-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_7603872-7857830

-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 GeneMark_model.16051_t
Valid prediction for Augustus_model.g6469.t1
Valid prediction for GlimmerHMM_glimmerT_9882-T1
Valid prediction for Augustus_model.g6486.t1
Valid prediction for Augustus_model.g6475.t1
Valid prediction for Augustus_model.g6480.t1
Valid prediction for GlimmerHMM_glimmerT_9884-T1
Couldn't classify 31532, 31654
Couldn't classify 33514, 33639
Sorry, prediction pasa_asmbl_42842.p1 fails validation.
(CAG)	 AC	31532-31654	GT	AGG
(ATT)	 AG	31888-32025	GT	AGG
(TAC)	 AG	32235-32325	GT	TGG
(GCT)	 AG	32531-32669	GT	AGG
(GGA)	 AG	33013-33065	GT	CGG
(GTG)	 AG	33192-33346	GT	GGG
(AGT)	 AG	33514-33639	GA	AGG
-recovered pasa_asmbl_42842.p1, internal, 31888, 32025
-recovered pasa_asmbl_42842.p1, internal, 32235, 32325
-recovered pasa_asmbl_42842.p1, internal, 32531, 32669
-recovered pasa_asmbl_42842.p1, internal, 33013, 33065
-recovered pasa_asmbl_42842.p1, internal, 33192, 33346
Valid prediction for snap_scaffold_4-snap.1615-T1
Couldn't classify 210421, 210918
Sorry, prediction pasa_asmbl_42855.p1 fails validation.
(CCA)	 GA	210421-210918	TG	GAT
Valid prediction for Augustus_model.g6483.t1
Valid prediction for GlimmerHMM_glimmerT_9872-T1
Valid prediction for GlimmerHMM_glimmerT_9888-T1
Valid prediction for GeneMark_model.16046_t
Valid prediction for snap_scaffold_4-snap.1636-T1
Valid prediction for snap_scaffold_4-snap.1637-T1
Valid prediction for GlimmerHMM_glimmerT_9891-T1
Valid prediction for snap_scaffold_4-snap.1651-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1630-T1
Valid prediction for GeneMark_model.16052_t
Valid prediction for snap_scaffold_4-snap.1618-T1
Valid prediction for GlimmerHMM_glimmerT_9887-T1
Valid prediction for GlimmerHMM_glimmerT_9885-T1
Valid prediction for GlimmerHMM_glimmerT_9889-T1
Valid prediction for snap_scaffold_4-snap.1639-T1
Couldn't classify 67408, 67487
Sorry, prediction pasa_asmbl_42845.p1 fails validation.
(ATG)	 AA	63724-63777	GT	AGG
(GTG)	 AG	64893-65042	GT	AGG
(CTG)	 AG	65322-65444	GT	TGG
(CAA)	 AG	65843-66002	GT	CGG
(ACG)	 AG	66805-66932	GT	AAG
(GAT)	 AG	67218-67263	GT	AGG
(AAG)	 AG	67408-67487	GA	ACG
-recovered pasa_asmbl_42845.p1, initial, 63724, 63777
-recovered pasa_asmbl_42845.p1, internal, 64893, 65042
-recovered pasa_asmbl_42845.p1, internal, 65322, 65444
-recovered pasa_asmbl_42845.p1, internal, 65843, 66002
-recovered pasa_asmbl_42845.p1, internal, 66805, 66932
-recovered pasa_asmbl_42845.p1, internal, 67218, 67263
Valid prediction for GeneMark_model.16067_t
Valid prediction for GlimmerHMM_glimmerT_9879-T1
Valid prediction for GlimmerHMM_glimmerT_9868-T1
Valid prediction for snap_scaffold_4-snap.1640-T1
Valid prediction for GlimmerHMM_glimmerT_9893-T1
Valid prediction for snap_scaffold_4-snap.1633-T1
Valid prediction for GlimmerHMM_glimmerT_9890-T1
Valid prediction for GlimmerHMM_glimmerT_9873-T1
Valid prediction for GeneMark_model.16068_t
Valid prediction for snap_scaffold_4-snap.1629-T1
Valid prediction for Augustus_model.g6484.t1
Valid prediction for snap_scaffold_4-snap.1649-T1
Valid prediction for snap_scaffold_4-snap.1624-T1
Valid prediction for snap_scaffold_4-snap.1632-T1
Valid prediction for snap_scaffold_4-snap.1641-T1
Valid prediction for GlimmerHMM_glimmerT_9892-T1
Valid prediction for GeneMark_model.16055_t
Valid prediction for Augustus_model.g6482.t1
Valid prediction for GeneMark_model.16064_t
Valid prediction for snap_scaffold_4-snap.1642-T1
Valid prediction for snap_scaffold_4-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_9881-T1
Valid prediction for GeneMark_model.16066_t
Valid prediction for GeneMark_model.16049_t
Valid prediction for GeneMark_model.16075_t
Valid prediction for GeneMark_model.16063_t
Valid prediction for Augustus_model.g6479.t1
Valid prediction for snap_scaffold_4-snap.1645-T1
Valid prediction for GeneMark_model.16073_t
