-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_17915769-18151146

-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 GlimmerHMM_glimmerT_13609-T1
Valid prediction for Augustus_model.g9023.t1
Valid prediction for GlimmerHMM_glimmerT_13589-T1
Valid prediction for CodingQuarry_transcript_52439-T1
Valid prediction for snap_scaffold_5-snap.3350-T1
Couldn't classify 60081, 60135
Sorry, prediction pasa_asmbl_46198.p1 fails validation.
(ACT)	 TC	60081-60135	GT	AGG
(GTA)	 AG	60392-60524	GT	AAG
(CTG)	 AG	60652-60829	GT	AGG
(ACC)	 AG	62895-62993	GC	AGG
(ATG)	 AG	63202-63426	GA	AGG
-recovered pasa_asmbl_46198.p1, terminal, 63202, 63426
-recovered pasa_asmbl_46198.p1, internal, 60392, 60524
-recovered pasa_asmbl_46198.p1, internal, 60652, 60829
-recovered pasa_asmbl_46198.p1, internal, 62895, 62993
Valid prediction for Augustus_model.g9024.t1
Valid prediction for Augustus_model.g9027.t1
Valid prediction for snap_scaffold_5-snap.3354-T1
Valid prediction for GlimmerHMM_glimmerT_13595-T1
Valid prediction for snap_scaffold_5-snap.3341-T1
Valid prediction for GlimmerHMM_glimmerT_13599-T1
Valid prediction for snap_scaffold_5-snap.3348-T1
Valid prediction for snap_scaffold_5-snap.3342-T1
Couldn't classify 58352, 58450
Couldn't classify 59053, 59070
Sorry, prediction pasa_asmbl_46348.p1 fails validation.
(CAG)	 CT	58352-58450	GT	AGG
(GCC)	 AG	58645-58860	GT	AAG
(CTG)	 AG	59053-59070	TA	ACT
-recovered pasa_asmbl_46348.p1, internal, 58645, 58860
Valid prediction for GlimmerHMM_glimmerT_13587-T1
Valid prediction for snap_scaffold_5-snap.3370-T1
Valid prediction for HiQ_model.g9026.t1
Couldn't classify 151876, 151970
Sorry, prediction pasa_asmbl_46203.p1 fails validation.
(TAC)	 TG	151876-151970	GT	AGG
(TAC)	 AG	152448-152537	GT	AGG
(TAA)	 AG	152809-152929	GT	AGG
(GAG)	 AG	153996-154121	GT	AGG
(ATG)	 AG	154200-154323	GT	GGG
(ACG)	 AG	154594-154684	GT	AGG
(GTG)	 AG	154834-154936	GC	GAG
-recovered pasa_asmbl_46203.p1, initial, 154200, 154323
-recovered pasa_asmbl_46203.p1, terminal, 154834, 154936
-recovered pasa_asmbl_46203.p1, internal, 152448, 152537
-recovered pasa_asmbl_46203.p1, internal, 152809, 152929
-recovered pasa_asmbl_46203.p1, internal, 153996, 154121
-recovered pasa_asmbl_46203.p1, internal, 154200, 154323
-recovered pasa_asmbl_46203.p1, internal, 154594, 154684
-recovered pasa_asmbl_46203.p1, internal, 154834, 154936
Couldn't classify 155707, 155747
Couldn't classify 155958, 156225
Sorry, prediction CodingQuarry_transcript_52441-T1 fails validation.
(ATG)	 GC	155707-155747	CT	GCC
(CTA)	 GC	155958-156225	TC	AGT
Couldn't classify 70953, 71082
Couldn't classify 81622, 81695
Sorry, prediction pasa_asmbl_46200.p1 fails validation.
