-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_1340071-1522058

-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_24-snap.349-T1
Valid prediction for GlimmerHMM_glimmerT_52011-T1
Valid prediction for snap_scaffold_24-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_52019-T1
Valid prediction for snap_scaffold_24-snap.364-T1
Valid prediction for snap_scaffold_24-snap.377-T1
Valid prediction for snap_scaffold_24-snap.375-T1
Couldn't classify 50466, 50678
Sorry, prediction pasa_asmbl_32074.p1 fails validation.
(CCA)	 AC	50466-50678	GT	TGG
(CAA)	 AG	51942-52061	GT	AGG
(GGT)	 AG	52655-52732	GT	AGG
(GTG)	 AG	53332-53466	AC	AAA
-recovered pasa_asmbl_32074.p1, terminal, 53332, 53466
-recovered pasa_asmbl_32074.p1, internal, 51942, 52061
-recovered pasa_asmbl_32074.p1, internal, 52655, 52732
Valid prediction for snap_scaffold_24-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_52010-T1
Valid prediction for GlimmerHMM_glimmerT_52020-T1
Valid prediction for snap_scaffold_24-snap.370-T1
Valid prediction for snap_scaffold_24-snap.328-T1
Valid prediction for Augustus_model.g34669.t1
Couldn't classify 103370, 103611
Sorry, prediction pasa_asmbl_32075.p1 fails validation.
(ATG)	 AC	100038-100163	GT	AGG
(CTT)	 AG	100748-100813	GT	AGG
(GAT)	 AG	101797-101881	GT	AGG
(CCA)	 AG	102208-102264	GT	GGG
(CAT)	 AG	103370-103611	AA	GGA
-recovered pasa_asmbl_32075.p1, initial, 100038, 100163
-recovered pasa_asmbl_32075.p1, internal, 100748, 100813
-recovered pasa_asmbl_32075.p1, internal, 101797, 101881
-recovered pasa_asmbl_32075.p1, internal, 102208, 102264
Valid prediction for GlimmerHMM_glimmerT_52007-T1
Valid prediction for snap_scaffold_24-snap.367-T1
Valid prediction for snap_scaffold_24-snap.351-T1
Valid prediction for snap_scaffold_24-snap.344-T1
Valid prediction for snap_scaffold_24-snap.368-T1
Valid prediction for Augustus_model.g34672.t1
Couldn't classify 49445, 49861
Sorry, prediction pasa_asmbl_32658.p1 fails validation.
(CCA)	 TA	49445-49861	CC	GAC
Valid prediction for snap_scaffold_24-snap.359-T1
Valid prediction for snap_scaffold_24-snap.357-T1
Valid prediction for snap_scaffold_24-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_52009-T1
Valid prediction for snap_scaffold_24-snap.333-T1
Valid prediction for snap_scaffold_24-snap.340-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52024-T1
Valid prediction for snap_scaffold_24-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_52012-T1
Valid prediction for snap_scaffold_24-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_52014-T1
Valid prediction for snap_scaffold_24-snap.329-T1
Valid prediction for snap_scaffold_24-snap.366-T1
Valid prediction for snap_scaffold_24-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_52016-T1
Valid prediction for snap_scaffold_24-snap.327-T1
Valid prediction for snap_scaffold_24-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_52022-T1
Valid prediction for HiQ_model.g34665.t1
Valid prediction for snap_scaffold_24-snap.355-T1
Valid prediction for snap_scaffold_24-snap.362-T1
Valid prediction for Augustus_model.g34666.t1
Valid prediction for HiQ_model.g34673.t1
Valid prediction for Augustus_model.g34664.t1
Valid prediction for snap_scaffold_24-snap.352-T1
Valid prediction for Augustus_model.g34671.t1
Valid prediction for pasa_asmbl_32078.p1
Valid prediction for GlimmerHMM_glimmerT_52018-T1
Valid prediction for snap_scaffold_24-snap.339-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_52013-T1
Valid prediction for Augustus_model.g34675.t1
Valid prediction for snap_scaffold_24-snap.345-T1
Valid prediction for Augustus_model.g34678.t1
Valid prediction for GlimmerHMM_glimmerT_52006-T1
Valid prediction for CodingQuarry_transcript_37235-T1
Valid prediction for GlimmerHMM_glimmerT_52026-T1
Valid prediction for HiQ_model.g34667.t1
Valid prediction for snap_scaffold_24-snap.332-T1
Valid prediction for snap_scaffold_24-snap.331-T1
Valid prediction for snap_scaffold_24-snap.348-T1
Valid prediction for snap_scaffold_24-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_52023-T1
Valid prediction for Augustus_model.g34663.t1
Valid prediction for CodingQuarry_transcript_37234-T1
Valid prediction for snap_scaffold_24-snap.378-T1
Valid prediction for snap_scaffold_24-snap.342-T1
Valid prediction for snap_scaffold_24-snap.337-T1
Valid prediction for snap_scaffold_24-snap.334-T1
Valid prediction for Augustus_model.g34670.t1
Valid prediction for snap_scaffold_24-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_52005-T1
Valid prediction for snap_scaffold_24-snap.376-T1
Valid prediction for snap_scaffold_24-snap.353-T1
Valid prediction for snap_scaffold_24-snap.363-T1
Valid prediction for Augustus_model.g34677.t1
Valid prediction for snap_scaffold_24-snap.358-T1
Valid prediction for snap_scaffold_24-snap.354-T1
Couldn't classify 104186, 104297
Sorry, prediction pasa_asmbl_32728.p1 fails validation.
(CTG)	 TA	104186-104297	GT	AGG
(GTA)	 AG	105747-105876	GC	ATG
(TTT)	 AG	106904-107051	GT	AGG
(GAT)	 AG	107826-107864	GC	GAG
-recovered pasa_asmbl_32728.p1, terminal, 107826, 107864
-recovered pasa_asmbl_32728.p1, internal, 105747, 105876
-recovered pasa_asmbl_32728.p1, internal, 106904, 107051
-recovered pasa_asmbl_32728.p1, internal, 107826, 107864
Valid prediction for snap_scaffold_24-snap.347-T1
Valid prediction for snap_scaffold_24-snap.371-T1
Valid prediction for snap_scaffold_24-snap.338-T1
Valid prediction for CodingQuarry_transcript_37237-T1
Valid prediction for GlimmerHMM_glimmerT_52017-T1
Valid prediction for Augustus_model.g34674.t1
Valid prediction for pasa_asmbl_32732.p2
Valid prediction for HiQ_model.g34668.t1
Valid prediction for snap_scaffold_24-snap.374-T1
Valid prediction for Augustus_model.g34676.t1
Valid prediction for snap_scaffold_24-snap.326-T1
Valid prediction for GlimmerHMM_glimmerT_52015-T1
Valid prediction for snap_scaffold_24-snap.343-T1
Valid prediction for Augustus_model.g34679.t1
Valid prediction for snap_scaffold_24-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_52025-T1
Valid prediction for GlimmerHMM_glimmerT_52021-T1
Valid prediction for pasa_asmbl_32729.p1
Valid prediction for snap_scaffold_24-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_52008-T1
Valid prediction for GlimmerHMM_glimmerT_52004-T1
Valid prediction for Augustus_model.g34661.t1
Couldn't classify 64912, 64991
Couldn't classify 67758, 67922
Sorry, prediction pasa_asmbl_32734.p1 fails validation.
(GCC)	 CC	64912-64991	GT	AGG
(GTT)	 AG	67345-67438	GT	TAG
(GAG)	 AG	67758-67922	TC	GCT
-recovered pasa_asmbl_32734.p1, internal, 67345, 67438
Valid prediction for CodingQuarry_transcript_37236-T1
Valid prediction for snap_scaffold_24-snap.341-T1
Valid prediction for snap_scaffold_24-snap.350-T1
Valid prediction for Augustus_model.g34662.t1
Valid prediction for snap_scaffold_24-snap.365-T1
Valid prediction for Augustus_model.g34660.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4490, rend_intergenic: 3639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17071, rend_intergenic: 4490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18614, rend_intergenic: 17135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20640, rend_intergenic: 19133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28540, rend_intergenic: 21114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38006, rend_intergenic: 34571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49861, rend_intergenic: 38990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53459, rend_intergenic: 51643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60388, rend_intergenic: 58555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69524, rend_intergenic: 60498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81915, rend_intergenic: 74657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90687, rend_intergenic: 86331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106939, rend_intergenic: 103421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111024, rend_intergenic: 110629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122847, rend_intergenic: 111125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124283, rend_intergenic: 122894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126172, rend_intergenic: 124389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135630, rend_intergenic: 127636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135927, rend_intergenic: 135700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138841, rend_intergenic: 136299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143063, rend_intergenic: 138917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150101, rend_intergenic: 144815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153858, rend_intergenic: 151091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172982, rend_intergenic: 154341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177207, rend_intergenic: 174007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180101, rend_intergenic: 178115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181988
-exon list size: 441


