-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_7181139-7405762

-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.g32046.t1
Valid prediction for Augustus_model.g32045.t1
Valid prediction for GlimmerHMM_glimmerT_48039-T1
Valid prediction for GlimmerHMM_glimmerT_48036-T1
Valid prediction for snap_scaffold_21-snap.1491-T1
Couldn't classify 133829, 133952
Sorry, prediction pasa_asmbl_28722.p1 fails validation.
(GTT)	 GG	133829-133952	GT	AGG
(CGC)	 AG	134254-134366	GT	AGG
(ACA)	 AG	134664-134757	GT	AGG
(ACG)	 AG	134965-135110	GT	CCG
(AAT)	 AG	135322-135415	GT	AGG
(ATG)	 AG	135560-135621	GT	TTG
(AGA)	 AG	135965-136133	GT	AGG
(CTT)	 AG	136287-136475	GT	AGG
(AAC)	 AG	136594-136767	GT	AGG
(GTG)	 AG	136929-137021	GT	AGG
(AGA)	 AG	137165-137298	GT	AAG
add_exon() Sorry, pasa_asmbl_28722.p1 135560-135621-initial-1 is invalid.
-recovered pasa_asmbl_28722.p1, initial, 135560, 135621
-recovered pasa_asmbl_28722.p1, terminal, 137165, 137298
-recovered pasa_asmbl_28722.p1, internal, 134254, 134366
-recovered pasa_asmbl_28722.p1, internal, 134664, 134757
-recovered pasa_asmbl_28722.p1, internal, 134965, 135110
-recovered pasa_asmbl_28722.p1, internal, 135322, 135415
-recovered pasa_asmbl_28722.p1, internal, 135560, 135621
-recovered pasa_asmbl_28722.p1, internal, 135965, 136133
-recovered pasa_asmbl_28722.p1, internal, 136287, 136475
-recovered pasa_asmbl_28722.p1, internal, 136594, 136767
-recovered pasa_asmbl_28722.p1, internal, 136929, 137021
-recovered pasa_asmbl_28722.p1, internal, 137165, 137298
Valid prediction for GlimmerHMM_glimmerT_48008-T1
Valid prediction for Augustus_model.g32043.t1
Valid prediction for GlimmerHMM_glimmerT_48028-T1
Valid prediction for HiQ_model.g32056.t1
Valid prediction for HiQ_model.g32057.t1
Valid prediction for Augustus_model.g32067.t1
Valid prediction for GlimmerHMM_glimmerT_48004-T1
Valid prediction for GlimmerHMM_glimmerT_47998-T1
Valid prediction for snap_scaffold_21-snap.1489-T1
Couldn't classify 202613, 202783
Sorry, prediction pasa_asmbl_28729.p1 fails validation.
(TAT)	 CT	202613-202783	GT	AGG
(CTG)	 AG	202963-203031	GT	AGG
(AAA)	 AG	203150-203200	GT	CTG
(GTG)	 AG	203290-203391	CC	AAC
-recovered pasa_asmbl_28729.p1, terminal, 203290, 203391
-recovered pasa_asmbl_28729.p1, internal, 202963, 203031
-recovered pasa_asmbl_28729.p1, internal, 203150, 203200
Valid prediction for snap_scaffold_21-snap.1521-T1
Valid prediction for snap_scaffold_21-snap.1501-T1
Valid prediction for snap_scaffold_21-snap.1538-T1
Valid prediction for pasa_asmbl_28730.p1
Valid prediction for snap_scaffold_21-snap.1522-T1
Valid prediction for GlimmerHMM_glimmerT_48010-T1
Valid prediction for GlimmerHMM_glimmerT_48022-T1
Valid prediction for GlimmerHMM_glimmerT_48003-T1
Valid prediction for snap_scaffold_21-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_48020-T1
Valid prediction for snap_scaffold_21-snap.1526-T1
Valid prediction for Augustus_model.g32055.t1
Valid prediction for snap_scaffold_21-snap.1505-T1
Valid prediction for Augustus_model.g32048.t1
Valid prediction for GlimmerHMM_glimmerT_48023-T1
Valid prediction for Augustus_model.g32054.t1
Valid prediction for snap_scaffold_21-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_48009-T1
Valid prediction for CodingQuarry_transcript_32613-T1
Couldn't classify 126194, 126286
Sorry, prediction pasa_asmbl_28720.p1 fails validation.
