-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_7964022-8096873

-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_51058-T1
Valid prediction for GeneMark_model.88524_t
Valid prediction for snap_scaffold_22-snap.1642-T1
Valid prediction for GlimmerHMM_glimmerT_51068-T1
Valid prediction for GlimmerHMM_glimmerT_51053-T1
Valid prediction for GlimmerHMM_glimmerT_51067-T1
Couldn't classify 109315, 109390
Sorry, prediction pasa_asmbl_29549.p1 fails validation.
(GTC)	 TT	109315-109390	GT	AAG
(ATG)	 AG	110012-110577	CA	GAC
-recovered pasa_asmbl_29549.p1, terminal, 110012, 110577
Couldn't classify 41121, 41194
Couldn't classify 42320, 42429
Sorry, prediction pasa_asmbl_29743.p1 fails validation.
(GAT)	 GG	41121-41194	GT	AGG
(GAG)	 AG	41602-41852	GT	AGG
(AAA)	 AG	41984-42178	GT	AGG
(GTA)	 AG	42320-42429	AC	TCA
add_exon() Sorry, pasa_asmbl_29743.p1 41602-41852-terminal-2 is invalid.
-recovered pasa_asmbl_29743.p1, terminal, 41602, 41852
-recovered pasa_asmbl_29743.p1, internal, 41602, 41852
-recovered pasa_asmbl_29743.p1, internal, 41984, 42178
Valid prediction for snap_scaffold_22-snap.1643-T1
Valid prediction for GeneMark_model.88490_t
Valid prediction for snap_scaffold_22-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_51062-T1
Couldn't classify 6346, 6390
Sorry, prediction pasa_asmbl_29536.p1 fails validation.
(ATG)	 AC	4727-4795	GT	AGG
(GAC)	 AG	5035-5079	GT	AGG
(GGG)	 AG	5230-5283	GT	AGG
(AGC)	 AG	5481-5540	GT	AGG
(AAC)	 AG	5730-5795	GT	AGG
(GTG)	 AG	6346-6390	AC	CAA
-recovered pasa_asmbl_29536.p1, initial, 4727, 4795
-recovered pasa_asmbl_29536.p1, internal, 5035, 5079
-recovered pasa_asmbl_29536.p1, internal, 5230, 5283
-recovered pasa_asmbl_29536.p1, internal, 5481, 5540
-recovered pasa_asmbl_29536.p1, internal, 5730, 5795
Valid prediction for GeneMark_model.88533_t
Valid prediction for GeneMark_model.88509_t
Valid prediction for snap_scaffold_22-snap.1634-T1
Valid prediction for snap_scaffold_22-snap.1629-T1
Valid prediction for GeneMark_model.88503_t
Valid prediction for GeneMark_model.88491_t
Valid prediction for GlimmerHMM_glimmerT_51055-T1
Valid prediction for GlimmerHMM_glimmerT_51073-T1
Valid prediction for Augustus_model.g34242.t1
Valid prediction for CodingQuarry_transcript_34178-T1
Valid prediction for GlimmerHMM_glimmerT_51071-T1
Valid prediction for Augustus_model.g34250.t1
Valid prediction for snap_scaffold_22-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_51063-T1
Couldn't classify 48750, 48917
Couldn't classify 52420, 52517
Sorry, prediction pasa_asmbl_29544.p1 fails validation.
(TTC)	 CC	48750-48917	GT	CGG
(GTT)	 AG	51587-51766	GT	AGG
(GCA)	 AG	51935-52115	GT	AGG
(AGC)	 AG	52420-52517	CT	CCC
-recovered pasa_asmbl_29544.p1, internal, 51587, 51766
-recovered pasa_asmbl_29544.p1, internal, 51935, 52115
Couldn't classify 7605, 7662
Couldn't classify 7813, 7925
Sorry, prediction CodingQuarry_transcript_34175-T1 fails validation.
