-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_1312664-1521876

-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_14054-T1
Couldn't classify 175069, 175581
Sorry, prediction pasa_asmbl_47929.p1 fails validation.
(TCT)	 TC	175069-175581	TC	GAT
Valid prediction for HiQ_model.g9328.t1
Valid prediction for snap_scaffold_6-snap.342-T1
Valid prediction for snap_scaffold_6-snap.335-T1
Valid prediction for snap_scaffold_6-snap.297-T1
Valid prediction for Augustus_model.g9319.t1
Valid prediction for Augustus_model.g9323.t1
Valid prediction for HiQ_model.g9324.t1
Valid prediction for snap_scaffold_6-snap.299-T1
Valid prediction for snap_scaffold_6-snap.315-T1
Valid prediction for snap_scaffold_6-snap.310-T1
Valid prediction for snap_scaffold_6-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_14036-T1
Valid prediction for snap_scaffold_6-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_14051-T1
Valid prediction for snap_scaffold_6-snap.324-T1
Valid prediction for snap_scaffold_6-snap.300-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.336-T1
Couldn't classify 173710, 174168
Sorry, prediction pasa_asmbl_47958.p1 fails validation.
(ACC)	 AC	173710-174168	CC	GAC
Valid prediction for Augustus_model.g9327.t1
Couldn't classify 180072, 180186
Couldn't classify 182265, 182319
Sorry, prediction CodingQuarry_transcript_54920-T1 fails validation.
(ATG)	 GA	179387-179489	GT	AAG
(CCT)	 AG	180072-180186	GA	CCG
(AGA)	 TA	182265-182319	TC	AGT
-recovered CodingQuarry_transcript_54920-T1, initial, 179387, 179489
Valid prediction for GlimmerHMM_glimmerT_14038-T1
Valid prediction for snap_scaffold_6-snap.305-T1
Couldn't classify 158449, 158471
Sorry, prediction HiQ_model.g9326.t1 fails validation.
(ATG)	 GG	149007-149121	GT	TTG
(TTT)	 AG	151049-151342	GT	AGG
(GCC)	 AG	151879-152015	GT	CTG
(GTA)	 AG	152424-152568	GT	AGG
(GTC)	 AG	153093-153353	GT	GGG
(AGC)	 AG	153906-154190	GT	AGG
(TCC)	 AG	154701-154997	GT	CGG
(AGC)	 AG	155094-155369	GT	AGG
(TGA)	 AG	155489-155621	GT	GTG
(GAA)	 AG	155746-155819	GT	TGG
(TCA)	 AG	156540-156593	GT	AGG
(AGT)	 AG	157055-157144	GT	AGG
(CTC)	 AG	157549-157605	GT	AGG
(GTG)	 AG	158449-158471	GT	GAG
-recovered HiQ_model.g9326.t1, initial, 149007, 149121
-recovered HiQ_model.g9326.t1, internal, 151049, 151342
-recovered HiQ_model.g9326.t1, internal, 151879, 152015
-recovered HiQ_model.g9326.t1, internal, 152424, 152568
-recovered HiQ_model.g9326.t1, internal, 153093, 153353
-recovered HiQ_model.g9326.t1, internal, 153906, 154190
-recovered HiQ_model.g9326.t1, internal, 154701, 154997
-recovered HiQ_model.g9326.t1, internal, 155094, 155369
-recovered HiQ_model.g9326.t1, internal, 155489, 155621
-recovered HiQ_model.g9326.t1, internal, 155746, 155819
-recovered HiQ_model.g9326.t1, internal, 156540, 156593
-recovered HiQ_model.g9326.t1, internal, 157055, 157144
-recovered HiQ_model.g9326.t1, internal, 157549, 157605
-recovered HiQ_model.g9326.t1, internal, 158449, 158471
Valid prediction for snap_scaffold_6-snap.313-T1
Couldn't classify 62296, 62467
Couldn't classify 62492, 62547
Sorry, prediction CodingQuarry_transcript_54917-T1 fails validation.
(ATG)	 CC	59594-59656	GT	CGG
(GCT)	 AG	61084-61233	GT	GGG
(ATG)	 AG	61423-61554	GT	CGG
(GTG)	 AG	62296-62467	TG	TCT
(TGT)	 TG	62492-62547	GC	GAG
-recovered CodingQuarry_transcript_54917-T1, initial, 59594, 59656
-recovered CodingQuarry_transcript_54917-T1, initial, 61423, 61554
-recovered CodingQuarry_transcript_54917-T1, internal, 61084, 61233
-recovered CodingQuarry_transcript_54917-T1, internal, 61423, 61554
Valid prediction for GlimmerHMM_glimmerT_14056-T1
Valid prediction for GlimmerHMM_glimmerT_14044-T1
Valid prediction for GlimmerHMM_glimmerT_14048-T1
Valid prediction for HiQ_model.g9329.t1
Valid prediction for snap_scaffold_6-snap.302-T1
Couldn't classify 58469, 58469
Couldn't classify 62903, 62938
Sorry, prediction pasa_asmbl_47996.p1 fails validation.