(GTT)	 GC	126194-126286	GT	AGG
(GGT)	 AG	126445-126565	GT	AGG
(CGT)	 AG	126779-126867	GT	GGG
(GTC)	 AG	127147-127236	GA	GAG
add_exon() Sorry, pasa_asmbl_28720.p1 126445-126565-terminal-3 is invalid.
-recovered pasa_asmbl_28720.p1, terminal, 126445, 126565
-recovered pasa_asmbl_28720.p1, terminal, 127147, 127236
-recovered pasa_asmbl_28720.p1, internal, 126445, 126565
-recovered pasa_asmbl_28720.p1, internal, 126779, 126867
Valid prediction for snap_scaffold_21-snap.1524-T1
Valid prediction for Augustus_model.g32042.t1
Couldn't classify 87067, 87124
Sorry, prediction pasa_asmbl_28716.p1 fails validation.
(CAG)	 CC	87067-87124	GT	TGG
(TGC)	 AG	87358-87482	GT	AGG
(GAG)	 AG	87720-87888	GT	TGG
(AGG)	 AG	88006-88105	GT	CGG
(GAG)	 AG	89725-89789	GT	AGG
(GGG)	 AG	89991-90104	GT	AGG
(GTG)	 AG	90262-90509	GT	GGG
(CTG)	 AG	90674-90889	GT	TGG
(GGC)	 AG	91151-91300	GT	ATG
(GTG)	 AG	91480-91673	GT	GGG
(GCC)	 AG	92184-92342	GT	GAG
(GGA)	 AG	92845-92956	CC	GAC
add_exon() Sorry, pasa_asmbl_28716.p1 92184-92342-terminal-1 is invalid.
-recovered pasa_asmbl_28716.p1, terminal, 92184, 92342
-recovered pasa_asmbl_28716.p1, terminal, 92845, 92956
-recovered pasa_asmbl_28716.p1, internal, 87358, 87482
-recovered pasa_asmbl_28716.p1, internal, 87720, 87888
-recovered pasa_asmbl_28716.p1, internal, 88006, 88105
-recovered pasa_asmbl_28716.p1, internal, 89725, 89789
-recovered pasa_asmbl_28716.p1, internal, 89991, 90104
-recovered pasa_asmbl_28716.p1, internal, 90262, 90509
-recovered pasa_asmbl_28716.p1, internal, 90674, 90889
-recovered pasa_asmbl_28716.p1, internal, 91151, 91300
-recovered pasa_asmbl_28716.p1, internal, 91480, 91673
-recovered pasa_asmbl_28716.p1, internal, 92184, 92342
Valid prediction for Augustus_model.g32050.t1
Valid prediction for GlimmerHMM_glimmerT_48007-T1
Valid prediction for snap_scaffold_21-snap.1535-T1
Valid prediction for Augustus_model.g32072.t1
Valid prediction for CodingQuarry_transcript_32609-T1
Valid prediction for snap_scaffold_21-snap.1495-T1
Valid prediction for GlimmerHMM_glimmerT_48029-T1
Valid prediction for snap_scaffold_21-snap.1540-T1
Valid prediction for snap_scaffold_21-snap.1513-T1
Valid prediction for HiQ_model.g32069.t1
Couldn't classify 171711, 171779
Couldn't classify 172551, 172574
Sorry, prediction pasa_asmbl_28961.p1 fails validation.
