-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_7393016-7618392

-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_14950-T1
Valid prediction for CodingQuarry_transcript_55104-T1
Valid prediction for snap_scaffold_6-snap.1683-T1
Valid prediction for Augustus_model.g9909.t1
Couldn't classify 145849, 146013
Couldn't classify 146698, 146778
Sorry, prediction pasa_asmbl_47972.p1 fails validation.
(GTG)	 TG	145849-146013	GT	AGG
(ATA)	 AG	146448-146543	GT	AGG
(AGT)	 AG	146698-146778	GT	GAG
-recovered pasa_asmbl_47972.p1, internal, 146448, 146543
-recovered pasa_asmbl_47972.p1, internal, 146698, 146778
Valid prediction for snap_scaffold_6-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_14972-T1
Valid prediction for snap_scaffold_6-snap.1656-T1
Valid prediction for snap_scaffold_6-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_14967-T1
Valid prediction for snap_scaffold_6-snap.1677-T1
Valid prediction for snap_scaffold_6-snap.1663-T1
Couldn't classify 142820, 143431
Sorry, prediction pasa_asmbl_47079.p1 fails validation.
(CTC)	 CT	142820-143431	AT	GCA
Valid prediction for Augustus_model.g9910.t1
Valid prediction for snap_scaffold_6-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_14943-T1
Valid prediction for GlimmerHMM_glimmerT_14962-T1
Valid prediction for snap_scaffold_6-snap.1676-T1
Valid prediction for Augustus_model.g9900.t1
Valid prediction for snap_scaffold_6-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_14942-T1
Valid prediction for snap_scaffold_6-snap.1669-T1
Valid prediction for Augustus_model.g9896.t1
Valid prediction for Augustus_model.g9903.t1
Valid prediction for GlimmerHMM_glimmerT_14968-T1
Valid prediction for Augustus_model.g9895.t1
Valid prediction for Augustus_model.g9914.t1
Valid prediction for Augustus_model.g9907.t1
Valid prediction for GlimmerHMM_glimmerT_14961-T1
Valid prediction for snap_scaffold_6-snap.1675-T1
Valid prediction for CodingQuarry_transcript_55103-T1
Valid prediction for GlimmerHMM_glimmerT_14956-T1
Valid prediction for Augustus_model.g9904.t1
Valid prediction for snap_scaffold_6-snap.1681-T1
Valid prediction for snap_scaffold_6-snap.1651-T1
Valid prediction for snap_scaffold_6-snap.1654-T1
Valid prediction for snap_scaffold_6-snap.1690-T1
Valid prediction for snap_scaffold_6-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_14974-T1
Couldn't classify 150799, 150831
Sorry, prediction pasa_asmbl_47080.p1 fails validation.
(CGC)	 TC	150799-150831	GT	AGG
(GAT)	 AG	151122-151192	GT	AAG
(GTA)	 AG	151295-151439	GT	AGG
(AAC)	 AG	151599-151688	GT	AGG
(GCA)	 AG	151828-151953	GT	TGG
(GCA)	 AG	152101-152229	GT	AGG
(GCA)	 AG	152393-152419	AG	AGA
add_exon() Sorry, pasa_asmbl_47080.p1 151122-151192-terminal-2 is invalid.
-recovered pasa_asmbl_47080.p1, terminal, 151122, 151192
-recovered pasa_asmbl_47080.p1, terminal, 152393, 152419
-recovered pasa_asmbl_47080.p1, internal, 151122, 151192
-recovered pasa_asmbl_47080.p1, internal, 151295, 151439
-recovered pasa_asmbl_47080.p1, internal, 151599, 151688
-recovered pasa_asmbl_47080.p1, internal, 151828, 151953
-recovered pasa_asmbl_47080.p1, internal, 152101, 152229
Valid prediction for GlimmerHMM_glimmerT_14964-T1
Valid prediction for HiQ_model.g9906.t1
Valid prediction for snap_scaffold_6-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_14958-T1
Valid prediction for snap_scaffold_6-snap.1658-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14955-T1
Valid prediction for snap_scaffold_6-snap.1672-T1
Valid prediction for GlimmerHMM_glimmerT_14949-T1
Valid prediction for Augustus_model.g9916.t1
Valid prediction for GlimmerHMM_glimmerT_14953-T1
Valid prediction for snap_scaffold_6-snap.1665-T1
Valid prediction for Augustus_model.g9892.t1
Valid prediction for GlimmerHMM_glimmerT_14965-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 GlimmerHMM_glimmerT_14939-T1
Valid prediction for GlimmerHMM_glimmerT_14954-T1
Valid prediction for Augustus_model.g9913.t1
Valid prediction for HiQ_model.g9911.t1
Valid prediction for snap_scaffold_6-snap.1670-T1
Valid prediction for snap_scaffold_6-snap.1678-T1
Valid prediction for Augustus_model.g9890.t1
Valid prediction for pasa_asmbl_48505.p1
Valid prediction for Augustus_model.g9901.t1
Valid prediction for snap_scaffold_6-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_14952-T1
Valid prediction for GlimmerHMM_glimmerT_14969-T1
Valid prediction for snap_scaffold_6-snap.1671-T1
Valid prediction for CodingQuarry_transcript_55102-T1
Valid prediction for GlimmerHMM_glimmerT_14975-T1
Valid prediction for snap_scaffold_6-snap.1668-T1
Valid prediction for snap_scaffold_6-snap.1653-T1
Valid prediction for Augustus_model.g9905.t1
Valid prediction for snap_scaffold_6-snap.1652-T1
Valid prediction for Augustus_model.g9902.t1
Valid prediction for snap_scaffold_6-snap.1686-T1
Valid prediction for pasa_asmbl_48502.p1
Valid prediction for snap_scaffold_6-snap.1648-T1
Valid prediction for snap_scaffold_6-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_14959-T1
Valid prediction for Augustus_model.g9908.t1
Valid prediction for HiQ_model.g9899.t1
Valid prediction for CodingQuarry_transcript_55107-T1
Valid prediction for snap_scaffold_6-snap.1689-T1
Valid prediction for CodingQuarry_transcript_55108-T1
Valid prediction for pasa_asmbl_48503.p1
Couldn't classify 182636, 182728
Couldn't classify 187510, 187547
Sorry, prediction pasa_asmbl_48494.p1 fails validation.
(AGT)	 GA	182636-182728	GT	AGG
(CCT)	 AG	183204-183336	GT	AGG
(CTC)	 AG	183611-183725	GT	ATG
(CTA)	 AG	184290-184365	GT	CGG
(GTT)	 AG	186800-187025	GT	GTG
(GTG)	 AG	187192-187338	GT	GGG
(GGA)	 AG	187510-187547	AA	ACA
-recovered pasa_asmbl_48494.p1, internal, 183204, 183336
-recovered pasa_asmbl_48494.p1, internal, 183611, 183725
-recovered pasa_asmbl_48494.p1, internal, 184290, 184365
-recovered pasa_asmbl_48494.p1, internal, 186800, 187025
