-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_6884068-7122305

-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 Augustus_model.g7982.t1
Valid prediction for GlimmerHMM_glimmerT_12137-T1
Valid prediction for GlimmerHMM_glimmerT_12145-T1
Valid prediction for snap_scaffold_5-snap.1358-T1
Valid prediction for snap_scaffold_5-snap.1395-T1
Valid prediction for GlimmerHMM_glimmerT_12146-T1
Valid prediction for snap_scaffold_5-snap.1384-T1
Valid prediction for snap_scaffold_5-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_12136-T1
Couldn't classify 36510, 36568
Couldn't classify 37381, 37433
Sorry, prediction pasa_asmbl_45460.p1 fails validation.
(ATC)	 CT	36510-36568	GT	AAG
(GAT)	 AG	36741-36847	GT	GGG
(ATT)	 AG	37031-37210	GT	AGG
(AGC)	 AG	37381-37433	CT	CCC
-recovered pasa_asmbl_45460.p1, internal, 36741, 36847
-recovered pasa_asmbl_45460.p1, internal, 37031, 37210
Valid prediction for GlimmerHMM_glimmerT_12135-T1
Valid prediction for snap_scaffold_5-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_12143-T1
Couldn't classify 18654, 19334
Sorry, prediction pasa_asmbl_45453.p1 fails validation.
(GGG)	 GG	18654-19334	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_12133-T1
Valid prediction for GlimmerHMM_glimmerT_12134-T1
Valid prediction for Augustus_model.g7980.t1
Valid prediction for snap_scaffold_5-snap.1398-T1
Valid prediction for pasa_asmbl_45463.p1
Valid prediction for snap_scaffold_5-snap.1359-T1
Valid prediction for snap_scaffold_5-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_12150-T1
Valid prediction for snap_scaffold_5-snap.1391-T1
Valid prediction for Augustus_model.g7973.t1
Valid prediction for Augustus_model.g7971.t1
Valid prediction for CodingQuarry_transcript_52110-T1
Valid prediction for snap_scaffold_5-snap.1362-T1
Valid prediction for Augustus_model.g7978.t1
Valid prediction for GlimmerHMM_glimmerT_12147-T1
Valid prediction for snap_scaffold_5-snap.1353-T1
Couldn't classify 63215, 63305
Sorry, prediction pasa_asmbl_45470.p1 fails validation.
(CCC)	 CC	63215-63305	GT	GAG
(TCC)	 AG	63406-63782	GT	AGG
(CCT)	 AG	64111-64269	GT	GGG
(AGC)	 AG	64413-64559	GT	AGG
(GTG)	 AG	64833-64961	GT	AGG
(GTG)	 AG	65065-65133	GC	GAG
-recovered pasa_asmbl_45470.p1, terminal, 65065, 65133
-recovered pasa_asmbl_45470.p1, internal, 63406, 63782
-recovered pasa_asmbl_45470.p1, internal, 64111, 64269
-recovered pasa_asmbl_45470.p1, internal, 64413, 64559
-recovered pasa_asmbl_45470.p1, internal, 64833, 64961
-recovered pasa_asmbl_45470.p1, internal, 65065, 65133
Valid prediction for pasa_asmbl_45457.p1
Valid prediction for snap_scaffold_5-snap.1360-T1
Couldn't classify 60361, 60420
Sorry, prediction pasa_asmbl_45468.p1 fails validation.
(ATG)	 AG	56915-57004	GT	AAG
(CTC)	 AG	57706-57834	GT	TGG
(GCG)	 AG	57995-58080	GT	AGG
(CCA)	 AG	58388-58472	GT	AGG
(GCA)	 AG	58623-58663	GT	AAG
(GAA)	 AG	58847-58943	GT	CTG
(GAG)	 AG	59025-59122	GT	AGG
(ACC)	 AG	59339-59443	GT	AGG
(GGT)	 AG	59586-59654	GT	AGG
(TGT)	 AG	59832-59958	GT	AGG
(ACA)	 AG	60188-60253	GT	AGG
(TTC)	 AG	60361-60420	GT	AGG
-recovered pasa_asmbl_45468.p1, initial, 56915, 57004
-recovered pasa_asmbl_45468.p1, internal, 56915, 57004
-recovered pasa_asmbl_45468.p1, internal, 57706, 57834
-recovered pasa_asmbl_45468.p1, internal, 57995, 58080
-recovered pasa_asmbl_45468.p1, internal, 58388, 58472
-recovered pasa_asmbl_45468.p1, internal, 58623, 58663
-recovered pasa_asmbl_45468.p1, internal, 58847, 58943
-recovered pasa_asmbl_45468.p1, internal, 59025, 59122
-recovered pasa_asmbl_45468.p1, internal, 59339, 59443
-recovered pasa_asmbl_45468.p1, internal, 59586, 59654
-recovered pasa_asmbl_45468.p1, internal, 59832, 59958
-recovered pasa_asmbl_45468.p1, internal, 60188, 60253
-recovered pasa_asmbl_45468.p1, internal, 60361, 60420
Valid prediction for Augustus_model.g7979.t1
Couldn't classify 53163, 53237
Sorry, prediction pasa_asmbl_45467.p1 fails validation.
