-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_5681187-5853506

-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_26-snap.1295-T1
Couldn't classify 156113, 156676
Couldn't classify 158129, 158252
Sorry, prediction pasa_asmbl_35042.p1 fails validation.
(TAC)	 AC	156113-156676	GT	AGG
(CTG)	 AG	156892-157099	GT	GAG
(ACT)	 AG	157518-157591	GT	GGG
(GAG)	 AG	157792-157967	GT	AAG
(ACA)	 AG	158129-158252	GT	CCG
-recovered pasa_asmbl_35042.p1, internal, 156892, 157099
-recovered pasa_asmbl_35042.p1, internal, 157518, 157591
-recovered pasa_asmbl_35042.p1, internal, 157792, 157967
-recovered pasa_asmbl_35042.p1, internal, 158129, 158252
Valid prediction for snap_scaffold_26-snap.1276-T1
Valid prediction for snap_scaffold_26-snap.1296-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g36949.t1
Valid prediction for snap_scaffold_26-snap.1303-T1
Valid prediction for Augustus_model.g36956.t1
Valid prediction for snap_scaffold_26-snap.1307-T1
Valid prediction for snap_scaffold_26-snap.1308-T1
Valid prediction for snap_scaffold_26-snap.1302-T1
Couldn't classify 141647, 141670
Sorry, prediction pasa_asmbl_35334.p1 fails validation.
(TCC)	 AG	141647-141670	GT	AGG
(AAC)	 AG	144103-144224	GT	GGG
(GAA)	 AG	144362-144527	GT	AGG
(AGA)	 AG	144704-144823	GT	AGG
(GGC)	 AG	145067-145142	GT	ATG
(GTT)	 AG	145246-145350	GT	AGG
(AGG)	 AG	145484-145558	GT	GAG
(ATC)	 AG	145885-145982	GT	AGG
(GAG)	 AG	146080-146202	GT	AGG
(CTG)	 AG	148139-148198	GT	GGG
(ATT)	 AG	148470-148579	GT	AAG
(ACG)	 AG	148697-148836	GT	CAG
(ATA)	 AG	148953-149087	GT	CGG
(CCC)	 AG	149288-149393	GT	AGG
(GAT)	 AG	149725-149887	GT	AGG
(GTC)	 AG	149993-150082	CT	AAC
add_exon() Sorry, pasa_asmbl_35334.p1 145484-145558-terminal-1 is invalid.
-recovered pasa_asmbl_35334.p1, terminal, 145484, 145558
-recovered pasa_asmbl_35334.p1, terminal, 149993, 150082
-recovered pasa_asmbl_35334.p1, internal, 141647, 141670
-recovered pasa_asmbl_35334.p1, internal, 144103, 144224
-recovered pasa_asmbl_35334.p1, internal, 144362, 144527
-recovered pasa_asmbl_35334.p1, internal, 144704, 144823
-recovered pasa_asmbl_35334.p1, internal, 145067, 145142
-recovered pasa_asmbl_35334.p1, internal, 145246, 145350
-recovered pasa_asmbl_35334.p1, internal, 145484, 145558
-recovered pasa_asmbl_35334.p1, internal, 145885, 145982
-recovered pasa_asmbl_35334.p1, internal, 146080, 146202
-recovered pasa_asmbl_35334.p1, internal, 148139, 148198
-recovered pasa_asmbl_35334.p1, internal, 148470, 148579
-recovered pasa_asmbl_35334.p1, internal, 148697, 148836
-recovered pasa_asmbl_35334.p1, internal, 148953, 149087
-recovered pasa_asmbl_35334.p1, internal, 149288, 149393
-recovered pasa_asmbl_35334.p1, internal, 149725, 149887
Valid prediction for snap_scaffold_26-snap.1304-T1
Valid prediction for GlimmerHMM_glimmerT_55768-T1
Valid prediction for snap_scaffold_26-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_55754-T1
Valid prediction for snap_scaffold_26-snap.1298-T1
Valid prediction for Augustus_model.g36958.t1
Valid prediction for pasa_asmbl_35036.p1
Valid prediction for snap_scaffold_26-snap.1292-T1
Couldn't classify 169641, 170012
Sorry, prediction pasa_asmbl_35046.p1 fails validation.
