-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_10842835-11081636

-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: +)Couldn't classify 222444, 222926
Sorry, prediction pasa_asmbl_2054.p1 fails validation.
(ATG)	 GT	222444-222926	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_1457-T1
Valid prediction for snap_scaffold_1-snap.1886-T1
Valid prediction for Augustus_model.g1078.t1
Valid prediction for Augustus_model.g1064.t1
Valid prediction for GlimmerHMM_glimmerT_1465-T1
Valid prediction for pasa_asmbl_2035.p1
Valid prediction for GlimmerHMM_glimmerT_1463-T1
Valid prediction for GlimmerHMM_glimmerT_1455-T1
Valid prediction for pasa_asmbl_2056.p1
Valid prediction for Augustus_model.g1088.t1
Valid prediction for snap_scaffold_1-snap.1874-T1
Valid prediction for snap_scaffold_1-snap.1860-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1869-T1
Valid prediction for snap_scaffold_1-snap.1898-T1
Valid prediction for snap_scaffold_1-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_1458-T1
Valid prediction for snap_scaffold_1-snap.1873-T1
Valid prediction for CodingQuarry_transcript_2757-T1
Valid prediction for snap_scaffold_1-snap.1890-T1
Valid prediction for snap_scaffold_1-snap.1855-T1
Valid prediction for snap_scaffold_1-snap.1880-T1
Couldn't classify 148003, 148146
Couldn't classify 151140, 151334
Sorry, prediction pasa_asmbl_2048.p1 fails validation.
(TAC)	 AG	148003-148146	GT	AGG
(GAG)	 AG	151140-151334	AC	GCA
-recovered pasa_asmbl_2048.p1, internal, 148003, 148146
Valid prediction for snap_scaffold_1-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_1471-T1
Valid prediction for CodingQuarry_transcript_2758-T1
Valid prediction for snap_scaffold_1-snap.1896-T1
Valid prediction for CodingQuarry_transcript_2760-T1
Valid prediction for Augustus_model.g1070.t1
Valid prediction for GlimmerHMM_glimmerT_1449-T1
Couldn't classify 11809, 11974
Sorry, prediction pasa_asmbl_2031.p1 fails validation.
(GTG)	 CA	11809-11974	GT	AGG
(GTC)	 AG	12455-12539	GT	AGG
(GTA)	 AG	12618-12764	GT	GAG
(ACC)	 AG	15640-15688	TA	AGT
-recovered pasa_asmbl_2031.p1, terminal, 15640, 15688
-recovered pasa_asmbl_2031.p1, internal, 12455, 12539
-recovered pasa_asmbl_2031.p1, internal, 12618, 12764
Valid prediction for GlimmerHMM_glimmerT_1450-T1
Valid prediction for GlimmerHMM_glimmerT_1453-T1
Valid prediction for GlimmerHMM_glimmerT_1462-T1
Valid prediction for snap_scaffold_1-snap.1857-T1
Valid prediction for Augustus_model.g1060.t1
Valid prediction for snap_scaffold_1-snap.1875-T1
Valid prediction for CodingQuarry_transcript_2766-T1
Valid prediction for snap_scaffold_1-snap.1862-T1
Valid prediction for snap_scaffold_1-snap.1887-T1
Valid prediction for HiQ_model.g1077.t1
Valid prediction for HiQ_model.g1074.t1
Valid prediction for CodingQuarry_transcript_2756-T1
Valid prediction for GlimmerHMM_glimmerT_1466-T1
Valid prediction for Augustus_model.g1086.t1
Valid prediction for snap_scaffold_1-snap.1882-T1
Valid prediction for Augustus_model.g1069.t1
Valid prediction for snap_scaffold_1-snap.1878-T1
Valid prediction for Augustus_model.g1087.t1
Valid prediction for pasa_asmbl_2042.p1
Valid prediction for snap_scaffold_1-snap.1861-T1
Valid prediction for pasa_asmbl_2044.p1
Valid prediction for snap_scaffold_1-snap.1884-T1
Valid prediction for CodingQuarry_transcript_2765-T1
Valid prediction for snap_scaffold_1-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_1459-T1
Valid prediction for snap_scaffold_1-snap.1858-T1
Valid prediction for snap_scaffold_1-snap.1865-T1
Valid prediction for Augustus_model.g1071.t1
Valid prediction for snap_scaffold_1-snap.1881-T1
Valid prediction for Augustus_model.g1061.t1
Valid prediction for Augustus_model.g1076.t1
Couldn't classify 151389, 151640
Sorry, prediction pasa_asmbl_2049.p1 fails validation.
