-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_7463140-7714879

-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 Augustus_model.g6277.t1
Valid prediction for CodingQuarry_transcript_49059-T1
Valid prediction for snap_scaffold_4-snap.1631-T1
Valid prediction for snap_scaffold_4-snap.1604-T1
Valid prediction for snap_scaffold_4-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_9683-T1
Couldn't classify 20125, 20997
Sorry, prediction pasa_asmbl_41500.p1 fails validation.
(GCC)	 TG	20125-20997	TG	GAT
Valid prediction for Augustus_model.g6283.t1
Valid prediction for snap_scaffold_4-snap.1635-T1
Valid prediction for Augustus_model.g6275.t1
Valid prediction for snap_scaffold_4-snap.1615-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 81556, 81678
Sorry, prediction pasa_asmbl_41505.p1 fails validation.
(ATG)	 AA	78543-78569	GT	AGG
(CAA)	 AG	78836-78959	GT	AAG
(GTG)	 AG	79357-79450	GT	GGG
(GTA)	 AG	79875-79935	GT	CGG
(ATA)	 AG	80699-80785	GT	ACG
(GAG)	 AG	81556-81678	TA	CGT
-recovered pasa_asmbl_41505.p1, initial, 78543, 78569
add_exon() Sorry, pasa_asmbl_41505.p1 78836-78959-terminal-3 is invalid.
-recovered pasa_asmbl_41505.p1, terminal, 78836, 78959
-recovered pasa_asmbl_41505.p1, internal, 78836, 78959
-recovered pasa_asmbl_41505.p1, internal, 79357, 79450
-recovered pasa_asmbl_41505.p1, internal, 79875, 79935
-recovered pasa_asmbl_41505.p1, internal, 80699, 80785
Valid prediction for GlimmerHMM_glimmerT_9670-T1
Valid prediction for Augustus_model.g6274.t1
Valid prediction for GlimmerHMM_glimmerT_9667-T1
Valid prediction for snap_scaffold_4-snap.1584-T1
Couldn't classify 208140, 208219
Sorry, prediction pasa_asmbl_41511.p1 fails validation.
(ATG)	 AA	204456-204509	GT	AGG
(GTG)	 AG	205625-205774	GT	AGG
(CTG)	 AG	206054-206176	GT	TGG
(CAA)	 AG	206575-206734	GT	CGG
(ACG)	 AG	207537-207664	GT	AAG
(GAT)	 AG	207950-207995	GT	AGG
(AAG)	 AG	208140-208219	GA	ACG
-recovered pasa_asmbl_41511.p1, initial, 204456, 204509
-recovered pasa_asmbl_41511.p1, internal, 205625, 205774
-recovered pasa_asmbl_41511.p1, internal, 206054, 206176
-recovered pasa_asmbl_41511.p1, internal, 206575, 206734
-recovered pasa_asmbl_41511.p1, internal, 207537, 207664
-recovered pasa_asmbl_41511.p1, internal, 207950, 207995
Valid prediction for snap_scaffold_4-snap.1633-T1
Valid prediction for snap_scaffold_4-snap.1618-T1
Valid prediction for snap_scaffold_4-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_9680-T1
Valid prediction for snap_scaffold_4-snap.1624-T1
Valid prediction for Augustus_model.g6273.t1
Valid prediction for snap_scaffold_4-snap.1625-T1
Valid prediction for Augustus_model.g6281.t1
Valid prediction for snap_scaffold_4-snap.1622-T1
Valid prediction for Augustus_model.g6271.t1
Valid prediction for snap_scaffold_4-snap.1611-T1
Valid prediction for snap_scaffold_4-snap.1612-T1
Valid prediction for snap_scaffold_4-snap.1605-T1
Valid prediction for snap_scaffold_4-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_9679-T1
Valid prediction for snap_scaffold_4-snap.1586-T1
Valid prediction for Augustus_model.g6284.t1
Valid prediction for snap_scaffold_4-snap.1626-T1
Valid prediction for snap_scaffold_4-snap.1616-T1
Valid prediction for snap_scaffold_4-snap.1600-T1
Valid prediction for GlimmerHMM_glimmerT_9669-T1
Valid prediction for snap_scaffold_4-snap.1593-T1
Valid prediction for snap_scaffold_4-snap.1608-T1
Valid prediction for GlimmerHMM_glimmerT_9682-T1
Couldn't classify 56750, 56887
Sorry, prediction pasa_asmbl_41502.p2 fails validation.