(AGT)	 TA	58469-58469	GT	AAG
(TGT)	 AG	59565-59656	GT	CGG
(GCT)	 AG	61084-61233	GT	GGG
(ATG)	 AG	61423-61554	GT	CGG
(GTG)	 AG	62296-62424	GT	AGG
(GGG)	 AG	62903-62938	GA	TGG
-recovered pasa_asmbl_47996.p1, initial, 61423, 61554
-recovered pasa_asmbl_47996.p1, internal, 59565, 59656
-recovered pasa_asmbl_47996.p1, internal, 61084, 61233
-recovered pasa_asmbl_47996.p1, internal, 61423, 61554
-recovered pasa_asmbl_47996.p1, internal, 62296, 62424
Valid prediction for snap_scaffold_6-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_14037-T1
Valid prediction for CodingQuarry_transcript_54919-T1
Valid prediction for snap_scaffold_6-snap.348-T1
Valid prediction for CodingQuarry_transcript_54921-T1
Couldn't classify 63047, 63089
Sorry, prediction pasa_asmbl_46698.p1 fails validation.
(CCC)	 CC	63047-63089	GT	TGG
(ATA)	 AG	63181-63290	GT	AGG
(ATC)	 AG	63601-63790	GT	GGG
(ATG)	 AG	64121-64209	GT	AGG
(GTC)	 AG	64656-64726	GT	AGG
(CTG)	 AG	65017-65188	GT	TGG
(GTC)	 AG	65682-65816	GT	TGG
(TGT)	 AG	66143-66277	GT	AGG
(ATC)	 AG	67889-68155	GT	AGG
(GGC)	 AG	68439-68617	GT	AGG
(GGG)	 AG	69079-69184	CA	AGC
add_exon() Sorry, pasa_asmbl_46698.p1 64121-64209-initial-1 is invalid.
-recovered pasa_asmbl_46698.p1, initial, 64121, 64209
-recovered pasa_asmbl_46698.p1, terminal, 69079, 69184
-recovered pasa_asmbl_46698.p1, internal, 63181, 63290
-recovered pasa_asmbl_46698.p1, internal, 63601, 63790
-recovered pasa_asmbl_46698.p1, internal, 64121, 64209
-recovered pasa_asmbl_46698.p1, internal, 64656, 64726
-recovered pasa_asmbl_46698.p1, internal, 65017, 65188
-recovered pasa_asmbl_46698.p1, internal, 65682, 65816
-recovered pasa_asmbl_46698.p1, internal, 66143, 66277
-recovered pasa_asmbl_46698.p1, internal, 67889, 68155
-recovered pasa_asmbl_46698.p1, internal, 68439, 68617
Valid prediction for snap_scaffold_6-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_14039-T1
Valid prediction for snap_scaffold_6-snap.304-T1
Valid prediction for pasa_asmbl_46700.p1
Valid prediction for pasa_asmbl_46714.p1
Valid prediction for HiQ_model.g9330.t1
Valid prediction for snap_scaffold_6-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_14052-T1
Valid prediction for GlimmerHMM_glimmerT_14050-T1
Valid prediction for pasa_asmbl_46710.p1
Valid prediction for snap_scaffold_6-snap.325-T1
Valid prediction for snap_scaffold_6-snap.320-T1
Valid prediction for CodingQuarry_transcript_54922-T1
Valid prediction for snap_scaffold_6-snap.307-T1
Valid prediction for snap_scaffold_6-snap.339-T1
Valid prediction for snap_scaffold_6-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_14034-T1
Valid prediction for snap_scaffold_6-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_14041-T1
Valid prediction for GlimmerHMM_glimmerT_14032-T1
Valid prediction for GlimmerHMM_glimmerT_14045-T1
Valid prediction for snap_scaffold_6-snap.338-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 snap_scaffold_6-snap.337-T1
Valid prediction for snap_scaffold_6-snap.331-T1
Valid prediction for snap_scaffold_6-snap.333-T1
Valid prediction for snap_scaffold_6-snap.330-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14046-T1
Valid prediction for snap_scaffold_6-snap.296-T1
Valid prediction for Augustus_model.g9320.t1
Valid prediction for Augustus_model.g9321.t1
Valid prediction for GlimmerHMM_glimmerT_14055-T1
Valid prediction for GlimmerHMM_glimmerT_14042-T1
Valid prediction for snap_scaffold_6-snap.329-T1
Valid prediction for GlimmerHMM_glimmerT_14035-T1
Valid prediction for snap_scaffold_6-snap.301-T1
Valid prediction for snap_scaffold_6-snap.334-T1
Valid prediction for snap_scaffold_6-snap.340-T1
Valid prediction for GlimmerHMM_glimmerT_14049-T1
Valid prediction for snap_scaffold_6-snap.317-T1
Valid prediction for snap_scaffold_6-snap.308-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.309-T1
Valid prediction for GlimmerHMM_glimmerT_14047-T1
Valid prediction for snap_scaffold_6-snap.318-T1
Valid prediction for GlimmerHMM_glimmerT_14040-T1
Valid prediction for snap_scaffold_6-snap.326-T1
Valid prediction for CodingQuarry_transcript_54916-T1
Valid prediction for GlimmerHMM_glimmerT_14033-T1
Valid prediction for snap_scaffold_6-snap.314-T1
Valid prediction for GlimmerHMM_glimmerT_14053-T1
Valid prediction for Augustus_model.g9322.t1
Valid prediction for snap_scaffold_6-snap.327-T1
Valid prediction for snap_scaffold_6-snap.347-T1
Valid prediction for snap_scaffold_6-snap.346-T1
Valid prediction for snap_scaffold_6-snap.323-T1
Valid prediction for snap_scaffold_6-snap.332-T1
Valid prediction for Augustus_model.g9325.t1
Couldn't classify 185297, 185329
Couldn't classify 188412, 188567
Sorry, prediction pasa_asmbl_48095.p1 fails validation.
(ATT)	 AG	185297-185329	GT	AGG
(GCT)	 AG	185575-185677	GT	AGG
(GTA)	 AG	186342-186410	GT	AGG
(AGT)	 AG	186891-187052	GT	CCG
(ACA)	 AG	187417-187619	GT	AGG
(GCT)	 AG	188009-188137	GT	CGG
(GAC)	 AG	188412-188567	CC	TCC
-recovered pasa_asmbl_48095.p1, internal, 185297, 185329
-recovered pasa_asmbl_48095.p1, internal, 185575, 185677
-recovered pasa_asmbl_48095.p1, internal, 186342, 186410
-recovered pasa_asmbl_48095.p1, internal, 186891, 187052
