-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_4116244-4238594

-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_9381-T1
Couldn't classify 39187, 39391
Sorry, prediction pasa_asmbl_43577.p1 fails validation.
(GTG)	 CG	39187-39391	GT	AGG
(GAA)	 AG	39681-40084	CA	AAC
-recovered pasa_asmbl_43577.p1, terminal, 39681, 40084
Valid prediction for GlimmerHMM_glimmerT_9368-T1
Valid prediction for GlimmerHMM_glimmerT_9374-T1
Couldn't classify 16625, 16778
Couldn't classify 16934, 17091
Sorry, prediction pasa_asmbl_43634.p1 fails validation.
(CAG)	 GC	16625-16778	GT	AGG
(ACT)	 AG	16934-17091	TC	CCT
Couldn't classify 10982, 11060
Couldn't classify 11295, 11593
Sorry, prediction pasa_asmbl_43513.p1 fails validation.
(GGG)	 AG	10982-11060	GT	AGG
(GTG)	 AG	11295-11593	GC	GGG
-recovered pasa_asmbl_43513.p1, internal, 10982, 11060
-recovered pasa_asmbl_43513.p1, internal, 11295, 11593
Valid prediction for snap_scaffold_4-snap.960-T1
Valid prediction for snap_scaffold_4-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_9367-T1
Valid prediction for GeneMark_model.15433_t
Valid prediction for Augustus_model.g6098.t1
Valid prediction for GeneMark_model.15422_t
Valid prediction for GlimmerHMM_glimmerT_9379-T1
Valid prediction for GlimmerHMM_glimmerT_9385-T1
Valid prediction for GeneMark_model.15416_t
Valid prediction for snap_scaffold_4-snap.958-T1
Valid prediction for GeneMark_model.15412_t
Valid prediction for GeneMark_model.15403_t
Valid prediction for snap_scaffold_4-snap.941-T1
Couldn't classify 25625, 27756
Sorry, prediction pasa_asmbl_42564.p1 fails validation.
(TTG)	 AC	25625-27756	GT	AGG
(GCC)	 AG	28094-28200	GT	AGG
(GTG)	 AG	28343-28483	GT	GGG
(TGG)	 AG	28738-28990	GT	AGG
(AAA)	 AG	29178-29285	GT	AGG
(ACG)	 AG	29457-29540	GT	AGG
(GTC)	 AG	29773-29902	GT	AGG
(GGC)	 AG	30067-30342	GG	AGG
add_exon() Sorry, pasa_asmbl_42564.p1 29457-29540-terminal-1 is invalid.
-recovered pasa_asmbl_42564.p1, terminal, 29457, 29540
-recovered pasa_asmbl_42564.p1, terminal, 30067, 30342
-recovered pasa_asmbl_42564.p1, internal, 28094, 28200
-recovered pasa_asmbl_42564.p1, internal, 28343, 28483
-recovered pasa_asmbl_42564.p1, internal, 28738, 28990
-recovered pasa_asmbl_42564.p1, internal, 29178, 29285
-recovered pasa_asmbl_42564.p1, internal, 29457, 29540
-recovered pasa_asmbl_42564.p1, internal, 29773, 29902
Valid prediction for GeneMark_model.15431_t
Valid prediction for snap_scaffold_4-snap.951-T1
Valid prediction for Augustus_model.g6096.t1
Valid prediction for snap_scaffold_4-snap.948-T1
Valid prediction for GeneMark_model.15424_t
Valid prediction for GeneMark_model.15410_t
Valid prediction for snap_scaffold_4-snap.945-T1
Valid prediction for snap_scaffold_4-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_9376-T1
Valid prediction for GeneMark_model.15428_t
Valid prediction for Augustus_model.g6094.t1
Couldn't classify 24833, 25438
Sorry, prediction pasa_asmbl_42563.p1 fails validation.
(TCA)	 CC	24833-25438	AC	GCA
Valid prediction for GlimmerHMM_glimmerT_9383-T1
Valid prediction for GeneMark_model.15409_t
Couldn't classify 14696, 14873
Couldn't classify 14969, 15126
Sorry, prediction pasa_asmbl_43600.p1 fails validation.
(CTC)	 GT	14696-14873	GT	AGG
(AAG)	 AG	14969-15126	GA	TCG
Valid prediction for snap_scaffold_4-snap.938-T1
Valid prediction for Augustus_model.g6099.t1
Valid prediction for GeneMark_model.15401_t
Valid prediction for GeneMark_model.15414_t
Valid prediction for GlimmerHMM_glimmerT_9384-T1
Valid prediction for GlimmerHMM_glimmerT_9372-T1
Valid prediction for GlimmerHMM_glimmerT_9378-T1
Valid prediction for GeneMark_model.15407_t
Valid prediction for GlimmerHMM_glimmerT_9382-T1
Valid prediction for snap_scaffold_4-snap.957-T1
Couldn't classify 1578, 1766
Sorry, prediction pasa_asmbl_43544.p1 fails validation.
(GCA)	 CA	1578-1766	GT	AGG
(GTT)	 AG	1872-2395	GT	AGG
(GGC)	 AG	2477-2687	GT	AGG
(GTC)	 AG	2857-3028	GT	AGG
(ATT)	 AG	3524-3609	GT	AAG
(GTA)	 AG	3810-3845	TA	GAT
-recovered pasa_asmbl_43544.p1, terminal, 3810, 3845
-recovered pasa_asmbl_43544.p1, internal, 1872, 2395
-recovered pasa_asmbl_43544.p1, internal, 2477, 2687
-recovered pasa_asmbl_43544.p1, internal, 2857, 3028
-recovered pasa_asmbl_43544.p1, internal, 3524, 3609
Valid prediction for Augustus_model.g6092.t1
Valid prediction for snap_scaffold_4-snap.954-T1
Valid prediction for snap_scaffold_4-snap.952-T1
Valid prediction for snap_scaffold_4-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_9370-T1
Valid prediction for snap_scaffold_4-snap.959-T1
Valid prediction for GeneMark_model.15435_t
Valid prediction for GeneMark_model.15421_t
Valid prediction for GeneMark_model.15400_t