(ATG)	 AG	52188-52234	GT	AGG
(GCA)	 AG	54626-54833	GT	AGG
(ACG)	 AG	56750-56887	TA	GGT
-recovered pasa_asmbl_41502.p2, initial, 52188, 52234
-recovered pasa_asmbl_41502.p2, internal, 52188, 52234
-recovered pasa_asmbl_41502.p2, internal, 54626, 54833
Valid prediction for GlimmerHMM_glimmerT_9671-T1
Valid prediction for snap_scaffold_4-snap.1594-T1
Valid prediction for snap_scaffold_4-snap.1628-T1
Couldn't classify 172264, 172386
Couldn't classify 174246, 174371
Sorry, prediction pasa_asmbl_41508.p1 fails validation.
(CAG)	 AC	172264-172386	GT	AGG
(ATT)	 AG	172620-172757	GT	AGG
(TAC)	 AG	172967-173057	GT	TGG
(GCT)	 AG	173263-173401	GT	AGG
(GGA)	 AG	173745-173797	GT	CGG
(GTG)	 AG	173924-174078	GT	GGG
(AGT)	 AG	174246-174371	GA	AGG
-recovered pasa_asmbl_41508.p1, internal, 172620, 172757
-recovered pasa_asmbl_41508.p1, internal, 172967, 173057
-recovered pasa_asmbl_41508.p1, internal, 173263, 173401
-recovered pasa_asmbl_41508.p1, internal, 173745, 173797
-recovered pasa_asmbl_41508.p1, internal, 173924, 174078
Valid prediction for snap_scaffold_4-snap.1627-T1
Valid prediction for GlimmerHMM_glimmerT_9677-T1
Valid prediction for GlimmerHMM_glimmerT_9673-T1
Valid prediction for snap_scaffold_4-snap.1589-T1
Couldn't classify 57654, 57819
Couldn't classify 59938, 60068
Sorry, prediction pasa_asmbl_41503.p1 fails validation.
(CCC)	 CC	57654-57819	GT	AAG
(GCT)	 AG	59938-60068	GC	TGG
-recovered pasa_asmbl_41503.p1, internal, 59938, 60068
Valid prediction for GlimmerHMM_glimmerT_9685-T1
Valid prediction for snap_scaffold_4-snap.1599-T1
Valid prediction for snap_scaffold_4-snap.1590-T1
Valid prediction for snap_scaffold_4-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_9666-T1
Valid prediction for snap_scaffold_4-snap.1591-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_9668-T1
Valid prediction for snap_scaffold_4-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_9676-T1
Valid prediction for snap_scaffold_4-snap.1621-T1
Valid prediction for snap_scaffold_4-snap.1609-T1
Valid prediction for GlimmerHMM_glimmerT_9674-T1
Valid prediction for GlimmerHMM_glimmerT_9686-T1
Valid prediction for snap_scaffold_4-snap.1634-T1
Valid prediction for snap_scaffold_4-snap.1632-T1
Valid prediction for Augustus_model.g6282.t1
Couldn't classify 88465, 88648
Sorry, prediction pasa_asmbl_42723.p1 fails validation.