-recovered pasa_asmbl_48095.p1, internal, 187417, 187619
-recovered pasa_asmbl_48095.p1, internal, 188009, 188137
Valid prediction for snap_scaffold_6-snap.341-T1
Valid prediction for snap_scaffold_6-snap.311-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.306-T1
Valid prediction for snap_scaffold_6-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_14043-T1
Valid prediction for snap_scaffold_6-snap.321-T1
Valid prediction for snap_scaffold_6-snap.312-T1
Valid prediction for snap_scaffold_6-snap.298-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7409, rend_intergenic: 4472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12378, rend_intergenic: 9205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17478, rend_intergenic: 12449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31656, rend_intergenic: 22386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41823, rend_intergenic: 40122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53293, rend_intergenic: 42184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57795, rend_intergenic: 53445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63118, rend_intergenic: 59594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69184, rend_intergenic: 63571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85990, rend_intergenic: 72879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91877, rend_intergenic: 86591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108812, rend_intergenic: 106583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109735, rend_intergenic: 109519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114173, rend_intergenic: 110433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134745, rend_intergenic: 114346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136697, rend_intergenic: 134982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143763, rend_intergenic: 138599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166254, rend_intergenic: 144193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172067, rend_intergenic: 168147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176673, rend_intergenic: 173626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192065, rend_intergenic: 190113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205848, rend_intergenic: 192750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209213
-exon list size: 405


building trellis

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27.3    
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27.8    
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28.7    
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29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
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31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
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46.4    
46.7    
46.9    
47.2    
47.4    
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47.9    
48.2    
48.4    
48.6    
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49.1    
49.4    
49.6    
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55.3    
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96.6    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 7409, rend_intergenic: 4472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12378, rend_intergenic: 9205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17478, rend_intergenic: 12449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31656, rend_intergenic: 22386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41823, rend_intergenic: 40122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53293, rend_intergenic: 42184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57795, rend_intergenic: 53445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63118, rend_intergenic: 59594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69184, rend_intergenic: 63571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85990, rend_intergenic: 72879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91877, rend_intergenic: 86591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108812, rend_intergenic: 106583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109735, rend_intergenic: 109519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114173, rend_intergenic: 110433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134745, rend_intergenic: 114346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136697, rend_intergenic: 134982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143763, rend_intergenic: 138599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166254, rend_intergenic: 144193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172067, rend_intergenic: 168147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176673, rend_intergenic: 173626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192065, rend_intergenic: 190113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205848, rend_intergenic: 192750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support