(AAG)	 AC	151389-151640	GT	AGG
(GCC)	 AG	151834-152029	GT	AGG
(ACG)	 AG	153343-153581	GT	AGG
(ATC)	 AG	153678-153761	GT	AGG
(ATC)	 AG	154087-154263	GT	AGG
(CTG)	 AG	154741-154870	GT	TGG
(GCA)	 AG	155545-155701	GT	AGG
(GTC)	 AG	156914-157046	GT	AGG
(GCT)	 AG	157393-157506	GT	TGG
(TTG)	 AG	157611-157725	GT	AGG
(GAA)	 AG	158011-158145	GT	AGG
(GTG)	 AG	158371-158558	AA	GAA
-recovered pasa_asmbl_2049.p1, terminal, 158371, 158558
-recovered pasa_asmbl_2049.p1, internal, 151834, 152029
-recovered pasa_asmbl_2049.p1, internal, 153343, 153581
-recovered pasa_asmbl_2049.p1, internal, 153678, 153761
-recovered pasa_asmbl_2049.p1, internal, 154087, 154263
-recovered pasa_asmbl_2049.p1, internal, 154741, 154870
-recovered pasa_asmbl_2049.p1, internal, 155545, 155701
-recovered pasa_asmbl_2049.p1, internal, 156914, 157046
-recovered pasa_asmbl_2049.p1, internal, 157393, 157506
-recovered pasa_asmbl_2049.p1, internal, 157611, 157725
-recovered pasa_asmbl_2049.p1, internal, 158011, 158145
Valid prediction for HiQ_model.g1068.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_1-snap.1879-T1
Valid prediction for snap_scaffold_1-snap.1871-T1
Valid prediction for snap_scaffold_1-snap.1863-T1
Valid prediction for CodingQuarry_transcript_2759-T1
Valid prediction for CodingQuarry_transcript_2764-T1
Valid prediction for snap_scaffold_1-snap.1883-T1
Valid prediction for snap_scaffold_1-snap.1866-T1
Valid prediction for GlimmerHMM_glimmerT_1454-T1
Valid prediction for Augustus_model.g1083.t1
Valid prediction for Augustus_model.g1082.t1
Valid prediction for Augustus_model.g1066.t1
Valid prediction for snap_scaffold_1-snap.1856-T1
Valid prediction for Augustus_model.g1081.t1
Valid prediction for snap_scaffold_1-snap.1872-T1
Valid prediction for pasa_asmbl_601.p1
Valid prediction for GlimmerHMM_glimmerT_1467-T1
Valid prediction for CodingQuarry_transcript_2763-T1
Couldn't classify 101257, 101278
Sorry, prediction pasa_asmbl_602.p1 fails validation.