(GTG)	 TA	88465-88648	GT	TGG
(TAA)	 AG	90173-90310	GT	AGG
(TGC)	 AG	93153-93223	GT	CCG
(ATT)	 AG	93803-93907	GT	AGG
(GTC)	 AG	96024-96152	GG	GAG
-recovered pasa_asmbl_42723.p1, terminal, 96024, 96152
-recovered pasa_asmbl_42723.p1, internal, 90173, 90310
-recovered pasa_asmbl_42723.p1, internal, 93153, 93223
-recovered pasa_asmbl_42723.p1, internal, 93803, 93907
Valid prediction for snap_scaffold_4-snap.1619-T1
Valid prediction for snap_scaffold_4-snap.1613-T1
Valid prediction for Augustus_model.g6279.t1
Valid prediction for Augustus_model.g6285.t1
Valid prediction for snap_scaffold_4-snap.1623-T1
Valid prediction for Augustus_model.g6278.t1
Couldn't classify 164047, 164355
Sorry, prediction pasa_asmbl_42722.p1 fails validation.
(GTT)	 AT	164047-164355	CA	GAC
Couldn't classify 84970, 85159
Sorry, prediction pasa_asmbl_42728.p1 fails validation.
(ATG)	 CA	80643-80656	GT	AGG
(TTG)	 AG	80934-81029	GT	AGG
(GCT)	 AG	81995-82173	GT	TGG
(TTT)	 AG	82354-82477	GT	AAG
(GCT)	 AG	84970-85159	AG	CAA
-recovered pasa_asmbl_42728.p1, initial, 80643, 80656
-recovered pasa_asmbl_42728.p1, internal, 80934, 81029
-recovered pasa_asmbl_42728.p1, internal, 81995, 82173
-recovered pasa_asmbl_42728.p1, internal, 82354, 82477
Valid prediction for snap_scaffold_4-snap.1595-T1
Valid prediction for snap_scaffold_4-snap.1607-T1
Valid prediction for Augustus_model.g6280.t1
Valid prediction for GlimmerHMM_glimmerT_9678-T1
Valid prediction for snap_scaffold_4-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_9684-T1
Valid prediction for snap_scaffold_4-snap.1629-T1
Valid prediction for GlimmerHMM_glimmerT_9672-T1
Valid prediction for snap_scaffold_4-snap.1614-T1
Valid prediction for snap_scaffold_4-snap.1617-T1
Valid prediction for snap_scaffold_4-snap.1636-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9681-T1
Valid prediction for snap_scaffold_4-snap.1601-T1
Valid prediction for snap_scaffold_4-snap.1588-T1
Valid prediction for snap_scaffold_4-snap.1585-T1
Valid prediction for snap_scaffold_4-snap.1603-T1
Valid prediction for Augustus_model.g6276.t1
Valid prediction for snap_scaffold_4-snap.1606-T1
Valid prediction for Augustus_model.g6272.t1
Valid prediction for snap_scaffold_4-snap.1598-T1
Valid prediction for snap_scaffold_4-snap.1630-T1
Valid prediction for snap_scaffold_4-snap.1610-T1
Valid prediction for GlimmerHMM_glimmerT_9675-T1
Valid prediction for snap_scaffold_4-snap.1597-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35533, rend_intergenic: 31728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70555, rend_intergenic: 64978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94201, rend_intergenic: 90456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100962, rend_intergenic: 97866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107844, rend_intergenic: 104381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118082, rend_intergenic: 113140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122971, rend_intergenic: 119188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132812, rend_intergenic: 127693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142754, rend_intergenic: 140182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224637, rend_intergenic: 222761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244775, rend_intergenic: 244441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251740
-exon list size: 380


building trellis

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35.3    
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36.6    
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39.5    
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40.1    
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41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
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75.4    
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84.8    
85.1    
85.3    
85.6    
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86.1    
86.4    
86.6    
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87.4    
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88.5    
88.7    
89.0    
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90.1    
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91.1    
91.4    
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96.1    
96.3    
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97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 35533, rend_intergenic: 31728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70555, rend_intergenic: 64978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94201, rend_intergenic: 90456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100962, rend_intergenic: 97866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107844, rend_intergenic: 104381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118082, rend_intergenic: 113140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122971, rend_intergenic: 119188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132812, rend_intergenic: 127693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142754, rend_intergenic: 140182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224637, rend_intergenic: 222761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244775, rend_intergenic: 244441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16129
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support