(ATG)	 CC	169641-170012	AC	GGA
Valid prediction for snap_scaffold_26-snap.1309-T1
Valid prediction for snap_scaffold_26-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_55751-T1
Valid prediction for GlimmerHMM_glimmerT_55762-T1
Valid prediction for CodingQuarry_transcript_40367-T1
Valid prediction for pasa_asmbl_35040.p1
Couldn't classify 127311, 127856
Sorry, prediction pasa_asmbl_35041.p1 fails validation.
(ATG)	 GC	127311-127856	AT	AGA
Valid prediction for GlimmerHMM_glimmerT_55743-T1
Valid prediction for GlimmerHMM_glimmerT_55752-T1
Valid prediction for snap_scaffold_26-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_55757-T1
Couldn't classify 63536, 63583
Sorry, prediction pasa_asmbl_35035.p1 fails validation.
(CAT)	 GG	63536-63583	GT	TGG
(GCT)	 AG	64770-64845	GT	GGG
(GTC)	 AG	65158-65262	GC	GGG
(GTG)	 AG	65398-65480	GT	GAG
-recovered pasa_asmbl_35035.p1, terminal, 65398, 65480
-recovered pasa_asmbl_35035.p1, internal, 64770, 64845
-recovered pasa_asmbl_35035.p1, internal, 65158, 65262
-recovered pasa_asmbl_35035.p1, internal, 65398, 65480
Valid prediction for Augustus_model.g36955.t1
Valid prediction for GlimmerHMM_glimmerT_55737-T1
Valid prediction for GlimmerHMM_glimmerT_55758-T1
Valid prediction for Augustus_model.g36937.t1
Valid prediction for snap_scaffold_26-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_55760-T1
Couldn't classify 160881, 161020
Couldn't classify 162149, 162265
Sorry, prediction pasa_asmbl_35043.p2 fails validation.
(GTA)	 CA	160881-161020	GT	CGG
(GGA)	 AG	161118-161220	GT	AGG
(AAC)	 AG	162149-162265	GC	AGG
-recovered pasa_asmbl_35043.p2, internal, 161118, 161220
-recovered pasa_asmbl_35043.p2, internal, 162149, 162265
Valid prediction for GlimmerHMM_glimmerT_55745-T1
Valid prediction for GlimmerHMM_glimmerT_55765-T1
Valid prediction for CodingQuarry_transcript_40370-T1
Valid prediction for HiQ_model.g36944.t1
Valid prediction for Augustus_model.g36954.t1
Valid prediction for GlimmerHMM_glimmerT_55759-T1
Valid prediction for GlimmerHMM_glimmerT_55735-T1
Valid prediction for Augustus_model.g36959.t1
Valid prediction for Augustus_model.g36942.t1
Valid prediction for GlimmerHMM_glimmerT_55753-T1
Valid prediction for pasa_asmbl_35039.p1
Valid prediction for snap_scaffold_26-snap.1299-T1
Valid prediction for snap_scaffold_26-snap.1306-T1
Valid prediction for snap_scaffold_26-snap.1291-T1
Valid prediction for snap_scaffold_26-snap.1281-T1
Valid prediction for Augustus_model.g36945.t1
Valid prediction for HiQ_model.g36943.t1
Valid prediction for Augustus_model.g36951.t1
Valid prediction for GlimmerHMM_glimmerT_55767-T1
Valid prediction for GlimmerHMM_glimmerT_55741-T1
Valid prediction for Augustus_model.g36957.t1
Valid prediction for snap_scaffold_26-snap.1273-T1
Valid prediction for snap_scaffold_26-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_55738-T1
Valid prediction for CodingQuarry_transcript_40366-T1
Valid prediction for GlimmerHMM_glimmerT_55770-T1
Valid prediction for GlimmerHMM_glimmerT_55739-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 GlimmerHMM_glimmerT_55755-T1
Valid prediction for Augustus_model.g36941.t1
Valid prediction for HiQ_model.g36952.t1
Valid prediction for GlimmerHMM_glimmerT_55746-T1
Valid prediction for GlimmerHMM_glimmerT_55756-T1
Valid prediction for snap_scaffold_26-snap.1274-T1
Valid prediction for snap_scaffold_26-snap.1293-T1
Valid prediction for snap_scaffold_26-snap.1285-T1
Valid prediction for HiQ_model.g36946.t1
Valid prediction for GlimmerHMM_glimmerT_55750-T1
Valid prediction for GlimmerHMM_glimmerT_55764-T1
Valid prediction for GlimmerHMM_glimmerT_55740-T1
Valid prediction for snap_scaffold_26-snap.1300-T1
Couldn't classify 62557, 62622
Sorry, prediction pasa_asmbl_35626.p1 fails validation.
