-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_6607370-6874534

-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 HiQ_model.g6191.t1
Valid prediction for GlimmerHMM_glimmerT_9571-T1
Couldn't classify 235762, 235824
Couldn't classify 236860, 237068
Sorry, prediction pasa_asmbl_41430.p1 fails validation.
(CAG)	 AC	235762-235824	GT	AGG
(CAC)	 AG	236060-236164	GT	AGG
(AAC)	 AG	236528-236663	GT	GGG
(GGT)	 AG	236860-237068	CA	CCC
-recovered pasa_asmbl_41430.p1, internal, 236060, 236164
-recovered pasa_asmbl_41430.p1, internal, 236528, 236663
Valid prediction for snap_scaffold_4-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_9556-T1
Valid prediction for pasa_asmbl_41421.p1
Valid prediction for snap_scaffold_4-snap.1409-T1
Valid prediction for snap_scaffold_4-snap.1448-T1
Valid prediction for pasa_asmbl_41422.p1
Valid prediction for snap_scaffold_4-snap.1450-T1
Valid prediction for snap_scaffold_4-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_9559-T1
Valid prediction for GlimmerHMM_glimmerT_9573-T1
Valid prediction for GlimmerHMM_glimmerT_9550-T1
Valid prediction for snap_scaffold_4-snap.1441-T1
Couldn't classify 97876, 98028
Sorry, prediction pasa_asmbl_41425.p1 fails validation.
(GGT)	 TG	97876-98028	GT	TGG
(GAG)	 AG	98313-98483	AC	GAA
-recovered pasa_asmbl_41425.p1, terminal, 98313, 98483
Valid prediction for pasa_asmbl_41431.p1
Valid prediction for Augustus_model.g6207.t1
Valid prediction for snap_scaffold_4-snap.1425-T1
Valid prediction for GlimmerHMM_glimmerT_9551-T1
Valid prediction for GlimmerHMM_glimmerT_9545-T1
Valid prediction for GlimmerHMM_glimmerT_9574-T1
Valid prediction for GlimmerHMM_glimmerT_9567-T1
Valid prediction for Augustus_model.g6202.t1
Valid prediction for GlimmerHMM_glimmerT_9561-T1
Couldn't classify 231577, 231609
Couldn't classify 235474, 235522
Sorry, prediction pasa_asmbl_41428.p1 fails validation.
(AAG)	 TC	231577-231609	GT	AAG
(GAT)	 AG	231825-231971	GT	AGG
(GTT)	 AG	233575-233601	GT	AGG
(GAC)	 AG	234782-234904	GT	TGG
(GAC)	 AG	235090-235169	GT	ATG
(TAA)	 AG	235474-235522	AC	GGA
-recovered pasa_asmbl_41428.p1, internal, 231825, 231971
-recovered pasa_asmbl_41428.p1, internal, 233575, 233601
-recovered pasa_asmbl_41428.p1, internal, 234782, 234904
-recovered pasa_asmbl_41428.p1, internal, 235090, 235169
Valid prediction for snap_scaffold_4-snap.1429-T1
Valid prediction for HiQ_model.g6196.t1
Valid prediction for snap_scaffold_4-snap.1440-T1
Valid prediction for Augustus_model.g6200.t1
Valid prediction for CodingQuarry_transcript_49029-T1
Valid prediction for snap_scaffold_4-snap.1437-T1
Valid prediction for snap_scaffold_4-snap.1426-T1
Valid prediction for Augustus_model.g6208.t1
Valid prediction for GlimmerHMM_glimmerT_9553-T1
Valid prediction for snap_scaffold_4-snap.1408-T1
Valid prediction for GlimmerHMM_glimmerT_9563-T1
Valid prediction for GlimmerHMM_glimmerT_9572-T1
Valid prediction for snap_scaffold_4-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_9546-T1
Valid prediction for Augustus_model.g6190.t1
Valid prediction for Augustus_model.g6194.t1
Couldn't classify 202325, 202651
Sorry, prediction pasa_asmbl_42699.p1 fails validation.