(CTC)	 AC	53163-53237	GT	CAG
(ATG)	 AG	53425-53550	GT	ATG
(GTG)	 AG	53845-54135	GG	GAG
-recovered pasa_asmbl_45467.p1, initial, 53425, 53550
-recovered pasa_asmbl_45467.p1, terminal, 53845, 54135
-recovered pasa_asmbl_45467.p1, internal, 53425, 53550
Couldn't classify 60912, 61003
Couldn't classify 62220, 62417
Sorry, prediction pasa_asmbl_45469.p1 fails validation.
(CAG)	 TG	60912-61003	GT	AGG
(TGC)	 AG	61100-61167	GT	AGG
(AGG)	 AG	61354-61507	GT	AGG
(CCA)	 AG	61623-61751	GC	GGG
(CCT)	 AG	61847-62015	GT	AGG
(GTG)	 AG	62220-62417	GA	ACG
add_exon() Sorry, pasa_asmbl_45469.p1 61100-61167-terminal-2 is invalid.
-recovered pasa_asmbl_45469.p1, terminal, 61100, 61167
-recovered pasa_asmbl_45469.p1, internal, 61100, 61167
-recovered pasa_asmbl_45469.p1, internal, 61354, 61507
-recovered pasa_asmbl_45469.p1, internal, 61623, 61751
-recovered pasa_asmbl_45469.p1, internal, 61847, 62015
Valid prediction for Augustus_model.g7981.t1
Valid prediction for snap_scaffold_5-snap.1374-T1
Valid prediction for snap_scaffold_5-snap.1375-T1
Valid prediction for snap_scaffold_5-snap.1371-T1
Valid prediction for CodingQuarry_transcript_52112-T1
Valid prediction for snap_scaffold_5-snap.1388-T1
Valid prediction for snap_scaffold_5-snap.1361-T1
Valid prediction for pasa_asmbl_45461.p1
Valid prediction for snap_scaffold_5-snap.1357-T1
Valid prediction for HiQ_model.g7969.t1
Valid prediction for Augustus_model.g7972.t1
Valid prediction for Augustus_model.g7970.t1
Valid prediction for pasa_asmbl_45456.p1
Valid prediction for snap_scaffold_5-snap.1373-T1
Valid prediction for snap_scaffold_5-snap.1385-T1
Valid prediction for snap_scaffold_5-snap.1364-T1
Couldn't classify 145720, 145888
Sorry, prediction pasa_asmbl_45472.p1 fails validation.
(GTG)	 GT	145720-145888	GT	CGG
(ACC)	 AG	147064-148028	TC	AAT
-recovered pasa_asmbl_45472.p1, terminal, 147064, 148028
Valid prediction for snap_scaffold_5-snap.1401-T1
Valid prediction for CodingQuarry_transcript_52111-T1
Valid prediction for snap_scaffold_5-snap.1382-T1
Valid prediction for Augustus_model.g7968.t1
Valid prediction for Augustus_model.g7974.t1
Valid prediction for snap_scaffold_5-snap.1378-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_5-snap.1372-T1
Valid prediction for snap_scaffold_5-snap.1394-T1
Valid prediction for snap_scaffold_5-snap.1376-T1
Valid prediction for Augustus_model.g7975.t1
Valid prediction for snap_scaffold_5-snap.1377-T1
Valid prediction for snap_scaffold_5-snap.1390-T1
Valid prediction for snap_scaffold_5-snap.1393-T1
Valid prediction for Augustus_model.g7976.t1
Valid prediction for GlimmerHMM_glimmerT_12138-T1
Valid prediction for snap_scaffold_5-snap.1389-T1
Valid prediction for snap_scaffold_5-snap.1392-T1
Valid prediction for snap_scaffold_5-snap.1369-T1
Valid prediction for snap_scaffold_5-snap.1383-T1
Valid prediction for snap_scaffold_5-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_12148-T1
Valid prediction for GlimmerHMM_glimmerT_12149-T1
Valid prediction for snap_scaffold_5-snap.1368-T1
Couldn't classify 155507, 155524
Couldn't classify 157675, 157864
Sorry, prediction pasa_asmbl_45022.p1 fails validation.
