-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_11121299-11280479

-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_16-snap.2085-T1
Valid prediction for snap_scaffold_16-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_39898-T1
Valid prediction for GeneMark_model.68405_t
Valid prediction for GeneMark_model.68395_t
Valid prediction for snap_scaffold_16-snap.2096-T1
Valid prediction for GlimmerHMM_glimmerT_39897-T1
Valid prediction for GlimmerHMM_glimmerT_39888-T1
Couldn't classify 126602, 126703
Couldn't classify 129968, 130047
Sorry, prediction pasa_asmbl_17371.p1 fails validation.
(GGA)	 TA	126602-126703	GT	AGG
(GCC)	 AG	127887-127997	GT	CAG
(GAC)	 AG	128261-128351	GT	TGG
(AAG)	 AG	129968-130047	GT	TGG
-recovered pasa_asmbl_17371.p1, internal, 127887, 127997
-recovered pasa_asmbl_17371.p1, internal, 128261, 128351
-recovered pasa_asmbl_17371.p1, internal, 129968, 130047
Valid prediction for snap_scaffold_16-snap.2104-T1
Valid prediction for GeneMark_model.68354_t
Valid prediction for GeneMark_model.68367_t
Valid prediction for snap_scaffold_16-snap.2091-T1
Valid prediction for GeneMark_model.68399_t
Valid prediction for Augustus_model.g26817.t1
Valid prediction for GeneMark_model.68383_t
Valid prediction for Augustus_model.g26818.t1
Valid prediction for snap_scaffold_16-snap.2107-T1
Valid prediction for snap_scaffold_16-snap.2111-T1
Valid prediction for snap_scaffold_16-snap.2108-T1
Valid prediction for GeneMark_model.68375_t
Valid prediction for GeneMark_model.68373_t
Valid prediction for GeneMark_model.68387_t
Valid prediction for GeneMark_model.68385_t
Valid prediction for GeneMark_model.68378_t
Valid prediction for GeneMark_model.68390_t
Valid prediction for GeneMark_model.68389_t
Valid prediction for snap_scaffold_16-snap.2100-T1
Valid prediction for GeneMark_model.68361_t
Valid prediction for Augustus_model.g26810.t1
Valid prediction for GeneMark_model.68381_t
Valid prediction for snap_scaffold_16-snap.2092-T1
Valid prediction for snap_scaffold_16-snap.2089-T1
Valid prediction for GeneMark_model.68359_t
Valid prediction for GeneMark_model.68369_t
Valid prediction for GeneMark_model.68403_t
Valid prediction for snap_scaffold_16-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_39900-T1
Valid prediction for snap_scaffold_16-snap.2079-T1
Valid prediction for snap_scaffold_16-snap.2095-T1
Valid prediction for GeneMark_model.68357_t
Valid prediction for GeneMark_model.68376_t
Valid prediction for GeneMark_model.68365_t
Valid prediction for snap_scaffold_16-snap.2086-T1
Valid prediction for snap_scaffold_16-snap.2080-T1
Valid prediction for snap_scaffold_16-snap.2084-T1
Valid prediction for snap_scaffold_16-snap.2113-T1
Valid prediction for GeneMark_model.68397_t
Valid prediction for GlimmerHMM_glimmerT_39895-T1
Valid prediction for GeneMark_model.68363_t
Valid prediction for GeneMark_model.68371_t
Valid prediction for GeneMark_model.68380_t
Valid prediction for snap_scaffold_16-snap.2102-T1
Valid prediction for snap_scaffold_16-snap.2087-T1
Valid prediction for snap_scaffold_16-snap.2097-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.68356_t
Valid prediction for GeneMark_model.68388_t
Valid prediction for snap_scaffold_16-snap.2090-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: -)Couldn't classify 121572, 121753
Couldn't classify 125286, 125375
Sorry, prediction pasa_asmbl_16509.p1 fails validation.
