-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_1396491-1540337

-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_20-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_45456-T1
Valid prediction for Augustus_model.g30207.t1
Valid prediction for GlimmerHMM_glimmerT_45474-T1
Valid prediction for pasa_asmbl_26417.p1
Valid prediction for snap_scaffold_20-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_45449-T1
Valid prediction for Augustus_model.g30190.t1
Valid prediction for GlimmerHMM_glimmerT_45470-T1
Valid prediction for HiQ_model.g30205.t1
Valid prediction for Augustus_model.g30210.t1
Couldn't classify 139889, 140040
Sorry, prediction pasa_asmbl_26422.p1 fails validation.
(AAC)	 TC	139889-140040	GT	AGG
(ACT)	 AG	140534-140713	GT	AGG
(ACT)	 AG	140921-141014	GG	AGG
-recovered pasa_asmbl_26422.p1, terminal, 140921, 141014
-recovered pasa_asmbl_26422.p1, internal, 140534, 140713
Valid prediction for snap_scaffold_20-snap.314-T1
Valid prediction for snap_scaffold_20-snap.326-T1
Valid prediction for snap_scaffold_20-snap.340-T1
Valid prediction for snap_scaffold_20-snap.324-T1
Valid prediction for snap_scaffold_20-snap.302-T1
Valid prediction for snap_scaffold_20-snap.321-T1
Valid prediction for GlimmerHMM_glimmerT_45471-T1
Valid prediction for CodingQuarry_transcript_30417-T1
Valid prediction for snap_scaffold_20-snap.313-T1
Valid prediction for Augustus_model.g30211.t1
Valid prediction for snap_scaffold_20-snap.305-T1
Valid prediction for snap_scaffold_20-snap.332-T1
Valid prediction for snap_scaffold_20-snap.334-T1
Valid prediction for snap_scaffold_20-snap.337-T1
Valid prediction for GlimmerHMM_glimmerT_45475-T1
Valid prediction for snap_scaffold_20-snap.336-T1
Valid prediction for Augustus_model.g30206.t1
Valid prediction for snap_scaffold_20-snap.301-T1
Valid prediction for snap_scaffold_20-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_45453-T1
Valid prediction for GlimmerHMM_glimmerT_45467-T1
Valid prediction for snap_scaffold_20-snap.342-T1
Valid prediction for snap_scaffold_20-snap.307-T1
Valid prediction for snap_scaffold_20-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_45469-T1
Valid prediction for snap_scaffold_20-snap.306-T1
Valid prediction for snap_scaffold_20-snap.310-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 CodingQuarry_transcript_30419-T1
Valid prediction for snap_scaffold_20-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_45465-T1
Valid prediction for snap_scaffold_20-snap.323-T1
Valid prediction for Augustus_model.g30197.t1
Couldn't classify 115692, 117061
Couldn't classify 117328, 117484
Sorry, prediction pasa_asmbl_25558.p1 fails validation.
(CTT)	 GT	115692-117061	GT	GTG
(ACT)	 AG	117328-117484	AC	AGA
Valid prediction for snap_scaffold_20-snap.316-T1
Valid prediction for snap_scaffold_20-snap.330-T1
Valid prediction for CodingQuarry_transcript_30413-T1
Valid prediction for Augustus_model.g30195.t1
Couldn't classify 21180, 21251
Couldn't classify 25827, 26012
Sorry, prediction pasa_asmbl_25581.p1 fails validation.
(CCA)	 GA	21180-21251	GT	TGG
(AAA)	 AG	21684-21756	GT	TGG
(GTA)	 AG	22288-22410	GT	CGG
(AGT)	 AG	22900-23001	GT	CAG
(AAA)	 AG	23666-23930	GT	GTG
(CCC)	 AG	24359-24437	GT	TGG
(CCG)	 AG	24547-24700	GT	AGG
(GTC)	 AG	24905-25029	GT	ATG
(TTC)	 AG	25419-25604	GT	CTG
(CGC)	 AG	25827-26012	TC	GCT
add_exon() Sorry, pasa_asmbl_25581.p1 24547-24700-terminal-3 is invalid.
-recovered pasa_asmbl_25581.p1, terminal, 24547, 24700
-recovered pasa_asmbl_25581.p1, internal, 21684, 21756
-recovered pasa_asmbl_25581.p1, internal, 22288, 22410
-recovered pasa_asmbl_25581.p1, internal, 22900, 23001
-recovered pasa_asmbl_25581.p1, internal, 23666, 23930
-recovered pasa_asmbl_25581.p1, internal, 24359, 24437
-recovered pasa_asmbl_25581.p1, internal, 24547, 24700
-recovered pasa_asmbl_25581.p1, internal, 24905, 25029
-recovered pasa_asmbl_25581.p1, internal, 25419, 25604
Valid prediction for HiQ_model.g30200.t1
Valid prediction for GlimmerHMM_glimmerT_45468-T1
Valid prediction for GlimmerHMM_glimmerT_45457-T1
Valid prediction for Augustus_model.g30193.t1
Couldn't classify 26465, 26550
Sorry, prediction pasa_asmbl_25580.p1 fails validation.