Valid prediction for Augustus_model.g6474.t1
Valid prediction for GlimmerHMM_glimmerT_9870-T1
Valid prediction for snap_scaffold_4-snap.1653-T1
Valid prediction for snap_scaffold_4-snap.1643-T1
Valid prediction for snap_scaffold_4-snap.1655-T1
Valid prediction for pasa_asmbl_42849.p1
Valid prediction for snap_scaffold_4-snap.1634-T1
Valid prediction for Augustus_model.g6478.t1
Valid prediction for GlimmerHMM_glimmerT_9883-T1
Valid prediction for GlimmerHMM_glimmerT_9877-T1
Valid prediction for snap_scaffold_4-snap.1619-T1
Valid prediction for Augustus_model.g6471.t1
Valid prediction for GeneMark_model.16065_t
Valid prediction for GlimmerHMM_glimmerT_9886-T1
Valid prediction for HiQ_model.g6476.t1
Valid prediction for Augustus_model.g6485.t1
Couldn't classify 153311, 153397
Sorry, prediction pasa_asmbl_42851.p1 fails validation.
(CTG)	 CC	153311-153397	GT	AGG
(GTG)	 AG	153581-153732	GT	AGG
(GCA)	 AG	153895-154027	GT	ACG
(GTG)	 AG	154205-154325	GT	AGG
(GTT)	 AG	154545-154726	AG	GAA
-recovered pasa_asmbl_42851.p1, terminal, 154545, 154726
-recovered pasa_asmbl_42851.p1, internal, 153581, 153732
-recovered pasa_asmbl_42851.p1, internal, 153895, 154027
-recovered pasa_asmbl_42851.p1, internal, 154205, 154325
Valid prediction for GeneMark_model.16057_t
Valid prediction for snap_scaffold_4-snap.1631-T1
Valid prediction for snap_scaffold_4-snap.1617-T1
Valid prediction for GlimmerHMM_glimmerT_9874-T1
Valid prediction for GeneMark_model.16069_t
Valid prediction for snap_scaffold_4-snap.1644-T1
Valid prediction for CodingQuarry_transcript_48956-T1
Valid prediction for GlimmerHMM_glimmerT_9871-T1
Couldn't classify 175707, 175814
Sorry, prediction pasa_asmbl_42853.p1 fails validation.
(GAA)	 AG	175707-175814	GT	AGG
(ACA)	 AG	176096-176298	GT	AGG
(TTC)	 AG	176639-176823	GT	TGG
(GTA)	 AG	177189-177347	GT	GGG
(GTC)	 AG	177511-177605	GT	AGG
(GAG)	 AG	178084-178242	GT	AGG
(ATG)	 AG	178435-178794	TG	GAT
-recovered pasa_asmbl_42853.p1, terminal, 178435, 178794
-recovered pasa_asmbl_42853.p1, internal, 175707, 175814
-recovered pasa_asmbl_42853.p1, internal, 176096, 176298
-recovered pasa_asmbl_42853.p1, internal, 176639, 176823
-recovered pasa_asmbl_42853.p1, internal, 177189, 177347
-recovered pasa_asmbl_42853.p1, internal, 177511, 177605
-recovered pasa_asmbl_42853.p1, internal, 178084, 178242
Valid prediction for Augustus_model.g6467.t1
Valid prediction for GeneMark_model.16061_t
Valid prediction for Augustus_model.g6477.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 GeneMark_model.16076_t
Valid prediction for snap_scaffold_4-snap.1623-T1
Valid prediction for GeneMark_model.16060_t
Valid prediction for GlimmerHMM_glimmerT_9878-T1
Valid prediction for snap_scaffold_4-snap.1638-T1
Valid prediction for snap_scaffold_4-snap.1650-T1
Valid prediction for snap_scaffold_4-snap.1626-T1
Valid prediction for Augustus_model.g6468.t1
Valid prediction for Augustus_model.g6487.t1
Valid prediction for snap_scaffold_4-snap.1612-T1
Valid prediction for Augustus_model.g6481.t1
Valid prediction for GeneMark_model.16056_t
Valid prediction for snap_scaffold_4-snap.1614-T1
Valid prediction for GeneMark_model.16071_t
Valid prediction for GeneMark_model.16050_t
Valid prediction for GeneMark_model.16054_t
Valid prediction for snap_scaffold_4-snap.1652-T1
Valid prediction for GeneMark_model.16070_t
Valid prediction for snap_scaffold_4-snap.1648-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9869-T1
Valid prediction for snap_scaffold_4-snap.1621-T1
Valid prediction for GeneMark_model.16047_t
Valid prediction for GeneMark_model.16072_t
Valid prediction for GeneMark_model.16059_t
Valid prediction for snap_scaffold_4-snap.1622-T1
Valid prediction for snap_scaffold_4-snap.1628-T1
Valid prediction for GlimmerHMM_glimmerT_9880-T1
Valid prediction for GeneMark_model.16045_t
Valid prediction for GlimmerHMM_glimmerT_9894-T1
Valid prediction for Augustus_model.g6466.t1
Valid prediction for GlimmerHMM_glimmerT_9867-T1
