-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_8039706-8308298

-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.g13376.t1
Valid prediction for snap_scaffold_8-snap.1573-T1
Valid prediction for snap_scaffold_8-snap.1570-T1
Valid prediction for snap_scaffold_8-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_20130-T1
Valid prediction for snap_scaffold_8-snap.1572-T1
Valid prediction for Augustus_model.g13389.t1
Valid prediction for snap_scaffold_8-snap.1560-T1
Valid prediction for Augustus_model.g13378.t1
Valid prediction for snap_scaffold_8-snap.1608-T1
Valid prediction for Augustus_model.g13369.t1
Valid prediction for GlimmerHMM_glimmerT_20106-T1
Valid prediction for snap_scaffold_8-snap.1574-T1
Valid prediction for snap_scaffold_8-snap.1581-T1
Valid prediction for Augustus_model.g13375.t1
Valid prediction for snap_scaffold_8-snap.1586-T1
Valid prediction for snap_scaffold_8-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_20107-T1
Valid prediction for GlimmerHMM_glimmerT_20098-T1
Valid prediction for snap_scaffold_8-snap.1568-T1
Valid prediction for snap_scaffold_8-snap.1571-T1
Valid prediction for Augustus_model.g13386.t1
Valid prediction for snap_scaffold_8-snap.1588-T1
Valid prediction for snap_scaffold_8-snap.1561-T1
Valid prediction for Augustus_model.g13367.t1
Valid prediction for snap_scaffold_8-snap.1584-T1
Valid prediction for snap_scaffold_8-snap.1605-T1
Valid prediction for snap_scaffold_8-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_20100-T1
Couldn't classify 135215, 135455
Sorry, prediction pasa_asmbl_53007.p1 fails validation.
(GTT)	 CA	135215-135455	GT	CGG
(GAC)	 AG	135612-135703	GT	AGG
(TAC)	 AG	137164-137295	GT	GGG
(AGC)	 AG	137626-137812	GT	CGG
(GCT)	 AG	138041-138311	GT	AGG
(GTT)	 AG	138412-138562	GT	AGG
(ATG)	 AG	138656-138808	GT	TGG
(ATC)	 AG	140984-141150	GT	AGG
(GTC)	 AG	141989-142170	GT	GGG
(GCA)	 AG	142278-142384	AC	AGA
-recovered pasa_asmbl_53007.p1, initial, 138656, 138808
-recovered pasa_asmbl_53007.p1, terminal, 142278, 142384
-recovered pasa_asmbl_53007.p1, internal, 135612, 135703
-recovered pasa_asmbl_53007.p1, internal, 137164, 137295
-recovered pasa_asmbl_53007.p1, internal, 137626, 137812
-recovered pasa_asmbl_53007.p1, internal, 138041, 138311
-recovered pasa_asmbl_53007.p1, internal, 138412, 138562
-recovered pasa_asmbl_53007.p1, internal, 138656, 138808
-recovered pasa_asmbl_53007.p1, internal, 140984, 141150
-recovered pasa_asmbl_53007.p1, internal, 141989, 142170
Valid prediction for CodingQuarry_transcript_59699-T1
Valid prediction for GlimmerHMM_glimmerT_20132-T1
Valid prediction for snap_scaffold_8-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_20105-T1
Valid prediction for snap_scaffold_8-snap.1577-T1
Valid prediction for snap_scaffold_8-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_20135-T1
Valid prediction for snap_scaffold_8-snap.1556-T1
Valid prediction for GlimmerHMM_glimmerT_20121-T1
Valid prediction for GlimmerHMM_glimmerT_20102-T1
Valid prediction for GlimmerHMM_glimmerT_20118-T1
Valid prediction for snap_scaffold_8-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_20137-T1
Valid prediction for GlimmerHMM_glimmerT_20099-T1
Valid prediction for snap_scaffold_8-snap.1616-T1
Valid prediction for snap_scaffold_8-snap.1607-T1
Valid prediction for GlimmerHMM_glimmerT_20101-T1
Valid prediction for snap_scaffold_8-snap.1587-T1
Valid prediction for snap_scaffold_8-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_20104-T1
Valid prediction for GlimmerHMM_glimmerT_20123-T1
Valid prediction for snap_scaffold_8-snap.1599-T1
Valid prediction for snap_scaffold_8-snap.1589-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_20113-T1
Valid prediction for snap_scaffold_8-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_20133-T1
Valid prediction for Augustus_model.g13371.t1
Valid prediction for GlimmerHMM_glimmerT_20096-T1
Valid prediction for GlimmerHMM_glimmerT_20115-T1
Valid prediction for snap_scaffold_8-snap.1611-T1
Valid prediction for snap_scaffold_8-snap.1595-T1
Valid prediction for Augustus_model.g13372.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 Augustus_model.g13373.t1
Valid prediction for Augustus_model.g13388.t1
Valid prediction for snap_scaffold_8-snap.1612-T1
Valid prediction for Augustus_model.g13390.t1
Valid prediction for GlimmerHMM_glimmerT_20120-T1
Valid prediction for GlimmerHMM_glimmerT_20131-T1
Valid prediction for snap_scaffold_8-snap.1613-T1
Couldn't classify 122029, 122263
Couldn't classify 122773, 122915
Sorry, prediction CodingQuarry_transcript_59700-T1 fails validation.