(TTC)	 TC	202325-202651	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_9557-T1
Valid prediction for snap_scaffold_4-snap.1428-T1
Valid prediction for snap_scaffold_4-snap.1422-T1
Valid prediction for snap_scaffold_4-snap.1446-T1
Valid prediction for GlimmerHMM_glimmerT_9554-T1
Valid prediction for snap_scaffold_4-snap.1420-T1
Valid prediction for CodingQuarry_transcript_49030-T1
Valid prediction for GlimmerHMM_glimmerT_9570-T1
Valid prediction for Augustus_model.g6199.t1
Couldn't classify 98313, 98313
Sorry, prediction CodingQuarry_transcript_49031-T1 fails validation.
(ATG)	 AC	95068-95214	GT	CGG
(TCC)	 AG	95789-95866	GT	AGG
(CAG)	 AG	96117-96236	GT	TGG
(AGT)	 AG	96534-96709	GT	TGG
(GCC)	 AG	96829-96954	GT	TAG
(GAG)	 AG	98313-98313	AG	GGA
-recovered CodingQuarry_transcript_49031-T1, initial, 95068, 95214
-recovered CodingQuarry_transcript_49031-T1, internal, 95789, 95866
-recovered CodingQuarry_transcript_49031-T1, internal, 96117, 96236
-recovered CodingQuarry_transcript_49031-T1, internal, 96534, 96709
-recovered CodingQuarry_transcript_49031-T1, internal, 96829, 96954
Valid prediction for CodingQuarry_transcript_49028-T1
Valid prediction for Augustus_model.g6195.t1
Valid prediction for snap_scaffold_4-snap.1443-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 pasa_asmbl_42693.p2
Valid prediction for snap_scaffold_4-snap.1413-T1
Valid prediction for GlimmerHMM_glimmerT_9562-T1
Valid prediction for Augustus_model.g6206.t1
Valid prediction for snap_scaffold_4-snap.1447-T1
Couldn't classify 261369, 261390
Couldn't classify 265244, 265620
Sorry, prediction pasa_asmbl_42691.p1 fails validation.
(GGA)	 CT	261369-261390	GT	GGG
(GCA)	 AG	263523-263738	GC	AGG
(ACG)	 AG	264487-264711	GT	AGG
(GTG)	 AG	265244-265620	CC	AGC
-recovered pasa_asmbl_42691.p1, internal, 263523, 263738
-recovered pasa_asmbl_42691.p1, internal, 264487, 264711
Valid prediction for snap_scaffold_4-snap.1407-T1
Valid prediction for snap_scaffold_4-snap.1417-T1
Valid prediction for Augustus_model.g6203.t1
Valid prediction for snap_scaffold_4-snap.1406-T1
Valid prediction for snap_scaffold_4-snap.1433-T1
Valid prediction for Augustus_model.g6205.t1
Valid prediction for GlimmerHMM_glimmerT_9547-T1
Valid prediction for snap_scaffold_4-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_9552-T1
Valid prediction for snap_scaffold_4-snap.1442-T1
Valid prediction for snap_scaffold_4-snap.1444-T1
Couldn't classify 185966, 186106
Couldn't classify 193538, 193727
Sorry, prediction pasa_asmbl_42697.p1 fails validation.