Valid prediction for snap_scaffold_4-snap.1654-T1
Valid prediction for GeneMark_model.16048_t
Valid prediction for snap_scaffold_4-snap.1616-T1
Valid prediction for snap_scaffold_4-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_9875-T1
Valid prediction for snap_scaffold_4-snap.1627-T1
Valid prediction for Augustus_model.g6472.t1
Valid prediction for GeneMark_model.16053_t
Valid prediction for Augustus_model.g6473.t1
Valid prediction for snap_scaffold_4-snap.1646-T1
Couldn't classify 227921, 228110
Sorry, prediction pasa_asmbl_41467.p1 fails validation.
(ATG)	 CA	223594-223607	GT	AGG
(TTG)	 AG	223885-223980	GT	AGG
(GCT)	 AG	224946-225124	GT	TGG
(TTT)	 AG	225305-225428	GT	AAG
(GCT)	 AG	227921-228110	AG	CAA
-recovered pasa_asmbl_41467.p1, initial, 223594, 223607
-recovered pasa_asmbl_41467.p1, internal, 223885, 223980
-recovered pasa_asmbl_41467.p1, internal, 224946, 225124
-recovered pasa_asmbl_41467.p1, internal, 225305, 225428
Valid prediction for GeneMark_model.16077_t
Valid prediction for GlimmerHMM_glimmerT_9876-T1
Valid prediction for snap_scaffold_4-snap.1647-T1
Valid prediction for snap_scaffold_4-snap.1625-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9895-T1
Valid prediction for GeneMark_model.16074_t
Valid prediction for snap_scaffold_4-snap.1613-T1
Valid prediction for HiQ_model.g6470.t1
Valid prediction for GeneMark_model.16058_t
Couldn't classify 231416, 231599
Sorry, prediction pasa_asmbl_41462.p1 fails validation.
(GTG)	 TA	231416-231599	GT	TGG
(TAA)	 AG	233124-233261	GT	AGG
(TGC)	 AG	236104-236174	GT	CCG
(ATT)	 AG	236754-236858	GT	AGG
(GTC)	 AG	238975-239103	GG	GAG
-recovered pasa_asmbl_41462.p1, terminal, 238975, 239103
-recovered pasa_asmbl_41462.p1, internal, 233124, 233261
-recovered pasa_asmbl_41462.p1, internal, 236104, 236174
-recovered pasa_asmbl_41462.p1, internal, 236754, 236858

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 104043, rend_intergenic: 103709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234429, rend_intergenic: 230156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241303, rend_intergenic: 235899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244687, rend_intergenic: 242628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246819, rend_intergenic: 245627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251558, rend_intergenic: 247867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253959
-exon list size: 579


building trellis

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80.7    
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86.7    
86.9    
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87.6    
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88.5    
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90.0    
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90.9    
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91.6    
91.7    
91.9    
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92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
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94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 104043, rend_intergenic: 103709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234429, rend_intergenic: 230156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241303, rend_intergenic: 235899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244687, rend_intergenic: 242628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246819, rend_intergenic: 245627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251558, rend_intergenic: 247867  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

-building DP trellis

-building trellis in range 1 - 14856
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1388 - 14856
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1388 - 14692
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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