-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_7714754-7867032

-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 128675, 128824
Sorry, prediction pasa_asmbl_30223.p1 fails validation.
(ATG)	 GT	126378-126977	GT	AGG
(GAC)	 AG	127919-128014	GT	AGG
(CGC)	 AG	128289-128522	GT	AGG
(AGC)	 AG	128675-128824	GG	CAG
-recovered pasa_asmbl_30223.p1, initial, 126378, 126977
-recovered pasa_asmbl_30223.p1, internal, 127919, 128014
-recovered pasa_asmbl_30223.p1, internal, 128289, 128522
Valid prediction for snap_scaffold_22-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_49793-T1
Valid prediction for snap_scaffold_22-snap.1541-T1
Valid prediction for snap_scaffold_22-snap.1538-T1
Valid prediction for GlimmerHMM_glimmerT_49786-T1
Valid prediction for GlimmerHMM_glimmerT_49803-T1
Valid prediction for snap_scaffold_22-snap.1549-T1
Valid prediction for pasa_asmbl_30220.p1
Valid prediction for GlimmerHMM_glimmerT_49804-T1
Valid prediction for snap_scaffold_22-snap.1553-T1
Couldn't classify 106012, 106434
Sorry, prediction pasa_asmbl_30221.p1 fails validation.
(GCT)	 CG	106012-106434	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_49808-T1
Valid prediction for GlimmerHMM_glimmerT_49791-T1
Valid prediction for Augustus_model.g33215.t1
Valid prediction for snap_scaffold_22-snap.1544-T1
Valid prediction for snap_scaffold_22-snap.1542-T1
Valid prediction for snap_scaffold_22-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_49787-T1
Valid prediction for snap_scaffold_22-snap.1555-T1
Valid prediction for Augustus_model.g33220.t1
Valid prediction for CodingQuarry_transcript_34218-T1
Valid prediction for snap_scaffold_22-snap.1536-T1
Valid prediction for Augustus_model.g33230.t1
Valid prediction for Augustus_model.g33232.t1
Valid prediction for snap_scaffold_22-snap.1556-T1
Valid prediction for Augustus_model.g33222.t1
Valid prediction for snap_scaffold_22-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_49800-T1
Valid prediction for Augustus_model.g33225.t1
Valid prediction for Augustus_model.g33224.t1
Valid prediction for Augustus_model.g33229.t1
Valid prediction for Augustus_model.g33217.t1
Valid prediction for snap_scaffold_22-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_49794-T1
Valid prediction for Augustus_model.g33218.t1
Valid prediction for snap_scaffold_22-snap.1540-T1
Valid prediction for snap_scaffold_22-snap.1550-T1
Valid prediction for Augustus_model.g33216.t1
Couldn't classify 40096, 40207
Sorry, prediction pasa_asmbl_30214.p1 fails validation.
(AAG)	 AG	40096-40207	GT	AGG
(GGA)	 AG	40337-40459	GT	TGG
(TCA)	 AG	41051-41133	GC	GAG
-recovered pasa_asmbl_30214.p1, terminal, 41051, 41133
-recovered pasa_asmbl_30214.p1, internal, 40096, 40207
-recovered pasa_asmbl_30214.p1, internal, 40337, 40459
-recovered pasa_asmbl_30214.p1, internal, 41051, 41133
Valid prediction for GlimmerHMM_glimmerT_49789-T1
Valid prediction for snap_scaffold_22-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_49802-T1
Couldn't classify 62075, 62120
Couldn't classify 62969, 63063
Sorry, prediction pasa_asmbl_30217.p1 fails validation.
(TCT)	 AG	62075-62120	GT	TGG
(TTG)	 AG	62212-62457	GT	AGG
(GTG)	 AG	62969-63063	TA	GCT
-recovered pasa_asmbl_30217.p1, internal, 62075, 62120
-recovered pasa_asmbl_30217.p1, internal, 62212, 62457
Valid prediction for snap_scaffold_22-snap.1551-T1
Valid prediction for snap_scaffold_22-snap.1543-T1
Valid prediction for GlimmerHMM_glimmerT_49788-T1
Valid prediction for GlimmerHMM_glimmerT_49807-T1
Valid prediction for GlimmerHMM_glimmerT_49810-T1
Valid prediction for Augustus_model.g33223.t1
Valid prediction for GlimmerHMM_glimmerT_49796-T1
Valid prediction for Augustus_model.g33233.t1
Valid prediction for GlimmerHMM_glimmerT_49801-T1
Valid prediction for Augustus_model.g33231.t1
Valid prediction for GlimmerHMM_glimmerT_49805-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_22-snap.1552-T1
Valid prediction for snap_scaffold_22-snap.1566-T1
Valid prediction for Augustus_model.g33228.t1
Valid prediction for pasa_asmbl_29423.p1
Valid prediction for snap_scaffold_22-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_49797-T1
Valid prediction for GlimmerHMM_glimmerT_49798-T1
Valid prediction for Augustus_model.g33234.t1
Valid prediction for Augustus_model.g33219.t1
Valid prediction for CodingQuarry_transcript_34220-T1
Valid prediction for snap_scaffold_22-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_49806-T1
Valid prediction for HiQ_model.g33226.t1
Valid prediction for GlimmerHMM_glimmerT_49790-T1
Valid prediction for snap_scaffold_22-snap.1547-T1
Valid prediction for snap_scaffold_22-snap.1560-T1
Valid prediction for Augustus_model.g33227.t1
Couldn't classify 62618, 62663
Sorry, prediction pasa_asmbl_29426.p1 fails validation.