(ATA)	 AG	171711-171779	GT	TGG
(TTA)	 AG	171976-172102	GT	AGG
(CTG)	 AG	172187-172264	GT	TGG
(GTC)	 AG	172367-172446	GT	AGG
(ACT)	 AG	172551-172574	AT	AGA
-recovered pasa_asmbl_28961.p1, internal, 171711, 171779
-recovered pasa_asmbl_28961.p1, internal, 171976, 172102
-recovered pasa_asmbl_28961.p1, internal, 172187, 172264
-recovered pasa_asmbl_28961.p1, internal, 172367, 172446
Valid prediction for Augustus_model.g32047.t1
Valid prediction for snap_scaffold_21-snap.1536-T1
Valid prediction for snap_scaffold_21-snap.1517-T1
Valid prediction for Augustus_model.g32041.t1
Valid prediction for snap_scaffold_21-snap.1496-T1
Valid prediction for HiQ_model.g32070.t1
Valid prediction for snap_scaffold_21-snap.1533-T1
Valid prediction for Augustus_model.g32062.t1
Valid prediction for Augustus_model.g32061.t1
Valid prediction for Augustus_model.g32049.t1
Valid prediction for GlimmerHMM_glimmerT_48038-T1
Valid prediction for Augustus_model.g32059.t1
Valid prediction for pasa_asmbl_28727.p1
Valid prediction for pasa_asmbl_28721.p1
Valid prediction for snap_scaffold_21-snap.1539-T1
Valid prediction for snap_scaffold_21-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_48013-T1
Valid prediction for GlimmerHMM_glimmerT_48014-T1
Valid prediction for GlimmerHMM_glimmerT_48041-T1
Valid prediction for GlimmerHMM_glimmerT_47999-T1
Valid prediction for snap_scaffold_21-snap.1510-T1
Valid prediction for CodingQuarry_transcript_32607-T1
Valid prediction for GlimmerHMM_glimmerT_48021-T1
Valid prediction for snap_scaffold_21-snap.1497-T1
Valid prediction for snap_scaffold_21-snap.1519-T1
Couldn't classify 176082, 176405
Sorry, prediction pasa_asmbl_28726.p1 fails validation.
(ACT)	 TC	176082-176405	GT	CGG
(GGC)	 AG	176578-176684	GT	AAG
(CAT)	 AG	176800-176935	GT	AGG
(GTG)	 AG	177042-177176	GG	GAG
-recovered pasa_asmbl_28726.p1, terminal, 177042, 177176
-recovered pasa_asmbl_28726.p1, internal, 176578, 176684
-recovered pasa_asmbl_28726.p1, internal, 176800, 176935
Valid prediction for CodingQuarry_transcript_32608-T1
Valid prediction for GlimmerHMM_glimmerT_48016-T1
Valid prediction for snap_scaffold_21-snap.1499-T1
Valid prediction for GlimmerHMM_glimmerT_48027-T1
Valid prediction for snap_scaffold_21-snap.1502-T1
Valid prediction for GlimmerHMM_glimmerT_48025-T1
Valid prediction for snap_scaffold_21-snap.1520-T1
Valid prediction for snap_scaffold_21-snap.1504-T1
Valid prediction for CodingQuarry_transcript_32614-T1
Valid prediction for snap_scaffold_21-snap.1527-T1
Valid prediction for snap_scaffold_21-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_48035-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.g32068.t1
Valid prediction for GlimmerHMM_glimmerT_48005-T1
Valid prediction for snap_scaffold_21-snap.1541-T1
Valid prediction for GlimmerHMM_glimmerT_48033-T1
Valid prediction for snap_scaffold_21-snap.1500-T1
Valid prediction for pasa_asmbl_27796.p1
Valid prediction for GlimmerHMM_glimmerT_48011-T1
Valid prediction for GlimmerHMM_glimmerT_48030-T1
Valid prediction for CodingQuarry_transcript_32605-T1
Valid prediction for snap_scaffold_21-snap.1498-T1
Valid prediction for CodingQuarry_transcript_32612-T1
Valid prediction for GlimmerHMM_glimmerT_48031-T1
Valid prediction for GlimmerHMM_glimmerT_48019-T1
Valid prediction for GlimmerHMM_glimmerT_48034-T1
Valid prediction for GlimmerHMM_glimmerT_48000-T1
Valid prediction for snap_scaffold_21-snap.1537-T1
Valid prediction for Augustus_model.g32066.t1
Valid prediction for snap_scaffold_21-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_48037-T1
Valid prediction for snap_scaffold_21-snap.1493-T1
Valid prediction for GlimmerHMM_glimmerT_48001-T1
Valid prediction for Augustus_model.g32065.t1
Valid prediction for snap_scaffold_21-snap.1492-T1
Valid prediction for snap_scaffold_21-snap.1507-T1