(CTC)	 GC	121572-121753	GT	AGG
(TGA)	 AG	122022-122116	GT	AGG
(GAG)	 AG	124208-124290	GT	AGG
(GTG)	 AG	125286-125375	GG	TAG
-recovered pasa_asmbl_16509.p1, internal, 122022, 122116
-recovered pasa_asmbl_16509.p1, internal, 124208, 124290
Valid prediction for snap_scaffold_16-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_39890-T1
Valid prediction for snap_scaffold_16-snap.2114-T1
Valid prediction for Augustus_model.g26808.t1
Valid prediction for Augustus_model.g26811.t1
Valid prediction for GlimmerHMM_glimmerT_39899-T1
Valid prediction for GlimmerHMM_glimmerT_39892-T1
Valid prediction for GlimmerHMM_glimmerT_39893-T1
Valid prediction for GlimmerHMM_glimmerT_39894-T1
Valid prediction for snap_scaffold_16-snap.2088-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.2098-T1
Valid prediction for snap_scaffold_16-snap.2099-T1
Valid prediction for GeneMark_model.68391_t
Valid prediction for Augustus_model.g26809.t1
Valid prediction for GeneMark_model.68358_t
Valid prediction for GlimmerHMM_glimmerT_39889-T1
Couldn't classify 84114, 84232
Couldn't classify 87110, 87237
Sorry, prediction pasa_asmbl_16513.p1 fails validation.
(GAC)	 CA	84114-84232	GT	AGG
(GCG)	 AG	84770-84873	GT	AGG
(CCG)	 AG	85882-86031	GT	AAG
(GTC)	 AG	87110-87237	AA	CCA
-recovered pasa_asmbl_16513.p1, internal, 84770, 84873
-recovered pasa_asmbl_16513.p1, internal, 85882, 86031
Valid prediction for snap_scaffold_16-snap.2109-T1
Valid prediction for snap_scaffold_16-snap.2078-T1
Valid prediction for snap_scaffold_16-snap.2075-T1
Valid prediction for GeneMark_model.68384_t
Valid prediction for GeneMark_model.68379_t
Valid prediction for snap_scaffold_16-snap.2105-T1
Valid prediction for GeneMark_model.68404_t
Valid prediction for Augustus_model.g26814.t1
Couldn't classify 128893, 129082
Couldn't classify 133678, 133710
Sorry, prediction pasa_asmbl_16508.p1 fails validation.
(CTT)	 GG	128893-129082	GT	AGG
(AGG)	 AG	130345-130386	GT	AGG
(ACT)	 AG	131308-131405	GT	AGG
(ACC)	 AG	131759-131896	GT	TGG
(ACC)	 AG	133678-133710	GT	AGG
-recovered pasa_asmbl_16508.p1, internal, 130345, 130386
-recovered pasa_asmbl_16508.p1, internal, 131308, 131405
-recovered pasa_asmbl_16508.p1, internal, 131759, 131896
-recovered pasa_asmbl_16508.p1, internal, 133678, 133710
Valid prediction for GeneMark_model.68402_t
Valid prediction for GeneMark_model.68396_t
Couldn't classify 105301, 105432
Couldn't classify 108109, 108290
Sorry, prediction pasa_asmbl_16511.p1 fails validation.
(GTG)	 CA	105301-105432	GT	AGG
(CAA)	 AG	107053-107170	GT	AGG
(AGG)	 AG	108109-108290	AA	CCA
-recovered pasa_asmbl_16511.p1, internal, 107053, 107170
Valid prediction for GeneMark_model.68374_t
Valid prediction for Augustus_model.g26812.t1
Valid prediction for snap_scaffold_16-snap.2101-T1
Valid prediction for snap_scaffold_16-snap.2103-T1
Valid prediction for GeneMark_model.68362_t
Valid prediction for snap_scaffold_16-snap.2081-T1
Valid prediction for GeneMark_model.68394_t
Valid prediction for GeneMark_model.68364_t
Valid prediction for snap_scaffold_16-snap.2112-T1
Valid prediction for GeneMark_model.68386_t
Couldn't classify 103807, 103931
Sorry, prediction pasa_asmbl_16512.p2 fails validation.