(CCT)	 GC	62618-62663	GT	CGG
(ACA)	 AG	62877-62958	GT	ACG
(ATG)	 AG	63107-63187	GT	TCG
(CTC)	 AG	63282-63340	GT	AGG
(ACG)	 AG	63426-63578	GT	TGG
(TTG)	 AG	63663-63896	GT	AGG
(CTT)	 AG	64320-64421	GT	GGG
(GTA)	 AG	64897-65168	GT	AGG
(GAC)	 AG	65394-65526	GT	AGG
(GAT)	 AG	65715-65767	CC	GAC
-recovered pasa_asmbl_29426.p1, initial, 63107, 63187
-recovered pasa_asmbl_29426.p1, terminal, 65715, 65767
-recovered pasa_asmbl_29426.p1, internal, 62877, 62958
-recovered pasa_asmbl_29426.p1, internal, 63107, 63187
-recovered pasa_asmbl_29426.p1, internal, 63282, 63340
-recovered pasa_asmbl_29426.p1, internal, 63426, 63578
-recovered pasa_asmbl_29426.p1, internal, 63663, 63896
-recovered pasa_asmbl_29426.p1, internal, 64320, 64421
-recovered pasa_asmbl_29426.p1, internal, 64897, 65168
-recovered pasa_asmbl_29426.p1, internal, 65394, 65526
Valid prediction for GlimmerHMM_glimmerT_49809-T1
Valid prediction for snap_scaffold_22-snap.1548-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 60872, 60986
Couldn't classify 62481, 62512
Sorry, prediction pasa_asmbl_29741.p1 fails validation.
(CTG)	 AC	60872-60986	GT	CGG
(CCA)	 AG	61102-61178	GT	GGG
(TTT)	 AG	61360-61485	GT	AGG
(GAG)	 AG	61591-61708	GT	GGG
(CCG)	 AG	61836-61984	GT	AGG
(AAT)	 AG	62089-62164	GT	AGG
(AGA)	 AG	62481-62512	GT	TGG
add_exon() Sorry, pasa_asmbl_29741.p1 62089-62164-terminal-3 is invalid.
-recovered pasa_asmbl_29741.p1, terminal, 62089, 62164
-recovered pasa_asmbl_29741.p1, internal, 61102, 61178
-recovered pasa_asmbl_29741.p1, internal, 61360, 61485
-recovered pasa_asmbl_29741.p1, internal, 61591, 61708
-recovered pasa_asmbl_29741.p1, internal, 61836, 61984
-recovered pasa_asmbl_29741.p1, internal, 62089, 62164
-recovered pasa_asmbl_29741.p1, internal, 62481, 62512
Couldn't classify 57716, 57831
Couldn't classify 59241, 59269
Sorry, prediction pasa_asmbl_29764.p2 fails validation.
(CAG)	 AG	57716-57831	GT	CTG
(CTC)	 AG	58307-58330	GT	AGG
(CTC)	 AG	58638-58767	GT	AGG
(CTG)	 AG	58920-59019	GT	CAG
(CAT)	 AG	59241-59269	GG	AAG
-recovered pasa_asmbl_29764.p2, internal, 57716, 57831
-recovered pasa_asmbl_29764.p2, internal, 58307, 58330
-recovered pasa_asmbl_29764.p2, internal, 58638, 58767
-recovered pasa_asmbl_29764.p2, internal, 58920, 59019
Valid prediction for snap_scaffold_22-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_49811-T1
Valid prediction for CodingQuarry_transcript_34219-T1
Valid prediction for snap_scaffold_22-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_49795-T1
Valid prediction for GlimmerHMM_glimmerT_49799-T1
Valid prediction for snap_scaffold_22-snap.1545-T1
Valid prediction for GlimmerHMM_glimmerT_49792-T1
Valid prediction for snap_scaffold_22-snap.1546-T1
Valid prediction for Augustus_model.g33221.t1
Valid prediction for snap_scaffold_22-snap.1537-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33369, rend_intergenic: 26993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101228, rend_intergenic: 87924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110871, rend_intergenic: 107413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130028, rend_intergenic: 125664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134378, rend_intergenic: 130122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137981, rend_intergenic: 134921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144024, rend_intergenic: 139385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152279
-exon list size: 396


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 33369, rend_intergenic: 26993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101228, rend_intergenic: 87924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110871, rend_intergenic: 107413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130028, rend_intergenic: 125664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134378, rend_intergenic: 130122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137981, rend_intergenic: 134921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144024, rend_intergenic: 139385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support