-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3366386-3498030

-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: +)Couldn't classify 42741, 43733
Sorry, prediction pasa_asmbl_36163.p1 fails validation.
(CCG)	 CT	42741-43733	GC	AGG
Valid prediction for snap_scaffold_27-snap.818-T1
Valid prediction for snap_scaffold_27-snap.809-T1
Valid prediction for GeneMark_model.101531_t
Valid prediction for GlimmerHMM_glimmerT_58402-T1
Valid prediction for Augustus_model.g38905.t1
Valid prediction for Augustus_model.g38908.t1
Valid prediction for GlimmerHMM_glimmerT_58390-T1
Valid prediction for snap_scaffold_27-snap.825-T1
Valid prediction for snap_scaffold_27-snap.811-T1
Valid prediction for GeneMark_model.101538_t
Valid prediction for Augustus_model.g38901.t1
Valid prediction for GeneMark_model.101557_t
Valid prediction for GlimmerHMM_glimmerT_58400-T1
Valid prediction for Augustus_model.g38900.t1
Valid prediction for Augustus_model.g38903.t1
Valid prediction for GlimmerHMM_glimmerT_58391-T1
Valid prediction for GlimmerHMM_glimmerT_58408-T1
Valid prediction for GeneMark_model.101546_t
Valid prediction for GeneMark_model.101534_t
Valid prediction for GeneMark_model.101536_t
Valid prediction for pasa_asmbl_36563.p1
Valid prediction for Augustus_model.g38899.t1
Valid prediction for snap_scaffold_27-snap.833-T1
Valid prediction for GlimmerHMM_glimmerT_58399-T1
Valid prediction for snap_scaffold_27-snap.815-T1
Valid prediction for GeneMark_model.101539_t
Valid prediction for CodingQuarry_transcript_41762-T1
Valid prediction for snap_scaffold_27-snap.823-T1
Couldn't classify 38935, 38955
Sorry, prediction pasa_asmbl_36160.p1 fails validation.
(ATG)	 CA	37048-37053	GT	AAG
(TTG)	 AG	37256-37300	GT	AGG
(TGC)	 AG	37440-37601	GT	GGG
(AGT)	 AG	37714-37849	GT	AGG
(GTT)	 AG	37951-38087	GT	AGG
(CTT)	 AG	38935-38955	TT	CGT
-recovered pasa_asmbl_36160.p1, initial, 37048, 37053
-recovered pasa_asmbl_36160.p1, internal, 37256, 37300
-recovered pasa_asmbl_36160.p1, internal, 37440, 37601
-recovered pasa_asmbl_36160.p1, internal, 37714, 37849
-recovered pasa_asmbl_36160.p1, internal, 37951, 38087
Valid prediction for GlimmerHMM_glimmerT_58392-T1
Valid prediction for snap_scaffold_27-snap.824-T1
Valid prediction for HiQ_model.g38902.t1
Valid prediction for snap_scaffold_27-snap.812-T1
Valid prediction for pasa_asmbl_36165.p1
Valid prediction for GeneMark_model.101537_t
Valid prediction for snap_scaffold_27-snap.821-T1
Valid prediction for GeneMark_model.101553_t
Valid prediction for GeneMark_model.101550_t
Valid prediction for GlimmerHMM_glimmerT_58395-T1
Valid prediction for GeneMark_model.101533_t
Valid prediction for GlimmerHMM_glimmerT_58397-T1
Valid prediction for GeneMark_model.101540_t
Valid prediction for GlimmerHMM_glimmerT_58411-T1
Valid prediction for GeneMark_model.101554_t
Valid prediction for GlimmerHMM_glimmerT_58396-T1
Valid prediction for GlimmerHMM_glimmerT_58407-T1
Valid prediction for CodingQuarry_transcript_41759-T1
Valid prediction for snap_scaffold_27-snap.822-T1
Valid prediction for CodingQuarry_transcript_41761-T1
Valid prediction for snap_scaffold_27-snap.810-T1
Valid prediction for GeneMark_model.101529_t
Valid prediction for GlimmerHMM_glimmerT_58410-T1
Valid prediction for snap_scaffold_27-snap.831-T1
Valid prediction for snap_scaffold_27-snap.826-T1
Valid prediction for CodingQuarry_transcript_41760-T1
Valid prediction for Augustus_model.g38907.t1
Valid prediction for Augustus_model.g38904.t1
Valid prediction for GeneMark_model.101547_t
Valid prediction for GeneMark_model.101558_t
Valid prediction for GeneMark_model.101541_t
Valid prediction for snap_scaffold_27-snap.820-T1
Valid prediction for snap_scaffold_27-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_58406-T1
Valid prediction for GeneMark_model.101555_t
Valid prediction for GlimmerHMM_glimmerT_58393-T1
Valid prediction for snap_scaffold_27-snap.830-T1
Couldn't classify 40515, 40623
Sorry, prediction pasa_asmbl_36162.p1 fails validation.
(CGG)	 AC	40515-40623	GT	CGG
(TGT)	 AG	40715-40815	GT	ACG
(ATG)	 AG	40937-41050	GT	AGG
(ATC)	 AG	41301-41457	GT	TGG
(AGT)	 AG	41563-41678	GT	AGG
(GTC)	 AG	41829-41982	GT	AGG
(GGT)	 AG	42087-42316	TT	AGT
-recovered pasa_asmbl_36162.p1, initial, 40937, 41050
-recovered pasa_asmbl_36162.p1, terminal, 42087, 42316
-recovered pasa_asmbl_36162.p1, internal, 40715, 40815
-recovered pasa_asmbl_36162.p1, internal, 40937, 41050
-recovered pasa_asmbl_36162.p1, internal, 41301, 41457
-recovered pasa_asmbl_36162.p1, internal, 41563, 41678
-recovered pasa_asmbl_36162.p1, internal, 41829, 41982
Valid prediction for GlimmerHMM_glimmerT_58401-T1
Valid prediction for GlimmerHMM_glimmerT_58394-T1
Valid prediction for GeneMark_model.101544_t
Valid prediction for HiQ_model.g38898.t1
Valid prediction for pasa_asmbl_36157.p1