(CGC)	 AT	101257-101278	GT	AGG
(ATG)	 AG	101414-102456	GA	GAG
-recovered pasa_asmbl_602.p1, terminal, 101414, 102456
Valid prediction for GlimmerHMM_glimmerT_1448-T1
Valid prediction for Augustus_model.g1065.t1
Valid prediction for Augustus_model.g1063.t1
Valid prediction for GlimmerHMM_glimmerT_1468-T1
Valid prediction for snap_scaffold_1-snap.1868-T1
Valid prediction for snap_scaffold_1-snap.1888-T1
Valid prediction for snap_scaffold_1-snap.1895-T1
Valid prediction for GlimmerHMM_glimmerT_1460-T1
Valid prediction for Augustus_model.g1075.t1
Valid prediction for GlimmerHMM_glimmerT_1456-T1
Valid prediction for Augustus_model.g1080.t1
Valid prediction for snap_scaffold_1-snap.1876-T1
Valid prediction for snap_scaffold_1-snap.1889-T1
Valid prediction for snap_scaffold_1-snap.1854-T1
Valid prediction for GlimmerHMM_glimmerT_1470-T1
Valid prediction for snap_scaffold_1-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_1469-T1
Valid prediction for GlimmerHMM_glimmerT_1461-T1
Valid prediction for snap_scaffold_1-snap.1877-T1
Valid prediction for Augustus_model.g1067.t1
Valid prediction for snap_scaffold_1-snap.1892-T1
Valid prediction for Augustus_model.g1062.t1
Valid prediction for CodingQuarry_transcript_2762-T1
Valid prediction for GlimmerHMM_glimmerT_1464-T1
Valid prediction for Augustus_model.g1079.t1
Valid prediction for Augustus_model.g1084.t1
Valid prediction for Augustus_model.g1072.t1
Valid prediction for snap_scaffold_1-snap.1853-T1
Valid prediction for snap_scaffold_1-snap.1859-T1
Valid prediction for snap_scaffold_1-snap.1852-T1
Valid prediction for snap_scaffold_1-snap.1885-T1
Valid prediction for Augustus_model.g1085.t1
Couldn't classify 22109, 22198
Sorry, prediction pasa_asmbl_603.p1 fails validation.
(AAT)	 AG	22109-22198	GT	TGG
(GTT)	 AG	23972-24090	GT	AGG
(ATC)	 AG	24366-24479	GT	CTG
(GTA)	 AG	24799-24940	GT	AGG
(GAA)	 AG	25109-25225	GT	AGG
(ATG)	 AG	25445-25510	GT	AGG
(GAT)	 AG	25644-25720	GT	AGG
(ATC)	 AG	26299-26392	GG	AGG
-recovered pasa_asmbl_603.p1, initial, 25445, 25510
-recovered pasa_asmbl_603.p1, terminal, 26299, 26392
-recovered pasa_asmbl_603.p1, internal, 22109, 22198
-recovered pasa_asmbl_603.p1, internal, 23972, 24090
-recovered pasa_asmbl_603.p1, internal, 24366, 24479
-recovered pasa_asmbl_603.p1, internal, 24799, 24940
-recovered pasa_asmbl_603.p1, internal, 25109, 25225
-recovered pasa_asmbl_603.p1, internal, 25445, 25510
-recovered pasa_asmbl_603.p1, internal, 25644, 25720
Valid prediction for GlimmerHMM_glimmerT_1451-T1
Valid prediction for GlimmerHMM_glimmerT_1452-T1
Valid prediction for HiQ_model.g1073.t1
Valid prediction for snap_scaffold_1-snap.1891-T1
Valid prediction for snap_scaffold_1-snap.1897-T1
Valid prediction for snap_scaffold_1-snap.1867-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23736, rend_intergenic: 18579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60389, rend_intergenic: 38745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68815, rend_intergenic: 61602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75146, rend_intergenic: 72063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84067, rend_intergenic: 79157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97310, rend_intergenic: 84193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140522, rend_intergenic: 136918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158558, rend_intergenic: 153967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173706, rend_intergenic: 166605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189964, rend_intergenic: 185646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214466, rend_intergenic: 212411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238802
-exon list size: 416


building trellis

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19.6    
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23.9    
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24.6    
24.9    
25.1    
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25.6    
25.8    
26.1    
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26.6    
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27.0    
27.3    
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30.4    
30.6    
30.9    
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31.3    
31.6    
31.8    
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33.0    
33.3    
33.5    
33.7    
34.0    
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34.9    
35.2    
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35.6    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
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46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
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50.0    
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50.5    
50.7    
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51.9    
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52.6    
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55.3    
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97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 23736, rend_intergenic: 18579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60389, rend_intergenic: 38745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68815, rend_intergenic: 61602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75146, rend_intergenic: 72063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84067, rend_intergenic: 79157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97310, rend_intergenic: 84193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140522, rend_intergenic: 136918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158558, rend_intergenic: 153967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173706, rend_intergenic: 166605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189964, rend_intergenic: 185646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214466, rend_intergenic: 212411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support