-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_16511415-16709504

-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 snap_scaffold_5-snap.3071-T1
Valid prediction for snap_scaffold_5-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_13401-T1
Valid prediction for GlimmerHMM_glimmerT_13384-T1
Valid prediction for GlimmerHMM_glimmerT_13400-T1
Valid prediction for snap_scaffold_5-snap.3082-T1
Valid prediction for snap_scaffold_5-snap.3075-T1
Valid prediction for GlimmerHMM_glimmerT_13391-T1
Valid prediction for snap_scaffold_5-snap.3064-T1
Valid prediction for GlimmerHMM_glimmerT_13385-T1
Valid prediction for HiQ_model.g8910.t1
Valid prediction for GlimmerHMM_glimmerT_13381-T1
Valid prediction for snap_scaffold_5-snap.3066-T1
Valid prediction for GlimmerHMM_glimmerT_13399-T1
Valid prediction for GlimmerHMM_glimmerT_13390-T1
Valid prediction for Augustus_model.g8903.t1
Valid prediction for GlimmerHMM_glimmerT_13395-T1
Valid prediction for Augustus_model.g8907.t1
Valid prediction for HiQ_model.g8912.t1
Valid prediction for Augustus_model.g8899.t1
Valid prediction for snap_scaffold_5-snap.3073-T1
Valid prediction for snap_scaffold_5-snap.3080-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g8897.t1
Couldn't classify 152497, 152737
Couldn't classify 155494, 155624
Sorry, prediction pasa_asmbl_46119.p1 fails validation.
(GCA)	 CA	152497-152737	GT	CGG
(TGG)	 AG	152855-153091	GT	CGG
(GCC)	 AG	153413-153643	GT	AGG
(ACA)	 AG	153946-154113	GT	GGG
(GAA)	 AG	154647-154803	GT	AGG
(GTA)	 AG	155225-155349	GT	GGG
(GCA)	 AG	155494-155624	GT	AGG
-recovered pasa_asmbl_46119.p1, internal, 152855, 153091
-recovered pasa_asmbl_46119.p1, internal, 153413, 153643
-recovered pasa_asmbl_46119.p1, internal, 153946, 154113
-recovered pasa_asmbl_46119.p1, internal, 154647, 154803
-recovered pasa_asmbl_46119.p1, internal, 155225, 155349
-recovered pasa_asmbl_46119.p1, internal, 155494, 155624
Valid prediction for snap_scaffold_5-snap.3085-T1
Valid prediction for pasa_asmbl_46114.p1
Valid prediction for snap_scaffold_5-snap.3062-T1
Valid prediction for snap_scaffold_5-snap.3068-T1
Valid prediction for snap_scaffold_5-snap.3060-T1
Valid prediction for snap_scaffold_5-snap.3076-T1
Sorry, intron length (6) is less than minimum required (10)
Couldn't classify 125037, 125810
Sorry, prediction pasa_asmbl_46110.p1 fails validation.
(GCC)	 GG	125037-125810	GG	GAG
Valid prediction for Augustus_model.g8909.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.g8913.t1
Valid prediction for GlimmerHMM_glimmerT_13383-T1
Valid prediction for Augustus_model.g8895.t1
Valid prediction for Augustus_model.g8902.t1
Valid prediction for GlimmerHMM_glimmerT_13380-T1
Valid prediction for GlimmerHMM_glimmerT_13382-T1
Valid prediction for HiQ_model.g8904.t1
Valid prediction for snap_scaffold_5-snap.3065-T1
Valid prediction for GlimmerHMM_glimmerT_13387-T1
Valid prediction for HiQ_model.g8900.t1
Valid prediction for Augustus_model.g8911.t1
Valid prediction for snap_scaffold_5-snap.3078-T1
Valid prediction for GlimmerHMM_glimmerT_13397-T1
Valid prediction for snap_scaffold_5-snap.3063-T1
Valid prediction for snap_scaffold_5-snap.3084-T1
Valid prediction for GlimmerHMM_glimmerT_13394-T1
Valid prediction for snap_scaffold_5-snap.3072-T1
Valid prediction for snap_scaffold_5-snap.3067-T1
Valid prediction for Augustus_model.g8905.t1
Couldn't classify 82383, 82484
Sorry, prediction pasa_asmbl_44765.p2 fails validation.
(GAG)	 GG	82383-82484	GT	GGG
(CTT)	 AG	85033-85266	TC	AGT
-recovered pasa_asmbl_44765.p2, terminal, 85033, 85266
Valid prediction for snap_scaffold_5-snap.3056-T1
Valid prediction for snap_scaffold_5-snap.3086-T1
Valid prediction for Augustus_model.g8901.t1
Valid prediction for snap_scaffold_5-snap.3070-T1
Couldn't classify 34022, 34085
Sorry, prediction pasa_asmbl_44767.p1 fails validation.