(ATG)	 GG	7041-7085	GT	AGG
(GAC)	 AG	7605-7662	AC	CAA
(AGG)	 GC	7813-7925	CT	AAC
-recovered CodingQuarry_transcript_34175-T1, initial, 7041, 7085
Valid prediction for snap_scaffold_22-snap.1658-T1
Valid prediction for GeneMark_model.88499_t
Valid prediction for snap_scaffold_22-snap.1644-T1
Valid prediction for GlimmerHMM_glimmerT_51061-T1
Valid prediction for Augustus_model.g34247.t1
Valid prediction for Augustus_model.g34248.t1
Valid prediction for snap_scaffold_22-snap.1631-T1
Valid prediction for GeneMark_model.88518_t
Valid prediction for Augustus_model.g34245.t1
Valid prediction for GeneMark_model.88495_t
Valid prediction for HiQ_model.g34241.t1
Valid prediction for Augustus_model.g34243.t1
Valid prediction for GeneMark_model.88487_t
Couldn't classify 39482, 39886
Sorry, prediction pasa_asmbl_29543.p1 fails validation.
(CAC)	 AA	39482-39886	CT	TAC
Valid prediction for pasa_asmbl_29550.p1
Couldn't classify 10529, 10675
Sorry, prediction pasa_asmbl_29538.p1 fails validation.
(ATG)	 TC	9414-9797	GT	AGG
(GTG)	 AG	9966-10253	GT	AGG
(GGT)	 AG	10529-10675	GA	AGG
-recovered pasa_asmbl_29538.p1, initial, 9414, 9797
-recovered pasa_asmbl_29538.p1, internal, 9966, 10253
Valid prediction for GeneMark_model.88513_t
Valid prediction for GeneMark_model.88526_t
Valid prediction for Augustus_model.g34246.t1
Valid prediction for GeneMark_model.88508_t
Valid prediction for GeneMark_model.88505_t
Valid prediction for GeneMark_model.88497_t
Valid prediction for GeneMark_model.88529_t
Valid prediction for snap_scaffold_22-snap.1635-T1
Valid prediction for GeneMark_model.88501_t
Valid prediction for GlimmerHMM_glimmerT_51057-T1
Valid prediction for snap_scaffold_22-snap.1652-T1
Valid prediction for snap_scaffold_22-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_51056-T1
Valid prediction for GeneMark_model.88516_t
Valid prediction for snap_scaffold_22-snap.1655-T1
Valid prediction for GeneMark_model.88498_t
Valid prediction for GeneMark_model.88493_t
Valid prediction for GeneMark_model.88520_t
Valid prediction for GeneMark_model.88506_t
Valid prediction for Augustus_model.g34249.t1
Valid prediction for snap_scaffold_22-snap.1648-T1
Valid prediction for GeneMark_model.88530_t
Valid prediction for snap_scaffold_22-snap.1653-T1
Valid prediction for GeneMark_model.88510_t
Valid prediction for snap_scaffold_22-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_51069-T1
Valid prediction for snap_scaffold_22-snap.1638-T1
Valid prediction for GeneMark_model.88489_t
Valid prediction for snap_scaffold_22-snap.1633-T1
Valid prediction for GlimmerHMM_glimmerT_51066-T1
Valid prediction for GeneMark_model.88484_t
Valid prediction for GeneMark_model.88522_t
Valid prediction for GlimmerHMM_glimmerT_51054-T1
Valid prediction for GeneMark_model.88512_t
Valid prediction for Augustus_model.g34244.t1
Valid prediction for GeneMark_model.88515_t
Valid prediction for GlimmerHMM_glimmerT_51072-T1
Valid prediction for GeneMark_model.88527_t

-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_22-snap.1636-T1
Valid prediction for GeneMark_model.88504_t
Valid prediction for snap_scaffold_22-snap.1647-T1
Valid prediction for GeneMark_model.88521_t
Valid prediction for snap_scaffold_22-snap.1632-T1
Valid prediction for GeneMark_model.88532_t
Couldn't classify 1186, 1450
Sorry, prediction pasa_asmbl_30215.p1 fails validation.
