-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_9569169-9761981

-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_12-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_29857-T1
Valid prediction for Augustus_model.g19745.t1
Valid prediction for snap_scaffold_12-snap.1808-T1
Valid prediction for Augustus_model.g19740.t1
Valid prediction for GlimmerHMM_glimmerT_29850-T1
Valid prediction for GlimmerHMM_glimmerT_29843-T1
Valid prediction for GlimmerHMM_glimmerT_29865-T1
Valid prediction for GlimmerHMM_glimmerT_29852-T1
Valid prediction for GlimmerHMM_glimmerT_29845-T1
Valid prediction for GlimmerHMM_glimmerT_29838-T1
Valid prediction for GlimmerHMM_glimmerT_29862-T1
Valid prediction for snap_scaffold_12-snap.1811-T1
Valid prediction for snap_scaffold_12-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_29853-T1
Valid prediction for Augustus_model.g19739.t1
Valid prediction for GlimmerHMM_glimmerT_29842-T1
Valid prediction for snap_scaffold_12-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_29849-T1
Valid prediction for snap_scaffold_12-snap.1841-T1
Valid prediction for snap_scaffold_12-snap.1815-T1
Valid prediction for CodingQuarry_transcript_10338-T1
Valid prediction for snap_scaffold_12-snap.1820-T1
Valid prediction for Augustus_model.g19746.t1
Valid prediction for Augustus_model.g19738.t1
Valid prediction for snap_scaffold_12-snap.1825-T1
Valid prediction for snap_scaffold_12-snap.1816-T1
Valid prediction for snap_scaffold_12-snap.1822-T1
Valid prediction for Augustus_model.g19729.t1
Valid prediction for Augustus_model.g19743.t1
Valid prediction for GlimmerHMM_glimmerT_29835-T1
Valid prediction for snap_scaffold_12-snap.1803-T1
Valid prediction for snap_scaffold_12-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_29869-T1
Valid prediction for GlimmerHMM_glimmerT_29868-T1
Valid prediction for snap_scaffold_12-snap.1828-T1
Valid prediction for Augustus_model.g19726.t1
Valid prediction for snap_scaffold_12-snap.1831-T1
Valid prediction for snap_scaffold_12-snap.1836-T1
Valid prediction for snap_scaffold_12-snap.1832-T1
Valid prediction for pasa_asmbl_7867.p1
Valid prediction for GlimmerHMM_glimmerT_29839-T1
Valid prediction for GlimmerHMM_glimmerT_29855-T1
Valid prediction for Augustus_model.g19734.t1
Valid prediction for GlimmerHMM_glimmerT_29836-T1
Valid prediction for GlimmerHMM_glimmerT_29864-T1
Valid prediction for snap_scaffold_12-snap.1839-T1
Valid prediction for snap_scaffold_12-snap.1797-T1
Valid prediction for snap_scaffold_12-snap.1824-T1
Valid prediction for snap_scaffold_12-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_29841-T1
Valid prediction for GlimmerHMM_glimmerT_29866-T1
Valid prediction for Augustus_model.g19735.t1
Valid prediction for snap_scaffold_12-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_29848-T1
Valid prediction for GlimmerHMM_glimmerT_29861-T1
Valid prediction for CodingQuarry_transcript_10337-T1
Valid prediction for snap_scaffold_12-snap.1837-T1
Valid prediction for Augustus_model.g19736.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_12-snap.1840-T1
Valid prediction for snap_scaffold_12-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_29859-T1
Valid prediction for GlimmerHMM_glimmerT_29867-T1
Valid prediction for Augustus_model.g19741.t1
Valid prediction for CodingQuarry_transcript_10339-T1
Valid prediction for GlimmerHMM_glimmerT_29837-T1
Valid prediction for snap_scaffold_12-snap.1804-T1
Valid prediction for snap_scaffold_12-snap.1806-T1
Valid prediction for snap_scaffold_12-snap.1810-T1
Valid prediction for snap_scaffold_12-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_29834-T1
Valid prediction for snap_scaffold_12-snap.1812-T1
Valid prediction for snap_scaffold_12-snap.1827-T1
Valid prediction for snap_scaffold_12-snap.1802-T1
Valid prediction for Augustus_model.g19733.t1
Valid prediction for Augustus_model.g19731.t1
Valid prediction for snap_scaffold_12-snap.1826-T1
Valid prediction for Augustus_model.g19725.t1
Valid prediction for GlimmerHMM_glimmerT_29860-T1
Valid prediction for Augustus_model.g19730.t1
Valid prediction for snap_scaffold_12-snap.1814-T1
Valid prediction for snap_scaffold_12-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_29844-T1
Valid prediction for pasa_asmbl_8687.p1
Valid prediction for GlimmerHMM_glimmerT_29863-T1
Valid prediction for GlimmerHMM_glimmerT_29858-T1
Couldn't classify 123334, 123996
Sorry, prediction pasa_asmbl_8682.p1 fails validation.
(ATG)	 GG	123334-123996	TT	CCT
Valid prediction for snap_scaffold_12-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_29856-T1
Couldn't classify 117067, 117251
Sorry, prediction pasa_asmbl_8684.p1 fails validation.
(ATG)	 AC	114284-114377	GT	GGG
(GAA)	 AG	114535-114631	GT	AGG
(GAG)	 AG	114871-115109	GT	CAG
(AGG)	 AG	115255-115343	GT	GGG
(GTG)	 AG	115842-115923	GT	CGG
(GTT)	 AG	116285-116374	GT	AGG
(ATC)	 AG	116481-116594	GT	AGG
(AGA)	 AG	116694-116782	GT	AAG
(CTT)	 AG	116867-116954	GT	CGG
(GTG)	 AG	117067-117251	CC	CTC
-recovered pasa_asmbl_8684.p1, initial, 114284, 114377
add_exon() Sorry, pasa_asmbl_8684.p1 114535-114631-terminal-3 is invalid.
-recovered pasa_asmbl_8684.p1, terminal, 114535, 114631
add_exon() Sorry, pasa_asmbl_8684.p1 116285-116374-terminal-1 is invalid.
-recovered pasa_asmbl_8684.p1, terminal, 116285, 116374
-recovered pasa_asmbl_8684.p1, internal, 114535, 114631
-recovered pasa_asmbl_8684.p1, internal, 114871, 115109
-recovered pasa_asmbl_8684.p1, internal, 115255, 115343
-recovered pasa_asmbl_8684.p1, internal, 115842, 115923
-recovered pasa_asmbl_8684.p1, internal, 116285, 116374
-recovered pasa_asmbl_8684.p1, internal, 116481, 116594
-recovered pasa_asmbl_8684.p1, internal, 116694, 116782
-recovered pasa_asmbl_8684.p1, internal, 116867, 116954
Valid prediction for snap_scaffold_12-snap.1809-T1
Valid prediction for CodingQuarry_transcript_10340-T1
Valid prediction for Augustus_model.g19732.t1