-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_58398-T1
Valid prediction for Augustus_model.g38897.t1
Valid prediction for snap_scaffold_27-snap.834-T1
Valid prediction for GeneMark_model.101552_t
Valid prediction for GeneMark_model.101563_t
Valid prediction for GeneMark_model.101545_t
Valid prediction for GlimmerHMM_glimmerT_58413-T1
Valid prediction for snap_scaffold_27-snap.813-T1
Valid prediction for GeneMark_model.101561_t
Valid prediction for GlimmerHMM_glimmerT_58412-T1
Valid prediction for GlimmerHMM_glimmerT_58388-T1
Valid prediction for GeneMark_model.101548_t
Valid prediction for Augustus_model.g38906.t1
Valid prediction for snap_scaffold_27-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_58404-T1
Valid prediction for snap_scaffold_27-snap.827-T1
Valid prediction for snap_scaffold_27-snap.807-T1
Valid prediction for GeneMark_model.101532_t
Valid prediction for GeneMark_model.101542_t
Valid prediction for Augustus_model.g38909.t1
Valid prediction for GeneMark_model.101528_t
Valid prediction for GlimmerHMM_glimmerT_58389-T1
Valid prediction for Augustus_model.g38910.t1
Valid prediction for GlimmerHMM_glimmerT_58405-T1
Valid prediction for GlimmerHMM_glimmerT_58409-T1
Valid prediction for GeneMark_model.101556_t
Valid prediction for snap_scaffold_27-snap.819-T1
Valid prediction for GeneMark_model.101530_t
Valid prediction for GlimmerHMM_glimmerT_58415-T1
Valid prediction for GlimmerHMM_glimmerT_58387-T1
Valid prediction for snap_scaffold_27-snap.817-T1
Valid prediction for GeneMark_model.101549_t
Valid prediction for GeneMark_model.101564_t
Valid prediction for GlimmerHMM_glimmerT_58403-T1
Valid prediction for GeneMark_model.101559_t
Valid prediction for GeneMark_model.101560_t
Valid prediction for snap_scaffold_27-snap.832-T1
Valid prediction for snap_scaffold_27-snap.808-T1
Valid prediction for GeneMark_model.101551_t
Valid prediction for GeneMark_model.101543_t
Valid prediction for snap_scaffold_27-snap.816-T1
Valid prediction for GeneMark_model.101562_t
Valid prediction for GlimmerHMM_glimmerT_58414-T1
Valid prediction for snap_scaffold_27-snap.828-T1
Valid prediction for GeneMark_model.101565_t
Valid prediction for snap_scaffold_27-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_58386-T1
Valid prediction for snap_scaffold_27-snap.806-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43733, rend_intergenic: 36966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61941, rend_intergenic: 48771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67018, rend_intergenic: 62795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123419, rend_intergenic: 122294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 131645
-exon list size: 480


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 43733, rend_intergenic: 36966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61941, rend_intergenic: 48771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67018, rend_intergenic: 62795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123419, rend_intergenic: 122294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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