Valid prediction for CodingQuarry_transcript_32606-T1
Valid prediction for Augustus_model.g32071.t1
Valid prediction for snap_scaffold_21-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_48017-T1
Valid prediction for CodingQuarry_transcript_32615-T1
Valid prediction for GlimmerHMM_glimmerT_48018-T1
Valid prediction for snap_scaffold_21-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_48040-T1
Valid prediction for snap_scaffold_21-snap.1506-T1
Valid prediction for Augustus_model.g32052.t1
Valid prediction for Augustus_model.g32044.t1
Valid prediction for snap_scaffold_21-snap.1514-T1
Couldn't classify 25865, 26773
Sorry, prediction pasa_asmbl_27804.p1 fails validation.
(CCG)	 CC	25865-26773	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_48006-T1
Valid prediction for snap_scaffold_21-snap.1523-T1
Valid prediction for GlimmerHMM_glimmerT_48012-T1
Valid prediction for snap_scaffold_21-snap.1494-T1
Valid prediction for snap_scaffold_21-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_48032-T1
Valid prediction for CodingQuarry_transcript_32610-T1
Valid prediction for snap_scaffold_21-snap.1518-T1
Valid prediction for Augustus_model.g32063.t1
Valid prediction for Augustus_model.g32064.t1
Valid prediction for snap_scaffold_21-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_48015-T1
Valid prediction for Augustus_model.g32060.t1
Valid prediction for GlimmerHMM_glimmerT_48026-T1
Valid prediction for snap_scaffold_21-snap.1532-T1
Valid prediction for HiQ_model.g32058.t1
Valid prediction for HiQ_model.g32053.t1
Valid prediction for snap_scaffold_21-snap.1534-T1
Valid prediction for snap_scaffold_21-snap.1509-T1
Valid prediction for snap_scaffold_21-snap.1525-T1
Valid prediction for snap_scaffold_21-snap.1516-T1
Valid prediction for pasa_asmbl_27794.p1
Valid prediction for Augustus_model.g32051.t1
Valid prediction for GlimmerHMM_glimmerT_48024-T1
Valid prediction for GlimmerHMM_glimmerT_48002-T1
Valid prediction for snap_scaffold_21-snap.1515-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25472, rend_intergenic: 14600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27914, rend_intergenic: 26047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46966, rend_intergenic: 45228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51167, rend_intergenic: 48646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64943, rend_intergenic: 52173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68828, rend_intergenic: 66016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78600, rend_intergenic: 72424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83708, rend_intergenic: 79142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92956, rend_intergenic: 86725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101027, rend_intergenic: 96735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224624
-exon list size: 557


building trellis

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76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 25472, rend_intergenic: 14600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27914, rend_intergenic: 26047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46966, rend_intergenic: 45228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51167, rend_intergenic: 48646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64943, rend_intergenic: 52173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68828, rend_intergenic: 66016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78600, rend_intergenic: 72424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83708, rend_intergenic: 79142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92956, rend_intergenic: 86725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101027, rend_intergenic: 96735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support