(GGC)	 GC	185966-186106	GT	AGG
(GTG)	 AG	186583-186767	GT	AGG
(CAC)	 AG	186911-187024	GT	TGG
(GGC)	 AG	188474-188573	GT	AGG
(GAG)	 AG	188853-188938	GT	AAG
(CCC)	 AG	190064-190199	GT	AGG
(GTG)	 AG	190615-190769	GT	GTG
(AGA)	 AG	190999-191113	GT	TGG
(GGT)	 AG	192121-192230	GT	CGG
(AAA)	 AG	192373-192438	GT	GAG
(CGC)	 AG	193538-193727	AT	ACA
-recovered pasa_asmbl_42697.p1, internal, 186583, 186767
-recovered pasa_asmbl_42697.p1, internal, 186911, 187024
-recovered pasa_asmbl_42697.p1, internal, 188474, 188573
-recovered pasa_asmbl_42697.p1, internal, 188853, 188938
-recovered pasa_asmbl_42697.p1, internal, 190064, 190199
-recovered pasa_asmbl_42697.p1, internal, 190615, 190769
-recovered pasa_asmbl_42697.p1, internal, 190999, 191113
-recovered pasa_asmbl_42697.p1, internal, 192121, 192230
-recovered pasa_asmbl_42697.p1, internal, 192373, 192438
Valid prediction for snap_scaffold_4-snap.1436-T1
Valid prediction for snap_scaffold_4-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_9548-T1
Valid prediction for snap_scaffold_4-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_9549-T1
Valid prediction for snap_scaffold_4-snap.1414-T1
Valid prediction for GlimmerHMM_glimmerT_9564-T1
Valid prediction for Augustus_model.g6204.t1
Valid prediction for snap_scaffold_4-snap.1435-T1
Valid prediction for snap_scaffold_4-snap.1412-T1
Valid prediction for Augustus_model.g6192.t1
Valid prediction for snap_scaffold_4-snap.1411-T1
Valid prediction for snap_scaffold_4-snap.1431-T1
Valid prediction for Augustus_model.g6197.t1
Valid prediction for snap_scaffold_4-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_9544-T1
Valid prediction for Augustus_model.g6209.t1
Valid prediction for Augustus_model.g6198.t1
Valid prediction for Augustus_model.g6189.t1
Valid prediction for snap_scaffold_4-snap.1410-T1
Valid prediction for GlimmerHMM_glimmerT_9568-T1
Valid prediction for GlimmerHMM_glimmerT_9555-T1
Valid prediction for snap_scaffold_4-snap.1424-T1
Valid prediction for GlimmerHMM_glimmerT_9569-T1
Valid prediction for snap_scaffold_4-snap.1438-T1
Valid prediction for GlimmerHMM_glimmerT_9558-T1
Valid prediction for snap_scaffold_4-snap.1415-T1
Couldn't classify 215932, 216062
Sorry, prediction pasa_asmbl_42692.p1 fails validation.
(ATA)	 GG	215932-216062	GT	CAG
(GTA)	 AG	216600-216753	GT	ACG
(AGG)	 AG	217878-218048	TC	GAT
-recovered pasa_asmbl_42692.p1, terminal, 217878, 218048
-recovered pasa_asmbl_42692.p1, internal, 216600, 216753
Valid prediction for snap_scaffold_4-snap.1451-T1
Valid prediction for GlimmerHMM_glimmerT_9566-T1
Valid prediction for snap_scaffold_4-snap.1416-T1
Valid prediction for snap_scaffold_4-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_9565-T1
Valid prediction for snap_scaffold_4-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_9560-T1
Valid prediction for Augustus_model.g6193.t1
Valid prediction for snap_scaffold_4-snap.1423-T1
Valid prediction for Augustus_model.g6201.t1
Valid prediction for snap_scaffold_4-snap.1432-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 108342, rend_intergenic: 105682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121675, rend_intergenic: 118023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131374, rend_intergenic: 122686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205232, rend_intergenic: 204860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235866, rend_intergenic: 226060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237821, rend_intergenic: 236042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256708, rend_intergenic: 252371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260318, rend_intergenic: 259731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265059, rend_intergenic: 260400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 267165
-exon list size: 470


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 108342, rend_intergenic: 105682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121675, rend_intergenic: 118023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131374, rend_intergenic: 122686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205232, rend_intergenic: 204860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235866, rend_intergenic: 226060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237821, rend_intergenic: 236042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256708, rend_intergenic: 252371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260318, rend_intergenic: 259731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265059, rend_intergenic: 260400  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