(ATG)	 AC	120775-120864	GT	AGG
(ATT)	 AG	121260-121371	GT	TGG
(ATG)	 AG	121511-121674	GT	AGG
(GCG)	 AG	122029-122263	TC	CGT
(GTG)	 GT	122773-122915	GT	AGG
(ATC)	 AG	123028-123178	GT	AGG
(GTC)	 AG	124544-124653	CC	AAC
-recovered CodingQuarry_transcript_59700-T1, initial, 120775, 120864
add_exon() Sorry, CodingQuarry_transcript_59700-T1 121511-121674-initial-1 is invalid.
-recovered CodingQuarry_transcript_59700-T1, initial, 121511, 121674
-recovered CodingQuarry_transcript_59700-T1, terminal, 124544, 124653
-recovered CodingQuarry_transcript_59700-T1, internal, 121260, 121371
-recovered CodingQuarry_transcript_59700-T1, internal, 121511, 121674
-recovered CodingQuarry_transcript_59700-T1, internal, 123028, 123178
Valid prediction for Augustus_model.g13391.t1
Valid prediction for GlimmerHMM_glimmerT_20110-T1
Valid prediction for GlimmerHMM_glimmerT_20108-T1
Valid prediction for Augustus_model.g13370.t1
Valid prediction for snap_scaffold_8-snap.1591-T1
Valid prediction for Augustus_model.g13384.t1
Valid prediction for Augustus_model.g13383.t1
Valid prediction for snap_scaffold_8-snap.1557-T1
Valid prediction for snap_scaffold_8-snap.1585-T1
Valid prediction for snap_scaffold_8-snap.1579-T1
Valid prediction for snap_scaffold_8-snap.1575-T1
Valid prediction for Augustus_model.g13392.t1
Valid prediction for snap_scaffold_8-snap.1594-T1
Valid prediction for GlimmerHMM_glimmerT_20124-T1
Couldn't classify 122029, 122263
Couldn't classify 122773, 122915
Sorry, prediction CodingQuarry_transcript_59701-T1 fails validation.
(ATG)	 TC	121567-121674	GT	AGG
(GCG)	 AG	122029-122263	TC	CGT
(GTG)	 GT	122773-122915	GT	AGG
(ATC)	 AG	123028-123186	GT	TGG
(GTC)	 AG	124544-124549	AG	GAA
-recovered CodingQuarry_transcript_59701-T1, initial, 121567, 121674
-recovered CodingQuarry_transcript_59701-T1, terminal, 124544, 124549
-recovered CodingQuarry_transcript_59701-T1, internal, 123028, 123186
Valid prediction for GlimmerHMM_glimmerT_20097-T1
Valid prediction for HiQ_model.g13387.t1
Valid prediction for snap_scaffold_8-snap.1601-T1
Valid prediction for snap_scaffold_8-snap.1590-T1
Valid prediction for snap_scaffold_8-snap.1592-T1
Valid prediction for snap_scaffold_8-snap.1569-T1
Valid prediction for GlimmerHMM_glimmerT_20129-T1
Valid prediction for GlimmerHMM_glimmerT_20114-T1
Valid prediction for GlimmerHMM_glimmerT_20116-T1
Valid prediction for GlimmerHMM_glimmerT_20126-T1
Valid prediction for snap_scaffold_8-snap.1609-T1
Valid prediction for snap_scaffold_8-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_20109-T1
Valid prediction for snap_scaffold_8-snap.1596-T1
Valid prediction for pasa_asmbl_51947.p1
Valid prediction for GlimmerHMM_glimmerT_20103-T1
Valid prediction for GlimmerHMM_glimmerT_20111-T1
Valid prediction for Augustus_model.g13385.t1
Valid prediction for Augustus_model.g13382.t1
Valid prediction for snap_scaffold_8-snap.1600-T1
Valid prediction for GlimmerHMM_glimmerT_20134-T1
Valid prediction for GlimmerHMM_glimmerT_20117-T1
Couldn't classify 7375, 7833
Sorry, prediction pasa_asmbl_51954.p1 fails validation.