(GAT)	 TA	26465-26550	GT	AAG
(GGG)	 AG	27081-27270	GT	AGG
(ACC)	 AG	29772-29919	GT	TGG
(ATG)	 AG	30240-30367	GT	AGG
(GAC)	 AG	30687-30810	GT	AGG
(ACC)	 AG	31059-31126	GT	AGG
(AAG)	 AG	31444-31626	CA	AGC
add_exon() Sorry, pasa_asmbl_25580.p1 30240-30367-initial-1 is invalid.
-recovered pasa_asmbl_25580.p1, initial, 30240, 30367
-recovered pasa_asmbl_25580.p1, terminal, 31444, 31626
-recovered pasa_asmbl_25580.p1, internal, 27081, 27270
-recovered pasa_asmbl_25580.p1, internal, 29772, 29919
-recovered pasa_asmbl_25580.p1, internal, 30240, 30367
-recovered pasa_asmbl_25580.p1, internal, 30687, 30810
-recovered pasa_asmbl_25580.p1, internal, 31059, 31126
Valid prediction for snap_scaffold_20-snap.315-T1
Valid prediction for Augustus_model.g30209.t1
Valid prediction for snap_scaffold_20-snap.327-T1
Valid prediction for pasa_asmbl_25566.p1
Couldn't classify 119792, 120286
Sorry, prediction pasa_asmbl_25557.p1 fails validation.
(TAT)	 TG	119792-120286	CC	AGC
Valid prediction for snap_scaffold_20-snap.309-T1
Valid prediction for GlimmerHMM_glimmerT_45458-T1
Valid prediction for snap_scaffold_20-snap.312-T1
Valid prediction for snap_scaffold_20-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_45450-T1
Valid prediction for CodingQuarry_transcript_30408-T1
Valid prediction for snap_scaffold_20-snap.311-T1
Valid prediction for snap_scaffold_20-snap.333-T1
Couldn't classify 27613, 27709
Sorry, prediction CodingQuarry_transcript_30418-T1 fails validation.
(ATG)	 GC	27223-27270	GT	AGG
(TAC)	 TG	27613-27709	GT	AGG
(TCC)	 AG	28537-28736	GT	CTG
(ACC)	 AG	29772-29919	GT	TGG
(ATG)	 AG	30240-30367	GT	AGG
(GAC)	 AG	30687-30810	GT	AGG
(ACC)	 AG	31059-31126	GT	AGG
(AAG)	 AG	31444-31626	CA	AGC
-recovered CodingQuarry_transcript_30418-T1, initial, 27223, 27270
add_exon() Sorry, CodingQuarry_transcript_30418-T1 30240-30367-initial-1 is invalid.
-recovered CodingQuarry_transcript_30418-T1, initial, 30240, 30367
-recovered CodingQuarry_transcript_30418-T1, terminal, 31444, 31626
-recovered CodingQuarry_transcript_30418-T1, internal, 28537, 28736
-recovered CodingQuarry_transcript_30418-T1, internal, 29772, 29919
-recovered CodingQuarry_transcript_30418-T1, internal, 30240, 30367
-recovered CodingQuarry_transcript_30418-T1, internal, 30687, 30810
-recovered CodingQuarry_transcript_30418-T1, internal, 31059, 31126
Valid prediction for snap_scaffold_20-snap.331-T1
Valid prediction for Augustus_model.g30199.t1
Valid prediction for GlimmerHMM_glimmerT_45472-T1
Valid prediction for CodingQuarry_transcript_30414-T1
Couldn't classify 88425, 88676
Couldn't classify 89806, 89979
Sorry, prediction pasa_asmbl_25567.p1 fails validation.
(TTT)	 GG	88425-88676	GT	GTG
(CAA)	 AG	89806-89979	GG	ATG
Valid prediction for CodingQuarry_transcript_30415-T1
Valid prediction for pasa_asmbl_25572.p1
Valid prediction for HiQ_model.g30202.t1
Valid prediction for Augustus_model.g30191.t1
Valid prediction for snap_scaffold_20-snap.329-T1
Valid prediction for CodingQuarry_transcript_30409-T1
Valid prediction for GlimmerHMM_glimmerT_45451-T1
Valid prediction for snap_scaffold_20-snap.318-T1
Valid prediction for pasa_asmbl_25569.p1
Valid prediction for snap_scaffold_20-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_45452-T1
Valid prediction for GlimmerHMM_glimmerT_45455-T1
Valid prediction for snap_scaffold_20-snap.341-T1
Valid prediction for Augustus_model.g30198.t1
Valid prediction for snap_scaffold_20-snap.308-T1
Couldn't classify 100777, 100887
Couldn't classify 105506, 105531
Sorry, prediction pasa_asmbl_25564.p1 fails validation.