Valid prediction for snap_scaffold_4-snap.943-T1
Valid prediction for snap_scaffold_4-snap.942-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_4-snap.955-T1
Valid prediction for snap_scaffold_4-snap.939-T1
Valid prediction for pasa_asmbl_42256.p1
Valid prediction for GeneMark_model.15427_t
Valid prediction for GeneMark_model.15415_t
Valid prediction for snap_scaffold_4-snap.961-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.15419_t
Valid prediction for snap_scaffold_4-snap.963-T1
Valid prediction for snap_scaffold_4-snap.944-T1
Valid prediction for snap_scaffold_4-snap.956-T1
Valid prediction for GeneMark_model.15429_t
Valid prediction for GeneMark_model.15423_t
Valid prediction for snap_scaffold_4-snap.940-T1
Couldn't classify 60278, 60476
Couldn't classify 61975, 62004
Sorry, prediction pasa_asmbl_41243.p1 fails validation.
(GTG)	 AG	60278-60476	GT	CTG
(TGC)	 AG	61180-61307	GT	GGG
(ATC)	 AG	61706-61780	GT	AGG
(CAC)	 AG	61975-62004	GA	AGG
-recovered pasa_asmbl_41243.p1, internal, 60278, 60476
-recovered pasa_asmbl_41243.p1, internal, 61180, 61307
-recovered pasa_asmbl_41243.p1, internal, 61706, 61780
Valid prediction for GeneMark_model.15436_t
Valid prediction for HiQ_model.g6091.t1
Valid prediction for GeneMark_model.15413_t
Valid prediction for GeneMark_model.15408_t
Valid prediction for GlimmerHMM_glimmerT_9371-T1
Valid prediction for HiQ_model.g6090.t1
Valid prediction for snap_scaffold_4-snap.949-T1
Valid prediction for GeneMark_model.15425_t
Valid prediction for GeneMark_model.15402_t
Valid prediction for GeneMark_model.15418_t
Valid prediction for snap_scaffold_4-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_9377-T1
Valid prediction for GeneMark_model.15420_t
Valid prediction for GlimmerHMM_glimmerT_9380-T1
Valid prediction for GlimmerHMM_glimmerT_9386-T1
Valid prediction for GeneMark_model.15404_t
Valid prediction for GlimmerHMM_glimmerT_9373-T1
Valid prediction for snap_scaffold_4-snap.947-T1
Valid prediction for GeneMark_model.15399_t
Valid prediction for GeneMark_model.15434_t
Valid prediction for GeneMark_model.15406_t
Valid prediction for Augustus_model.g6095.t1
Valid prediction for GeneMark_model.15411_t
Valid prediction for pasa_asmbl_41237.p1
Valid prediction for GeneMark_model.15417_t
Valid prediction for snap_scaffold_4-snap.950-T1
Valid prediction for HiQ_model.g6093.t1
Valid prediction for GlimmerHMM_glimmerT_9369-T1
Valid prediction for CodingQuarry_transcript_48839-T1
Valid prediction for GlimmerHMM_glimmerT_9375-T1
Valid prediction for GeneMark_model.15432_t
Valid prediction for Augustus_model.g6097.t1
Couldn't classify 62089, 62133
Sorry, prediction pasa_asmbl_41242.p1 fails validation.
(GCC)	 TG	62089-62133	GT	AGG
(CCT)	 AG	62630-62758	GT	AGG
(GTG)	 AG	63340-63439	GT	CCG
(AGG)	 AG	63776-63943	GT	CGG
(ATC)	 AG	64172-64195	GT	AGG
(CAT)	 AG	64314-64381	GT	AGG
(ATA)	 AG	64595-64660	GT	TGG
(CAA)	 AG	64863-65006	GT	AGG
(CAG)	 AG	65161-65262	GG	GAG
-recovered pasa_asmbl_41242.p1, terminal, 65161, 65262
-recovered pasa_asmbl_41242.p1, internal, 62630, 62758
-recovered pasa_asmbl_41242.p1, internal, 63340, 63439
-recovered pasa_asmbl_41242.p1, internal, 63776, 63943
-recovered pasa_asmbl_41242.p1, internal, 64172, 64195
-recovered pasa_asmbl_41242.p1, internal, 64314, 64381
-recovered pasa_asmbl_41242.p1, internal, 64595, 64660
-recovered pasa_asmbl_41242.p1, internal, 64863, 65006
Valid prediction for GeneMark_model.15430_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 68563, rend_intergenic: 64382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77007, rend_intergenic: 75647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81303, rend_intergenic: 79519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98857, rend_intergenic: 98602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101696, rend_intergenic: 99141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118883, rend_intergenic: 115859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 122351
-exon list size: 470


building trellis

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-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 68563, rend_intergenic: 64382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77007, rend_intergenic: 75647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81303, rend_intergenic: 79519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98857, rend_intergenic: 98602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101696, rend_intergenic: 99141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118883, rend_intergenic: 115859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support