-recovered pasa_asmbl_48494.p1, internal, 187192, 187338
Valid prediction for GlimmerHMM_glimmerT_14970-T1
Couldn't classify 187773, 188693
Sorry, prediction pasa_asmbl_48493.p1 fails validation.
(TCC)	 AC	187773-188693	GA	ACG
Valid prediction for snap_scaffold_6-snap.1666-T1
Valid prediction for snap_scaffold_6-snap.1647-T1
Valid prediction for snap_scaffold_6-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_14966-T1
Valid prediction for snap_scaffold_6-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_14973-T1
Valid prediction for snap_scaffold_6-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_14963-T1
Valid prediction for snap_scaffold_6-snap.1673-T1
Valid prediction for snap_scaffold_6-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_14947-T1
Valid prediction for Augustus_model.g9917.t1
Valid prediction for HiQ_model.g9915.t1
Valid prediction for Augustus_model.g9897.t1
Valid prediction for snap_scaffold_6-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_14945-T1
Valid prediction for GlimmerHMM_glimmerT_14940-T1
Valid prediction for GlimmerHMM_glimmerT_14948-T1
Valid prediction for GlimmerHMM_glimmerT_14957-T1
Valid prediction for Augustus_model.g9898.t1
Valid prediction for Augustus_model.g9894.t1
Valid prediction for snap_scaffold_6-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_14960-T1
Valid prediction for snap_scaffold_6-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_14971-T1
Valid prediction for Augustus_model.g9912.t1
Valid prediction for GlimmerHMM_glimmerT_14944-T1
Valid prediction for snap_scaffold_6-snap.1685-T1
Valid prediction for snap_scaffold_6-snap.1684-T1
Valid prediction for snap_scaffold_6-snap.1679-T1
Valid prediction for GlimmerHMM_glimmerT_14941-T1
Valid prediction for snap_scaffold_6-snap.1682-T1
Valid prediction for Augustus_model.g9893.t1
Valid prediction for GlimmerHMM_glimmerT_14946-T1
Valid prediction for Augustus_model.g9891.t1
Valid prediction for GlimmerHMM_glimmerT_14951-T1
Couldn't classify 180341, 180473
Couldn't classify 181875, 181948
Sorry, prediction pasa_asmbl_48495.p1 fails validation.
(AAG)	 GG	180341-180473	GT	GGG
(AAG)	 AG	181604-181774	GT	CGG
(GTT)	 AG	181875-181948	AC	GTA
-recovered pasa_asmbl_48495.p1, internal, 181604, 181774
Valid prediction for snap_scaffold_6-snap.1650-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 122380, rend_intergenic: 122377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43519, rend_intergenic: 35820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48838, rend_intergenic: 45924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50725, rend_intergenic: 48966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58175, rend_intergenic: 50781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61886, rend_intergenic: 59343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66609, rend_intergenic: 62096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79109, rend_intergenic: 67240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80984, rend_intergenic: 80358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85219, rend_intergenic: 81648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95869, rend_intergenic: 85224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150243, rend_intergenic: 145549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184635, rend_intergenic: 181666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225377
-exon list size: 428


building trellis

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24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
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27.4    
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27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
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34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
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49.5    
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50.0    
50.2    
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50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
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53.5    
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54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
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75.6    
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90.9    
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92.3    
92.6    
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93.7    
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94.2    
94.4    
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95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 122380, rend_intergenic: 122377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43519, rend_intergenic: 35820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48838, rend_intergenic: 45924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50725, rend_intergenic: 48966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58175, rend_intergenic: 50781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61886, rend_intergenic: 59343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66609, rend_intergenic: 62096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79109, rend_intergenic: 67240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80984, rend_intergenic: 80358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85219, rend_intergenic: 81648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95869, rend_intergenic: 85224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150243, rend_intergenic: 145549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184635, rend_intergenic: 181666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support