(AAG)	 AC	70953-71082	GT	TGG
(AGT)	 AG	71368-71563	GT	TGG
(GGA)	 AG	74287-74378	GT	AGG
(GAG)	 AG	74522-74625	GT	TGG
(TTT)	 AG	75149-75221	GT	TGG
(ACG)	 AG	75947-76022	GT	AAG
(GGG)	 AG	76584-76701	GT	AGG
(GAC)	 AG	77172-77216	GT	AGG
(GTA)	 AG	78422-78559	GT	AGG
(GGG)	 AG	78694-78864	GT	TGG
(TTT)	 AG	79085-79218	GT	AGG
(GTG)	 AG	79424-79556	GT	CGG
(GGG)	 AG	79957-80013	GT	CTG
(ACG)	 AG	80266-80346	GT	TGG
(GTG)	 AG	80474-80582	GT	TGG
(GTT)	 AG	80842-80910	GT	TGG
(GCC)	 AG	81018-81194	GT	AGG
(TGA)	 AG	81294-81368	GT	AGG
(GGA)	 AG	81622-81695	GA	CTG
-recovered pasa_asmbl_46200.p1, internal, 71368, 71563
-recovered pasa_asmbl_46200.p1, internal, 74287, 74378
-recovered pasa_asmbl_46200.p1, internal, 74522, 74625
-recovered pasa_asmbl_46200.p1, internal, 75149, 75221
-recovered pasa_asmbl_46200.p1, internal, 75947, 76022
-recovered pasa_asmbl_46200.p1, internal, 76584, 76701
-recovered pasa_asmbl_46200.p1, internal, 77172, 77216
-recovered pasa_asmbl_46200.p1, internal, 78422, 78559
-recovered pasa_asmbl_46200.p1, internal, 78694, 78864
-recovered pasa_asmbl_46200.p1, internal, 79085, 79218
-recovered pasa_asmbl_46200.p1, internal, 79424, 79556
-recovered pasa_asmbl_46200.p1, internal, 79957, 80013
-recovered pasa_asmbl_46200.p1, internal, 80266, 80346
-recovered pasa_asmbl_46200.p1, internal, 80474, 80582
-recovered pasa_asmbl_46200.p1, internal, 80842, 80910
-recovered pasa_asmbl_46200.p1, internal, 81018, 81194
-recovered pasa_asmbl_46200.p1, internal, 81294, 81368
Valid prediction for pasa_asmbl_46194.p1
Valid prediction for GlimmerHMM_glimmerT_13617-T1
Valid prediction for HiQ_model.g9029.t1
Valid prediction for GlimmerHMM_glimmerT_13601-T1
Valid prediction for snap_scaffold_5-snap.3340-T1
Valid prediction for GlimmerHMM_glimmerT_13597-T1
Valid prediction for GlimmerHMM_glimmerT_13610-T1
Valid prediction for snap_scaffold_5-snap.3359-T1
Valid prediction for snap_scaffold_5-snap.3352-T1
Valid prediction for snap_scaffold_5-snap.3347-T1
Valid prediction for snap_scaffold_5-snap.3336-T1
Valid prediction for Augustus_model.g9033.t1
Valid prediction for GlimmerHMM_glimmerT_13598-T1
Valid prediction for Augustus_model.g9025.t1
Valid prediction for snap_scaffold_5-snap.3339-T1
Valid prediction for snap_scaffold_5-snap.3335-T1
Valid prediction for GlimmerHMM_glimmerT_13604-T1
Valid prediction for snap_scaffold_5-snap.3337-T1
Valid prediction for Augustus_model.g9036.t1
Valid prediction for Augustus_model.g9034.t1
Valid prediction for snap_scaffold_5-snap.3366-T1
Valid prediction for snap_scaffold_5-snap.3349-T1
Valid prediction for snap_scaffold_5-snap.3361-T1
Valid prediction for snap_scaffold_5-snap.3368-T1
Valid prediction for snap_scaffold_5-snap.3334-T1
Valid prediction for Augustus_model.g9028.t1
Valid prediction for snap_scaffold_5-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_13590-T1
Valid prediction for GlimmerHMM_glimmerT_13593-T1
Valid prediction for GlimmerHMM_glimmerT_13591-T1
Valid prediction for snap_scaffold_5-snap.3338-T1
Valid prediction for GlimmerHMM_glimmerT_13613-T1
Valid prediction for GlimmerHMM_glimmerT_13596-T1
Valid prediction for snap_scaffold_5-snap.3371-T1
Valid prediction for GlimmerHMM_glimmerT_13592-T1
Valid prediction for snap_scaffold_5-snap.3332-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3362-T1
Valid prediction for snap_scaffold_5-snap.3346-T1
Valid prediction for snap_scaffold_5-snap.3374-T1
Couldn't classify 23126, 23197
Couldn't classify 24828, 24917
Sorry, prediction pasa_asmbl_46339.p1 fails validation.
(ACG)	 GC	23126-23197	GT	TTG
(GAG)	 AG	23615-23699	GT	TGG
(GCT)	 AG	23813-23958	GT	ACG
(ATT)	 AG	24828-24917	GG	ATG
-recovered pasa_asmbl_46339.p1, internal, 23615, 23699
-recovered pasa_asmbl_46339.p1, internal, 23813, 23958

-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_13607-T1
Couldn't classify 95109, 95495
Sorry, prediction pasa_asmbl_44828.p1 fails validation.
(CTC)	 CT	95109-95495	CA	GAC
Valid prediction for snap_scaffold_5-snap.3355-T1
Valid prediction for Augustus_model.g9035.t1
Valid prediction for GlimmerHMM_glimmerT_13616-T1
Valid prediction for Augustus_model.g9038.t1
Valid prediction for snap_scaffold_5-snap.3351-T1
Valid prediction for GlimmerHMM_glimmerT_13615-T1
Valid prediction for snap_scaffold_5-snap.3345-T1
Valid prediction for Augustus_model.g9030.t1
Valid prediction for GlimmerHMM_glimmerT_13603-T1
Valid prediction for snap_scaffold_5-snap.3344-T1
Valid prediction for snap_scaffold_5-snap.3365-T1
Valid prediction for GlimmerHMM_glimmerT_13611-T1
Couldn't classify 127611, 127649
Couldn't classify 131874, 131912
Sorry, prediction pasa_asmbl_44825.p1 fails validation.