building trellis

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29.1    
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29.8    
30.0    
30.2    
30.5    
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30.9    
31.2    
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31.6    
31.8    
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32.3    
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33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.8    
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35.4    
35.7    
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36.3    
36.6    
36.8    
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37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
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39.1    
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39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.1    
45.4    
45.6    
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47.0    
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99.5    
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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 4490, rend_intergenic: 3639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17071, rend_intergenic: 4490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18614, rend_intergenic: 17135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20640, rend_intergenic: 19133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28540, rend_intergenic: 21114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38006, rend_intergenic: 34571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49861, rend_intergenic: 38990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53459, rend_intergenic: 51643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60388, rend_intergenic: 58555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69524, rend_intergenic: 60498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81915, rend_intergenic: 74657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90687, rend_intergenic: 86331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106939, rend_intergenic: 103421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111024, rend_intergenic: 110629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122847, rend_intergenic: 111125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124283, rend_intergenic: 122894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126172, rend_intergenic: 124389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135630, rend_intergenic: 127636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135927, rend_intergenic: 135700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138841, rend_intergenic: 136299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143063, rend_intergenic: 138917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150101, rend_intergenic: 144815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153858, rend_intergenic: 151091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172982, rend_intergenic: 154341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177207, rend_intergenic: 174007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180101, rend_intergenic: 178115  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