(TTT)	 TG	34022-34085	GT	GGG
(GAA)	 AG	34353-34489	GT	CGG
(CTG)	 AG	34667-34797	GT	AGG
(GCC)	 AG	35997-36282	GT	AGG
(AAC)	 AG	36484-36557	GT	CGG
(CTA)	 AG	36738-36846	GT	AGG
(CTG)	 AG	36936-37028	TG	AAT
-recovered pasa_asmbl_44767.p1, terminal, 36936, 37028
-recovered pasa_asmbl_44767.p1, internal, 34353, 34489
-recovered pasa_asmbl_44767.p1, internal, 34667, 34797
-recovered pasa_asmbl_44767.p1, internal, 35997, 36282
-recovered pasa_asmbl_44767.p1, internal, 36484, 36557
-recovered pasa_asmbl_44767.p1, internal, 36738, 36846
Couldn't classify 113396, 113656
Couldn't classify 114416, 114517
Sorry, prediction pasa_asmbl_44762.p1 fails validation.
(CCC)	 CC	113396-113656	GT	TGG
(GAG)	 AG	114416-114517	AC	CAA
Couldn't classify 188292, 188293
Sorry, prediction CodingQuarry_transcript_52418-T1 fails validation.
(ATG)	 AG	188292-188293	GT	ATG
(GCA)	 AG	189219-189332	GT	TGG
(CTG)	 AG	189431-189500	GT	ATG
(GAA)	 AG	189608-189706	GT	AGG
(TTT)	 AG	189812-189901	GT	ATG
(ATG)	 AG	190007-190060	GT	AGG
(CAT)	 AG	190285-190312	GT	AAG
(AAA)	 AG	190582-190601	CA	AGC
-recovered CodingQuarry_transcript_52418-T1, initial, 190007, 190060
-recovered CodingQuarry_transcript_52418-T1, terminal, 190582, 190601
-recovered CodingQuarry_transcript_52418-T1, internal, 188292, 188293
-recovered CodingQuarry_transcript_52418-T1, internal, 189219, 189332
-recovered CodingQuarry_transcript_52418-T1, internal, 189431, 189500
-recovered CodingQuarry_transcript_52418-T1, internal, 189608, 189706
-recovered CodingQuarry_transcript_52418-T1, internal, 189812, 189901
-recovered CodingQuarry_transcript_52418-T1, internal, 190007, 190060
-recovered CodingQuarry_transcript_52418-T1, internal, 190285, 190312
Valid prediction for snap_scaffold_5-snap.3077-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 5740, 6111
Sorry, prediction pasa_asmbl_44771.p1 fails validation.
(GAA)	 AC	5740-6111	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_13386-T1
Valid prediction for CodingQuarry_transcript_52419-T1
Valid prediction for Augustus_model.g8915.t1
Couldn't classify 188292, 188293
Sorry, prediction pasa_asmbl_44750.p1 fails validation.
(ATG)	 AG	188292-188293	GT	ATG
(GCA)	 AG	189219-189332	GT	TGG
(CTG)	 AG	189431-189500	GT	ATG
(GAA)	 AG	189608-189706	GT	AGG
(TTT)	 AG	189812-189901	GT	ATG
(ATG)	 AG	190007-190060	GT	AGG
(AAA)	 AG	190582-190659	AA	GAA
-recovered pasa_asmbl_44750.p1, initial, 190007, 190060
-recovered pasa_asmbl_44750.p1, terminal, 190582, 190659
-recovered pasa_asmbl_44750.p1, internal, 188292, 188293
-recovered pasa_asmbl_44750.p1, internal, 189219, 189332
-recovered pasa_asmbl_44750.p1, internal, 189431, 189500
-recovered pasa_asmbl_44750.p1, internal, 189608, 189706
-recovered pasa_asmbl_44750.p1, internal, 189812, 189901
-recovered pasa_asmbl_44750.p1, internal, 190007, 190060
Valid prediction for snap_scaffold_5-snap.3061-T1
Valid prediction for snap_scaffold_5-snap.3074-T1
Couldn't classify 16026, 16349
Couldn't classify 16573, 16605
Sorry, prediction pasa_asmbl_44770.p1 fails validation.
(GAG)	 AG	16026-16349	GT	AGG
(GGG)	 AG	16573-16605	CC	GAC
-recovered pasa_asmbl_44770.p1, internal, 16026, 16349
Valid prediction for snap_scaffold_5-snap.3087-T1
Valid prediction for pasa_asmbl_44766.p4
Valid prediction for GlimmerHMM_glimmerT_13398-T1
Valid prediction for snap_scaffold_5-snap.3081-T1
Valid prediction for snap_scaffold_5-snap.3079-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g8898.t1
Valid prediction for snap_scaffold_5-snap.3059-T1
Valid prediction for snap_scaffold_5-snap.3069-T1
Valid prediction for GlimmerHMM_glimmerT_13402-T1
Valid prediction for snap_scaffold_5-snap.3083-T1
Valid prediction for Augustus_model.g8896.t1
Couldn't classify 94312, 94629
Sorry, prediction pasa_asmbl_44763.p1 fails validation.