(ATG)	 TC	97621-97630	GT	CGG
(TGT)	 AG	99012-99154	GT	TGG
(ATA)	 AG	100130-100222	GT	AGG
(ATG)	 AG	101778-101926	GT	GAG
(AAC)	 AG	102075-102160	GT	AGG
(GCA)	 AG	103807-103931	CG	GGC
-recovered pasa_asmbl_16512.p2, initial, 97621, 97630
-recovered pasa_asmbl_16512.p2, initial, 101778, 101926
-recovered pasa_asmbl_16512.p2, internal, 99012, 99154
-recovered pasa_asmbl_16512.p2, internal, 100130, 100222
-recovered pasa_asmbl_16512.p2, internal, 101778, 101926
-recovered pasa_asmbl_16512.p2, internal, 102075, 102160
Valid prediction for GlimmerHMM_glimmerT_39887-T1
Valid prediction for Augustus_model.g26815.t1
Valid prediction for snap_scaffold_16-snap.2106-T1
Valid prediction for GeneMark_model.68368_t
Valid prediction for snap_scaffold_16-snap.2110-T1
Valid prediction for GeneMark_model.68372_t
Valid prediction for GeneMark_model.68400_t
Valid prediction for snap_scaffold_16-snap.2077-T1
Valid prediction for GeneMark_model.68377_t
Valid prediction for GeneMark_model.68355_t
Valid prediction for GeneMark_model.68393_t
Valid prediction for GlimmerHMM_glimmerT_39891-T1
Valid prediction for snap_scaffold_16-snap.2093-T1
Valid prediction for GeneMark_model.68398_t
Valid prediction for GeneMark_model.68366_t
Valid prediction for GeneMark_model.68382_t
Valid prediction for GeneMark_model.68392_t
Valid prediction for Augustus_model.g26816.t1
Valid prediction for GeneMark_model.68353_t
Valid prediction for GeneMark_model.68360_t
Valid prediction for GlimmerHMM_glimmerT_39896-T1
Valid prediction for snap_scaffold_16-snap.2083-T1
Valid prediction for Augustus_model.g26813.t1
Valid prediction for GeneMark_model.68370_t
Couldn't classify 91060, 91162
Couldn't classify 95551, 95626
Sorry, prediction pasa_asmbl_16716.p1 fails validation.
(AGT)	 TC	91060-91162	GT	CGG
(TCA)	 AG	92215-92318	GT	AGG
(GGG)	 AG	92689-92738	GT	AGG
(GGA)	 AG	95551-95626	GT	AGG
-recovered pasa_asmbl_16716.p1, internal, 92215, 92318
-recovered pasa_asmbl_16716.p1, internal, 92689, 92738
-recovered pasa_asmbl_16716.p1, internal, 95551, 95626

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10262, rend_intergenic: 7112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17002, rend_intergenic: 11007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23737, rend_intergenic: 21704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32454, rend_intergenic: 24125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42746, rend_intergenic: 34189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45039, rend_intergenic: 44627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67154, rend_intergenic: 45704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79063, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86224, rend_intergenic: 81711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99652, rend_intergenic: 97533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101802, rend_intergenic: 100485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106197, rend_intergenic: 104633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113927, rend_intergenic: 111291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130870, rend_intergenic: 121337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153925, rend_intergenic: 147617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157760, rend_intergenic: 155191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159181
-exon list size: 731


building trellis

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83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 10262, rend_intergenic: 7112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17002, rend_intergenic: 11007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23737, rend_intergenic: 21704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32454, rend_intergenic: 24125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42746, rend_intergenic: 34189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45039, rend_intergenic: 44627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67154, rend_intergenic: 45704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79063, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86224, rend_intergenic: 81711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99652, rend_intergenic: 97533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101802, rend_intergenic: 100485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106197, rend_intergenic: 104633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113927, rend_intergenic: 111291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130870, rend_intergenic: 121337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153925, rend_intergenic: 147617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157760, rend_intergenic: 155191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support