(ATA)	 TT	155507-155524	GT	GGG
(TTC)	 AG	157230-157354	GT	AGG
(GCT)	 AG	157675-157864	CC	GTC
-recovered pasa_asmbl_45022.p1, internal, 157230, 157354
Valid prediction for Augustus_model.g7985.t1
Valid prediction for Augustus_model.g7967.t1
Valid prediction for GlimmerHMM_glimmerT_12132-T1
Valid prediction for pasa_asmbl_44162.p1
Valid prediction for GlimmerHMM_glimmerT_12142-T1
Valid prediction for snap_scaffold_5-snap.1403-T1
Valid prediction for snap_scaffold_5-snap.1396-T1
Valid prediction for snap_scaffold_5-snap.1354-T1
Valid prediction for snap_scaffold_5-snap.1379-T1
Valid prediction for CodingQuarry_transcript_52113-T1
Valid prediction for Augustus_model.g7984.t1
Valid prediction for Augustus_model.g7977.t1
Valid prediction for snap_scaffold_5-snap.1399-T1
Valid prediction for snap_scaffold_5-snap.1387-T1
Valid prediction for snap_scaffold_5-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_12151-T1
Couldn't classify 10960, 11088
Sorry, prediction pasa_asmbl_44165.p1 fails validation.
(TTC)	 CC	10960-11088	GT	AGG
(GAG)	 AG	11261-11403	GT	AAG
(GGT)	 AG	11570-11754	GT	AGG
(GCT)	 AG	12219-12307	GT	AGG
(GCG)	 AG	12449-12589	GT	AGG
(GTG)	 AG	12744-13055	GT	AGG
(GTG)	 AG	13213-13515	AT	AGA
add_exon() Sorry, pasa_asmbl_44165.p1 11570-11754-terminal-2 is invalid.
-recovered pasa_asmbl_44165.p1, terminal, 11570, 11754
-recovered pasa_asmbl_44165.p1, terminal, 13213, 13515
-recovered pasa_asmbl_44165.p1, internal, 11261, 11403
-recovered pasa_asmbl_44165.p1, internal, 11570, 11754
-recovered pasa_asmbl_44165.p1, internal, 12219, 12307
-recovered pasa_asmbl_44165.p1, internal, 12449, 12589
-recovered pasa_asmbl_44165.p1, internal, 12744, 13055
Valid prediction for CodingQuarry_transcript_52114-T1
Valid prediction for snap_scaffold_5-snap.1381-T1
Valid prediction for snap_scaffold_5-snap.1370-T1
Valid prediction for snap_scaffold_5-snap.1367-T1
Valid prediction for snap_scaffold_5-snap.1380-T1
Valid prediction for snap_scaffold_5-snap.1400-T1
Valid prediction for snap_scaffold_5-snap.1402-T1
Valid prediction for snap_scaffold_5-snap.1386-T1
Valid prediction for GlimmerHMM_glimmerT_12141-T1
Valid prediction for GlimmerHMM_glimmerT_12139-T1
Valid prediction for GlimmerHMM_glimmerT_12140-T1
Valid prediction for GlimmerHMM_glimmerT_12131-T1
Valid prediction for snap_scaffold_5-snap.1365-T1
Valid prediction for pasa_asmbl_44166.p1
Valid prediction for GlimmerHMM_glimmerT_12144-T1
Valid prediction for Augustus_model.g7983.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6868, rend_intergenic: 2221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65133, rend_intergenic: 57597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69981, rend_intergenic: 67753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73190, rend_intergenic: 70986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76884, rend_intergenic: 73861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92287, rend_intergenic: 90355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93230, rend_intergenic: 92290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111192, rend_intergenic: 93828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125385, rend_intergenic: 121928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136718, rend_intergenic: 125401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148800, rend_intergenic: 137100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167272, rend_intergenic: 158619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175675, rend_intergenic: 168329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179799, rend_intergenic: 176874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189485, rend_intergenic: 183929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196108, rend_intergenic: 194127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201489, rend_intergenic: 200592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202783, rend_intergenic: 202019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211669, rend_intergenic: 203259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216235, rend_intergenic: 213643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227351, rend_intergenic: 224306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 213732, rend_intergenic: 213729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238238
-exon list size: 564


building trellis

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80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 6868, rend_intergenic: 2221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65133, rend_intergenic: 57597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69981, rend_intergenic: 67753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73190, rend_intergenic: 70986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76884, rend_intergenic: 73861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92287, rend_intergenic: 90355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93230, rend_intergenic: 92290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111192, rend_intergenic: 93828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125385, rend_intergenic: 121928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136718, rend_intergenic: 125401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148800, rend_intergenic: 137100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167272, rend_intergenic: 158619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175675, rend_intergenic: 168329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179799, rend_intergenic: 176874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189485, rend_intergenic: 183929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196108, rend_intergenic: 194127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201489, rend_intergenic: 200592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202783, rend_intergenic: 202019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211669, rend_intergenic: 203259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216235, rend_intergenic: 213643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227351, rend_intergenic: 224306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 213732, rend_intergenic: 213729  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