(CCC)	 CT	94312-94629	CG	AGC
Valid prediction for GlimmerHMM_glimmerT_13392-T1
Valid prediction for GlimmerHMM_glimmerT_13396-T1
Valid prediction for GlimmerHMM_glimmerT_13389-T1
Valid prediction for GlimmerHMM_glimmerT_13393-T1
Valid prediction for snap_scaffold_5-snap.3057-T1
Couldn't classify 149437, 149548
Sorry, prediction pasa_asmbl_44754.p1 fails validation.
(GGT)	 CA	149437-149548	GT	GGG
(GCA)	 AG	149706-149863	GT	TGG
(CTC)	 AG	150106-150270	GT	AGG
(ACA)	 AG	150610-150762	GT	CGG
(GTC)	 AG	150912-150994	GT	GGG
(TTT)	 AG	151135-151282	GT	AGG
(GAG)	 AG	151575-151688	GT	AGG
(CTC)	 AG	151851-151928	GT	AGG
(GCA)	 AG	152029-152124	GT	TTG
(GTC)	 AG	152258-152364	GT	AGG
(GGC)	 AG	152527-152596	GT	AGG
(TGC)	 AG	152865-153044	GT	TGG
(GAG)	 AG	153351-153405	GT	TGG
(AAA)	 AG	153515-153603	GT	AGG
(ATG)	 AG	153710-153764	GT	CGG
(AGA)	 AG	153975-154081	GT	AGG
(GAG)	 AG	154192-154230	GA	GAG
-recovered pasa_asmbl_44754.p1, initial, 153710, 153764
-recovered pasa_asmbl_44754.p1, terminal, 154192, 154230
-recovered pasa_asmbl_44754.p1, internal, 149706, 149863
-recovered pasa_asmbl_44754.p1, internal, 150106, 150270
-recovered pasa_asmbl_44754.p1, internal, 150610, 150762
-recovered pasa_asmbl_44754.p1, internal, 150912, 150994
-recovered pasa_asmbl_44754.p1, internal, 151135, 151282
-recovered pasa_asmbl_44754.p1, internal, 151575, 151688
-recovered pasa_asmbl_44754.p1, internal, 151851, 151928
-recovered pasa_asmbl_44754.p1, internal, 152029, 152124
-recovered pasa_asmbl_44754.p1, internal, 152258, 152364
-recovered pasa_asmbl_44754.p1, internal, 152527, 152596
-recovered pasa_asmbl_44754.p1, internal, 152865, 153044
-recovered pasa_asmbl_44754.p1, internal, 153351, 153405
-recovered pasa_asmbl_44754.p1, internal, 153515, 153603
-recovered pasa_asmbl_44754.p1, internal, 153710, 153764
-recovered pasa_asmbl_44754.p1, internal, 153975, 154081
Valid prediction for snap_scaffold_5-snap.3054-T1
Valid prediction for Augustus_model.g8906.t1
Valid prediction for Augustus_model.g8914.t1
Valid prediction for Augustus_model.g8908.t1
Valid prediction for GlimmerHMM_glimmerT_13379-T1
Valid prediction for snap_scaffold_5-snap.3055-T1
Couldn't classify 32729, 33148
Sorry, prediction pasa_asmbl_44768.p1 fails validation.
(ATG)	 GG	31570-31744	GT	AAG
(CTT)	 AG	31864-31988	GT	AGG
(AAC)	 AG	32141-32267	GT	AGG
(GTG)	 AG	32377-32510	GT	AGG
(GAG)	 AG	32729-33148	AG	CTA
-recovered pasa_asmbl_44768.p1, initial, 31570, 31744
-recovered pasa_asmbl_44768.p1, internal, 31864, 31988
-recovered pasa_asmbl_44768.p1, internal, 32141, 32267
-recovered pasa_asmbl_44768.p1, internal, 32377, 32510
Valid prediction for GlimmerHMM_glimmerT_13388-T1
Couldn't classify 124010, 124282
Sorry, prediction pasa_asmbl_44757.p1 fails validation.
(CCC)	 CC	124010-124282	GT	AGG
(TCT)	 AG	124605-124754	GT	AGG
(AGA)	 AG	125775-125900	AC	GAA
-recovered pasa_asmbl_44757.p1, terminal, 125775, 125900
-recovered pasa_asmbl_44757.p1, internal, 124605, 124754

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54909, rend_intergenic: 51580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77006, rend_intergenic: 74915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81014, rend_intergenic: 78712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89720, rend_intergenic: 84241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97765, rend_intergenic: 95940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115702, rend_intergenic: 101605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125810, rend_intergenic: 115953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140120, rend_intergenic: 132808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155681, rend_intergenic: 149443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185855, rend_intergenic: 178310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198090
-exon list size: 457


building trellis

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99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 54909, rend_intergenic: 51580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77006, rend_intergenic: 74915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81014, rend_intergenic: 78712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89720, rend_intergenic: 84241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97765, rend_intergenic: 95940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115702, rend_intergenic: 101605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125810, rend_intergenic: 115953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140120, rend_intergenic: 132808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155681, rend_intergenic: 149443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185855, rend_intergenic: 178310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support