(ATG)	 CC	58483-58600	GT	CGG
(AGT)	 AG	59185-59202	GT	AGG
(GGA)	 AG	59285-59367	GT	TTG
(GTC)	 AG	61033-61137	GT	AGG
(GAG)	 AG	62557-62622	AG	ACA
-recovered pasa_asmbl_35626.p1, initial, 58483, 58600
-recovered pasa_asmbl_35626.p1, internal, 59185, 59202
-recovered pasa_asmbl_35626.p1, internal, 59285, 59367
-recovered pasa_asmbl_35626.p1, internal, 61033, 61137
Valid prediction for GlimmerHMM_glimmerT_55742-T1
Valid prediction for CodingQuarry_transcript_40369-T1
Valid prediction for pasa_asmbl_35621.p1
Couldn't classify 50003, 50128
Couldn't classify 55891, 55959
Sorry, prediction pasa_asmbl_35875.p1 fails validation.
(AAG)	 AG	50003-50128	GT	AGG
(TTC)	 AG	52049-52198	GT	TGG
(CAG)	 AG	53426-53554	GT	TGG
(GTG)	 AG	53748-53837	GT	AGG
(GAA)	 AG	54517-54603	GT	AGG
(GAC)	 AG	54851-54922	GT	AGG
(ATC)	 AG	55142-55227	GT	AGG
(GGA)	 AG	55542-55587	GT	AGG
(AAA)	 AG	55891-55959	CG	GGC
-recovered pasa_asmbl_35875.p1, internal, 50003, 50128
-recovered pasa_asmbl_35875.p1, internal, 52049, 52198
-recovered pasa_asmbl_35875.p1, internal, 53426, 53554
-recovered pasa_asmbl_35875.p1, internal, 53748, 53837
-recovered pasa_asmbl_35875.p1, internal, 54517, 54603
-recovered pasa_asmbl_35875.p1, internal, 54851, 54922
-recovered pasa_asmbl_35875.p1, internal, 55142, 55227
-recovered pasa_asmbl_35875.p1, internal, 55542, 55587
Valid prediction for snap_scaffold_26-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_55763-T1
Valid prediction for snap_scaffold_26-snap.1284-T1
Valid prediction for snap_scaffold_26-snap.1272-T1
Valid prediction for snap_scaffold_26-snap.1287-T1
Valid prediction for Augustus_model.g36947.t1
Valid prediction for Augustus_model.g36953.t1
Valid prediction for GlimmerHMM_glimmerT_55761-T1
Valid prediction for Augustus_model.g36935.t1
Valid prediction for GlimmerHMM_glimmerT_55747-T1
Valid prediction for GlimmerHMM_glimmerT_55749-T1
Valid prediction for GlimmerHMM_glimmerT_55748-T1
Valid prediction for GlimmerHMM_glimmerT_55769-T1
Valid prediction for snap_scaffold_26-snap.1280-T1
Valid prediction for Augustus_model.g36948.t1
Valid prediction for snap_scaffold_26-snap.1283-T1
Valid prediction for snap_scaffold_26-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_55744-T1
Valid prediction for Augustus_model.g36940.t1
Valid prediction for snap_scaffold_26-snap.1282-T1
Valid prediction for Augustus_model.g36950.t1
Couldn't classify 49422, 49487
Sorry, prediction pasa_asmbl_35629.p1 fails validation.