(ATC)	 CC	127611-127649	GT	AGG
(TCC)	 AG	127987-128154	GT	AGG
(TTG)	 AG	130783-131049	GT	TGG
(TCT)	 AG	131874-131912	AA	ACA
-recovered pasa_asmbl_44825.p1, internal, 127987, 128154
-recovered pasa_asmbl_44825.p1, internal, 130783, 131049
Couldn't classify 119549, 119611
Couldn't classify 121208, 121354
Sorry, prediction pasa_asmbl_44827.p1 fails validation.
(AAC)	 AG	119549-119611	GT	AGG
(GAG)	 AG	120521-120688	GT	AGG
(GTG)	 AG	120867-120968	GT	AGG
(GTG)	 AG	121208-121354	CT	AGC
-recovered pasa_asmbl_44827.p1, internal, 119549, 119611
-recovered pasa_asmbl_44827.p1, internal, 120521, 120688
-recovered pasa_asmbl_44827.p1, internal, 120867, 120968
Valid prediction for GlimmerHMM_glimmerT_13600-T1
Valid prediction for snap_scaffold_5-snap.3353-T1
Valid prediction for GlimmerHMM_glimmerT_13588-T1
Valid prediction for GlimmerHMM_glimmerT_13586-T1
Valid prediction for snap_scaffold_5-snap.3369-T1
Valid prediction for GlimmerHMM_glimmerT_13612-T1
Valid prediction for GlimmerHMM_glimmerT_13606-T1
Valid prediction for snap_scaffold_5-snap.3367-T1
Valid prediction for Augustus_model.g9031.t1
Valid prediction for snap_scaffold_5-snap.3363-T1
Valid prediction for snap_scaffold_5-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_13614-T1
Valid prediction for GlimmerHMM_glimmerT_13602-T1
Valid prediction for GlimmerHMM_glimmerT_13605-T1
Valid prediction for GlimmerHMM_glimmerT_13618-T1
Valid prediction for snap_scaffold_5-snap.3358-T1
Valid prediction for GlimmerHMM_glimmerT_13594-T1
Valid prediction for GlimmerHMM_glimmerT_13608-T1
Valid prediction for snap_scaffold_5-snap.3373-T1
Valid prediction for Augustus_model.g9037.t1
Couldn't classify 132473, 132817
Sorry, prediction pasa_asmbl_44824.p1 fails validation.
(GAG)	 TG	132473-132817	CA	GAC
Valid prediction for snap_scaffold_5-snap.3375-T1
Valid prediction for snap_scaffold_5-snap.3357-T1
Valid prediction for Augustus_model.g9032.t1
Valid prediction for HiQ_model.g9022.t1
Valid prediction for snap_scaffold_5-snap.3343-T1
Valid prediction for Augustus_model.g9039.t1
Couldn't classify 41059, 41808
Sorry, prediction pasa_asmbl_46205.p1 fails validation.
(CTC)	 TC	41059-41808	TC	AGT
Valid prediction for snap_scaffold_5-snap.3331-T1
Valid prediction for snap_scaffold_5-snap.3360-T1
Valid prediction for pasa_asmbl_44820.p1
Valid prediction for CodingQuarry_transcript_52438-T1
Valid prediction for snap_scaffold_5-snap.3356-T1
Valid prediction for snap_scaffold_5-snap.3364-T1
Valid prediction for snap_scaffold_5-snap.3372-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25270, rend_intergenic: 12247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81912, rend_intergenic: 73539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98297, rend_intergenic: 83055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102619, rend_intergenic: 101582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108870, rend_intergenic: 104572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111254, rend_intergenic: 109645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126802, rend_intergenic: 114758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138493, rend_intergenic: 126931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144638, rend_intergenic: 141763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154361, rend_intergenic: 147187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156249, rend_intergenic: 154587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187745, rend_intergenic: 185937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190693, rend_intergenic: 190432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201001, rend_intergenic: 196606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212606, rend_intergenic: 201160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216421, rend_intergenic: 213039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229836, rend_intergenic: 219240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235378
-exon list size: 503


building trellis

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90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 25270, rend_intergenic: 12247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81912, rend_intergenic: 73539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98297, rend_intergenic: 83055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102619, rend_intergenic: 101582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108870, rend_intergenic: 104572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111254, rend_intergenic: 109645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126802, rend_intergenic: 114758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138493, rend_intergenic: 126931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144638, rend_intergenic: 141763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154361, rend_intergenic: 147187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156249, rend_intergenic: 154587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187745, rend_intergenic: 185937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190693, rend_intergenic: 190432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201001, rend_intergenic: 196606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212606, rend_intergenic: 201160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216421, rend_intergenic: 213039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229836, rend_intergenic: 219240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support