(CCC)	 CC	100777-100887	GT	AGG
(CAG)	 AG	101025-101190	GT	AGG
(TGG)	 AG	101691-101887	GT	AGG
(TTT)	 AG	102263-102391	GT	AGG
(GAT)	 AG	103287-103508	GT	AGG
(CTG)	 AG	103902-104119	GT	AGG
(TAA)	 AG	104433-104527	GT	AGG
(GCG)	 AG	104641-104892	GT	AGG
(CAG)	 AG	105325-105429	GT	AGG
(GAC)	 AG	105506-105531	GC	AGG
-recovered pasa_asmbl_25564.p1, internal, 101025, 101190
-recovered pasa_asmbl_25564.p1, internal, 101691, 101887
-recovered pasa_asmbl_25564.p1, internal, 102263, 102391
-recovered pasa_asmbl_25564.p1, internal, 103287, 103508
-recovered pasa_asmbl_25564.p1, internal, 103902, 104119
-recovered pasa_asmbl_25564.p1, internal, 104433, 104527
-recovered pasa_asmbl_25564.p1, internal, 104641, 104892
-recovered pasa_asmbl_25564.p1, internal, 105325, 105429
-recovered pasa_asmbl_25564.p1, internal, 105506, 105531
Valid prediction for GlimmerHMM_glimmerT_45454-T1
Valid prediction for Augustus_model.g30208.t1
Valid prediction for GlimmerHMM_glimmerT_45473-T1
Couldn't classify 106058, 106580
Couldn't classify 107571, 107629
Sorry, prediction pasa_asmbl_25561.p1 fails validation.
(CCA)	 TC	106058-106580	GT	AGG
(GTC)	 AG	106915-107018	GT	CTG
(GAC)	 AG	107295-107406	GT	CAG
(GAT)	 AG	107571-107629	GC	TGG
-recovered pasa_asmbl_25561.p1, internal, 106915, 107018
-recovered pasa_asmbl_25561.p1, internal, 107295, 107406
-recovered pasa_asmbl_25561.p1, internal, 107571, 107629
Valid prediction for snap_scaffold_20-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_45461-T1
Valid prediction for CodingQuarry_transcript_30407-T1
Valid prediction for Augustus_model.g30204.t1
Valid prediction for GlimmerHMM_glimmerT_45464-T1
Valid prediction for Augustus_model.g30192.t1
Valid prediction for Augustus_model.g30201.t1
Valid prediction for GlimmerHMM_glimmerT_45459-T1
Valid prediction for snap_scaffold_20-snap.325-T1
Valid prediction for snap_scaffold_20-snap.338-T1
Valid prediction for CodingQuarry_transcript_30410-T1
Valid prediction for snap_scaffold_20-snap.339-T1
Valid prediction for Augustus_model.g30196.t1
Valid prediction for GlimmerHMM_glimmerT_45462-T1
Valid prediction for Augustus_model.g30203.t1
Couldn't classify 109089, 109334
Sorry, prediction pasa_asmbl_26250.p1 fails validation.
(AGC)	 GT	109089-109334	GT	CGG
(ATG)	 AG	110115-110183	GG	GAG
-recovered pasa_asmbl_26250.p1, terminal, 110115, 110183
Valid prediction for CodingQuarry_transcript_30411-T1
Valid prediction for GlimmerHMM_glimmerT_45460-T1
Valid prediction for GlimmerHMM_glimmerT_45463-T1
Valid prediction for CodingQuarry_transcript_30412-T1
Valid prediction for Augustus_model.g30194.t1
Valid prediction for GlimmerHMM_glimmerT_45466-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9271, rend_intergenic: 8828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19242, rend_intergenic: 9310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27991, rend_intergenic: 20845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37713, rend_intergenic: 32755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47067, rend_intergenic: 37741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56192, rend_intergenic: 49410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61404, rend_intergenic: 59962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64204, rend_intergenic: 61634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70580, rend_intergenic: 65453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79639, rend_intergenic: 75954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87319, rend_intergenic: 83804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103691, rend_intergenic: 87325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110670, rend_intergenic: 105298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115274, rend_intergenic: 112222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128799, rend_intergenic: 115284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131654, rend_intergenic: 129809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138653, rend_intergenic: 137886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140951, rend_intergenic: 138903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143847
-exon list size: 397


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 9271, rend_intergenic: 8828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19242, rend_intergenic: 9310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27991, rend_intergenic: 20845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37713, rend_intergenic: 32755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47067, rend_intergenic: 37741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56192, rend_intergenic: 49410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61404, rend_intergenic: 59962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64204, rend_intergenic: 61634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70580, rend_intergenic: 65453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79639, rend_intergenic: 75954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87319, rend_intergenic: 83804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103691, rend_intergenic: 87325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110670, rend_intergenic: 105298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115274, rend_intergenic: 112222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128799, rend_intergenic: 115284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131654, rend_intergenic: 129809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138653, rend_intergenic: 137886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140951, rend_intergenic: 138903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support