(ATG)	 CC	47742-47795	GT	GGG
(GTG)	 AG	48110-48220	GT	AAG
(CTC)	 AG	48497-48581	GT	AAG
(GTT)	 AG	49084-49247	GT	AGG
(ATT)	 AG	49422-49487	GA	TGG
-recovered pasa_asmbl_35629.p1, initial, 47742, 47795
-recovered pasa_asmbl_35629.p1, internal, 48110, 48220
-recovered pasa_asmbl_35629.p1, internal, 48497, 48581
-recovered pasa_asmbl_35629.p1, internal, 49084, 49247
Valid prediction for pasa_asmbl_35619.p1
Valid prediction for Augustus_model.g36938.t1
Valid prediction for snap_scaffold_26-snap.1279-T1
Valid prediction for snap_scaffold_26-snap.1278-T1
Couldn't classify 70444, 70548
Sorry, prediction pasa_asmbl_35622.p1 fails validation.
(TGC)	 GC	70444-70548	GT	CTG
(GGG)	 AG	70678-71142	GT	GGG
(ATG)	 AG	72629-72717	GT	GTG
(GTA)	 AG	72810-72912	GT	AGG
(TCC)	 AG	72993-73124	GT	CCG
(GTC)	 AG	73213-73332	GT	AGG
(GGT)	 AG	73420-73638	GT	AGG
(TCG)	 AG	73805-74140	GT	TGG
(ACT)	 AG	74229-74449	GT	TGG
(CAT)	 AG	74542-74744	GT	ATG
(GCT)	 AG	74860-74945	GT	TGG
(AGC)	 AG	75027-75160	GT	AGG
(TCT)	 AG	75287-75404	GT	CCG
(GTC)	 AG	75583-75703	GT	TGG
(CCA)	 AG	77888-77901	GC	AAG
-recovered pasa_asmbl_35622.p1, initial, 72629, 72717
-recovered pasa_asmbl_35622.p1, terminal, 77888, 77901
-recovered pasa_asmbl_35622.p1, internal, 70678, 71142
-recovered pasa_asmbl_35622.p1, internal, 72629, 72717
-recovered pasa_asmbl_35622.p1, internal, 72810, 72912
-recovered pasa_asmbl_35622.p1, internal, 72993, 73124
-recovered pasa_asmbl_35622.p1, internal, 73213, 73332
-recovered pasa_asmbl_35622.p1, internal, 73420, 73638
-recovered pasa_asmbl_35622.p1, internal, 73805, 74140
-recovered pasa_asmbl_35622.p1, internal, 74229, 74449
-recovered pasa_asmbl_35622.p1, internal, 74542, 74744
-recovered pasa_asmbl_35622.p1, internal, 74860, 74945
-recovered pasa_asmbl_35622.p1, internal, 75027, 75160
-recovered pasa_asmbl_35622.p1, internal, 75287, 75404
-recovered pasa_asmbl_35622.p1, internal, 75583, 75703
-recovered pasa_asmbl_35622.p1, internal, 77888, 77901
Valid prediction for GlimmerHMM_glimmerT_55736-T1
Valid prediction for CodingQuarry_transcript_40368-T1
Valid prediction for snap_scaffold_26-snap.1297-T1
Valid prediction for Augustus_model.g36936.t1
Valid prediction for snap_scaffold_26-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_55766-T1
Valid prediction for snap_scaffold_26-snap.1288-T1
Valid prediction for Augustus_model.g36939.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13960, rend_intergenic: 9857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17352, rend_intergenic: 14292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33692, rend_intergenic: 31119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36035, rend_intergenic: 35046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105502, rend_intergenic: 98124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125699, rend_intergenic: 123556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 7020, rend_intergenic: 7017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172320
-exon list size: 427


building trellis

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93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13960, rend_intergenic: 9857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17352, rend_intergenic: 14292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33692, rend_intergenic: 31119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36035, rend_intergenic: 35046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105502, rend_intergenic: 98124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125699, rend_intergenic: 123556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 7020, rend_intergenic: 7017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support