal, 93040, 93166
-recovered pasa_asmbl_13325.p1, internal, 93252, 93445
-recovered pasa_asmbl_13325.p1, internal, 94386, 94662
Valid prediction for GlimmerHMM_glimmerT_35123-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10849, rend_intergenic: 7002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40889, rend_intergenic: 31638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47564, rend_intergenic: 42059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60754, rend_intergenic: 52127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71845, rend_intergenic: 68462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73271, rend_intergenic: 72489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80780, rend_intergenic: 73391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88848, rend_intergenic: 82809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96026, rend_intergenic: 92937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100333, rend_intergenic: 96333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106945, rend_intergenic: 103809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109318, rend_intergenic: 107450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113442, rend_intergenic: 109489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118908, rend_intergenic: 113536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143923, rend_intergenic: 126061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159613, rend_intergenic: 156615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163671
-exon list size: 651


building trellis

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88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
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    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
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 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10849, rend_intergenic: 7002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40889, rend_intergenic: 31638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47564, rend_intergenic: 42059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60754, rend_intergenic: 52127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71845, rend_intergenic: 68462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73271, rend_intergenic: 72489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80780, rend_intergenic: 73391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88848, rend_intergenic: 82809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96026, rend_intergenic: 92937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100333, rend_intergenic: 96333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106945, rend_intergenic: 103809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109318, rend_intergenic: 107450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113442, rend_intergenic: 109489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118908, rend_intergenic: 113536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143923, rend_intergenic: 126061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159613, rend_intergenic: 156615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support