(GTT)	 AT	7375-7833	CA	GCC
Valid prediction for snap_scaffold_8-snap.1606-T1
Valid prediction for snap_scaffold_8-snap.1564-T1
Valid prediction for HiQ_model.g13379.t1
Valid prediction for Augustus_model.g13377.t1
Valid prediction for Augustus_model.g13368.t1
Valid prediction for GlimmerHMM_glimmerT_20119-T1
Valid prediction for snap_scaffold_8-snap.1614-T1
Valid prediction for snap_scaffold_8-snap.1563-T1
Valid prediction for snap_scaffold_8-snap.1567-T1
Valid prediction for snap_scaffold_8-snap.1582-T1
Valid prediction for snap_scaffold_8-snap.1559-T1
Valid prediction for pasa_asmbl_51949.p1
Valid prediction for GlimmerHMM_glimmerT_20125-T1
Valid prediction for CodingQuarry_transcript_59702-T1
Valid prediction for snap_scaffold_8-snap.1610-T1
Valid prediction for GlimmerHMM_glimmerT_20128-T1
Valid prediction for Augustus_model.g13381.t1
Valid prediction for GlimmerHMM_glimmerT_20127-T1
Valid prediction for snap_scaffold_8-snap.1562-T1
Valid prediction for Augustus_model.g13374.t1
Valid prediction for Augustus_model.g13380.t1
Valid prediction for GlimmerHMM_glimmerT_20112-T1
Valid prediction for GlimmerHMM_glimmerT_20136-T1
Valid prediction for snap_scaffold_8-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_20122-T1
Couldn't classify 12579, 12988
Sorry, prediction GlimmerHMM_glimmerT_20138-T1 fails validation.
(ATG)	 CC	3386-4135	GT	AGG
(ATC)	 AG	6844-8009	GT	TGG
(TGG)	 AG	11113-12520	GT	ATG
(AAC)	 AN	12579-12988	GT	TGG
(CCT)	 AG	13834-15209	GT	AGG
(CTG)	 AG	16243-16445	GT	TCG
(TCT)	 AG	17020-17214	GT	ATG
(GCC)	 AG	18883-19041	GC	GAG
-recovered GlimmerHMM_glimmerT_20138-T1, initial, 3386, 4135
-recovered GlimmerHMM_glimmerT_20138-T1, terminal, 18883, 19041
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 6844, 8009
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 11113, 12520
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 13834, 15209
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 16243, 16445
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 17020, 17214
-recovered GlimmerHMM_glimmerT_20138-T1, internal, 18883, 19041
Valid prediction for snap_scaffold_8-snap.1602-T1
Valid prediction for snap_scaffold_8-snap.1578-T1
Valid prediction for snap_scaffold_8-snap.1565-T1
Valid prediction for snap_scaffold_8-snap.1615-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10519, rend_intergenic: 6838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11565, rend_intergenic: 10965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16260, rend_intergenic: 12276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32564, rend_intergenic: 22044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40517, rend_intergenic: 38293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40614, rend_intergenic: 40544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42437, rend_intergenic: 41311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55542, rend_intergenic: 44678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71364, rend_intergenic: 68342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88963, rend_intergenic: 74045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106095, rend_intergenic: 103503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129075, rend_intergenic: 106671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144854, rend_intergenic: 132757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151253, rend_intergenic: 150059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160292, rend_intergenic: 159453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168197, rend_intergenic: 160649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169602, rend_intergenic: 169134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174726, rend_intergenic: 169889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181308, rend_intergenic: 180078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184732, rend_intergenic: 182965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193684, rend_intergenic: 184737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197944, rend_intergenic: 194895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207011, rend_intergenic: 199221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214588, rend_intergenic: 207119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268593
-exon list size: 528


building trellis

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80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 10519, rend_intergenic: 6838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11565, rend_intergenic: 10965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16260, rend_intergenic: 12276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32564, rend_intergenic: 22044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40517, rend_intergenic: 38293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40614, rend_intergenic: 40544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42437, rend_intergenic: 41311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55542, rend_intergenic: 44678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71364, rend_intergenic: 68342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88963, rend_intergenic: 74045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106095, rend_intergenic: 103503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129075, rend_intergenic: 106671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144854, rend_intergenic: 132757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151253, rend_intergenic: 150059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160292, rend_intergenic: 159453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168197, rend_intergenic: 160649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169602, rend_intergenic: 169134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174726, rend_intergenic: 169889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181308, rend_intergenic: 180078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184732, rend_intergenic: 182965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193684, rend_intergenic: 184737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197944, rend_intergenic: 194895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207011, rend_intergenic: 199221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214588, rend_intergenic: 207119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support