Valid prediction for GlimmerHMM_glimmerT_29840-T1
Valid prediction for GlimmerHMM_glimmerT_29846-T1
Couldn't classify 117837, 118586
Sorry, prediction pasa_asmbl_8683.p1 fails validation.
(GCC)	 CT	117837-118586	GT	AGG
(ATG)	 AG	118696-118811	GT	AGG
(TGG)	 AG	118904-118997	CC	GAC
-recovered pasa_asmbl_8683.p1, initial, 118696, 118811
-recovered pasa_asmbl_8683.p1, terminal, 118904, 118997
-recovered pasa_asmbl_8683.p1, internal, 118696, 118811
Valid prediction for GlimmerHMM_glimmerT_29847-T1
Valid prediction for snap_scaffold_12-snap.1830-T1
Couldn't classify 112292, 112366
Couldn't classify 113303, 113403
Sorry, prediction pasa_asmbl_8686.p1 fails validation.
(GAC)	 TC	112292-112366	GT	AGG
(AAC)	 AG	112621-112710	GT	GGG
(GTG)	 AG	112823-112951	GT	AGG
(GTA)	 AG	113104-113218	GT	CAG
(TTC)	 AG	113303-113403	GT	GAG
-recovered pasa_asmbl_8686.p1, internal, 112621, 112710
-recovered pasa_asmbl_8686.p1, internal, 112823, 112951
-recovered pasa_asmbl_8686.p1, internal, 113104, 113218
-recovered pasa_asmbl_8686.p1, internal, 113303, 113403
Valid prediction for snap_scaffold_12-snap.1823-T1
Valid prediction for Augustus_model.g19727.t1
Valid prediction for HiQ_model.g19737.t1
Valid prediction for snap_scaffold_12-snap.1833-T1
Valid prediction for snap_scaffold_12-snap.1835-T1
Valid prediction for Augustus_model.g19742.t1
Couldn't classify 124045, 124458
Sorry, prediction pasa_asmbl_8681.p1 fails validation.
(CGG)	 GT	124045-124458	AA	AGA
Valid prediction for snap_scaffold_12-snap.1807-T1
Valid prediction for snap_scaffold_12-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_29851-T1
Valid prediction for Augustus_model.g19744.t1
Valid prediction for snap_scaffold_12-snap.1813-T1
Valid prediction for snap_scaffold_12-snap.1818-T1
Valid prediction for snap_scaffold_12-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_29854-T1
Valid prediction for Augustus_model.g19728.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8618, rend_intergenic: 6612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20951, rend_intergenic: 14306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26390, rend_intergenic: 22839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28657, rend_intergenic: 26705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33863, rend_intergenic: 33011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39139, rend_intergenic: 33970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46835, rend_intergenic: 41738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85325, rend_intergenic: 80987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87388, rend_intergenic: 85453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92566, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132231, rend_intergenic: 123606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135524, rend_intergenic: 132441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137889, rend_intergenic: 135564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142565, rend_intergenic: 138496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153244, rend_intergenic: 151292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157497, rend_intergenic: 153276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164718, rend_intergenic: 157910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176175, rend_intergenic: 167638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176693, rend_intergenic: 176223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187850, rend_intergenic: 182299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192813
-exon list size: 424


building trellis

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27.9    
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28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
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35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
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39.4    
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40.6    
40.8    
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41.8    
42.0    
42.3    
42.5    
42.7    
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97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 8618, rend_intergenic: 6612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20951, rend_intergenic: 14306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26390, rend_intergenic: 22839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28657, rend_intergenic: 26705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33863, rend_intergenic: 33011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39139, rend_intergenic: 33970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46835, rend_intergenic: 41738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85325, rend_intergenic: 80987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87388, rend_intergenic: 85453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92566, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132231, rend_intergenic: 123606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135524, rend_intergenic: 132441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137889, rend_intergenic: 135564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142565, rend_intergenic: 138496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153244, rend_intergenic: 151292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157497, rend_intergenic: 153276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164718, rend_intergenic: 157910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176175, rend_intergenic: 167638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176693, rend_intergenic: 176223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187850, rend_intergenic: 182299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support