(TTA)	 AG	1186-1450	GT	AGG
(AGA)	 AG	1571-1699	GT	AGG
(GCA)	 AG	1919-2199	GG	AGG
-recovered pasa_asmbl_30215.p1, terminal, 1919, 2199
-recovered pasa_asmbl_30215.p1, internal, 1186, 1450
-recovered pasa_asmbl_30215.p1, internal, 1571, 1699
Valid prediction for GeneMark_model.88531_t
Valid prediction for GlimmerHMM_glimmerT_51070-T1
Valid prediction for snap_scaffold_22-snap.1630-T1
Valid prediction for GeneMark_model.88494_t
Valid prediction for GeneMark_model.88519_t
Valid prediction for snap_scaffold_22-snap.1640-T1
Valid prediction for snap_scaffold_22-snap.1654-T1
Valid prediction for Augustus_model.g34251.t1
Valid prediction for GlimmerHMM_glimmerT_51065-T1
Valid prediction for GeneMark_model.88507_t
Valid prediction for GlimmerHMM_glimmerT_51074-T1
Valid prediction for GeneMark_model.88485_t
Valid prediction for GeneMark_model.88525_t
Valid prediction for GlimmerHMM_glimmerT_51059-T1
Valid prediction for GeneMark_model.88486_t
Valid prediction for GeneMark_model.88500_t
Valid prediction for GeneMark_model.88492_t
Valid prediction for snap_scaffold_22-snap.1649-T1
Valid prediction for GeneMark_model.88528_t
Valid prediction for GeneMark_model.88488_t
Valid prediction for GeneMark_model.88483_t
Valid prediction for GeneMark_model.88511_t
Valid prediction for snap_scaffold_22-snap.1637-T1
Valid prediction for GeneMark_model.88534_t
Valid prediction for snap_scaffold_22-snap.1645-T1
Valid prediction for GeneMark_model.88523_t
Valid prediction for GeneMark_model.88502_t
Valid prediction for snap_scaffold_22-snap.1662-T1
Valid prediction for snap_scaffold_22-snap.1650-T1
Valid prediction for snap_scaffold_22-snap.1641-T1
Valid prediction for snap_scaffold_22-snap.1651-T1
Valid prediction for snap_scaffold_22-snap.1639-T1
Valid prediction for snap_scaffold_22-snap.1656-T1
Valid prediction for snap_scaffold_22-snap.1646-T1
Valid prediction for GeneMark_model.88517_t
Valid prediction for GeneMark_model.88514_t
Valid prediction for GeneMark_model.88496_t
Valid prediction for GlimmerHMM_glimmerT_51060-T1
Valid prediction for GlimmerHMM_glimmerT_51064-T1
Valid prediction for snap_scaffold_22-snap.1663-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 130657, rend_intergenic: 130654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7007, rend_intergenic: 5023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10726, rend_intergenic: 8101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44201, rend_intergenic: 30585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49188, rend_intergenic: 44547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55374, rend_intergenic: 49941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75940, rend_intergenic: 68739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94082, rend_intergenic: 88311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99883, rend_intergenic: 98607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105911, rend_intergenic: 102263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110577, rend_intergenic: 108864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127530, rend_intergenic: 125926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 132852
-exon list size: 628


building trellis

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-found 32 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 130657, rend_intergenic: 130654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7007, rend_intergenic: 5023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10726, rend_intergenic: 8101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44201, rend_intergenic: 30585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49188, rend_intergenic: 44547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55374, rend_intergenic: 49941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75940, rend_intergenic: 68739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94082, rend_intergenic: 88311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99883, rend_intergenic: 98607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105911, rend_intergenic: 102263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110577, rend_intergenic: 108864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127530, rend_intergenic: 125926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support