-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_10130646-10439008

-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 GlimmerHMM_glimmerT_28394-T1
Valid prediction for Augustus_model.g18955.t1
Valid prediction for GeneMark_model.49019_t
Valid prediction for snap_scaffold_11-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_28372-T1
Valid prediction for GeneMark_model.49026_t
Valid prediction for HiQ_model.g18937.t1
Valid prediction for GlimmerHMM_glimmerT_28397-T1
Valid prediction for GeneMark_model.49000_t
Valid prediction for GeneMark_model.49014_t
Valid prediction for HiQ_model.g18953.t1
Valid prediction for Augustus_model.g18954.t1
Valid prediction for snap_scaffold_11-snap.2325-T1
Valid prediction for GeneMark_model.49018_t
Couldn't classify 142232, 142366
Sorry, prediction pasa_asmbl_5895.p1 fails validation.
(GTG)	 GT	142232-142366	GT	AGG
(ATG)	 AG	142610-142788	GT	AAG
(ATT)	 AG	143010-143115	TG	GAT
-recovered pasa_asmbl_5895.p1, initial, 142610, 142788
-recovered pasa_asmbl_5895.p1, terminal, 143010, 143115
-recovered pasa_asmbl_5895.p1, internal, 142610, 142788
Valid prediction for snap_scaffold_11-snap.2327-T1
Valid prediction for Augustus_model.g18943.t1
Valid prediction for Augustus_model.g18934.t1
Couldn't classify 258636, 258766
Couldn't classify 259637, 259727
Sorry, prediction pasa_asmbl_5903.p1 fails validation.
(GAG)	 AG	258636-258766	GT	AAG
(GAA)	 AG	259024-259147	GT	GGG
(GCG)	 AG	259237-259349	GT	AGG
(TTC)	 AG	259637-259727	GT	CGG
-recovered pasa_asmbl_5903.p1, internal, 258636, 258766
-recovered pasa_asmbl_5903.p1, internal, 259024, 259147
-recovered pasa_asmbl_5903.p1, internal, 259237, 259349
-recovered pasa_asmbl_5903.p1, internal, 259637, 259727
Valid prediction for GeneMark_model.48999_t
Valid prediction for GeneMark_model.49007_t
Valid prediction for GlimmerHMM_glimmerT_28376-T1
Valid prediction for GeneMark_model.49016_t
Valid prediction for GlimmerHMM_glimmerT_28390-T1
Valid prediction for snap_scaffold_11-snap.2316-T1
Valid prediction for GeneMark_model.49005_t
Valid prediction for GlimmerHMM_glimmerT_28393-T1
Couldn't classify 264635, 264833
Sorry, prediction pasa_asmbl_5909.p1 fails validation.
(CAG)	 TC	264635-264833	GT	GGG
(GAG)	 AG	265119-265322	GT	GGG
(GCT)	 AG	265793-265969	GT	TGG
(CGG)	 AG	266141-266278	GT	AGG
(CTT)	 AG	266762-266998	GT	AGG
(ACT)	 AG	267198-267351	GT	AAG
(TTG)	 AG	267603-267760	GT	CTG
(CTC)	 AG	268006-268237	GT	AGG
(TGA)	 AG	268419-268636	GT	ATG
(ACA)	 AG	268838-269089	GT	TGG
(GCT)	 AG	269393-269596	GT	AGG
(AGC)	 AG	269913-270107	GT	GGG
(ATT)	 AG	270360-270494	GT	AGG
(CAC)	 AG	270793-270958	GT	AGG
(GCT)	 AG	271482-271698	AT	GAA
-recovered pasa_asmbl_5909.p1, terminal, 271482, 271698
-recovered pasa_asmbl_5909.p1, internal, 265119, 265322
-recovered pasa_asmbl_5909.p1, internal, 265793, 265969
-recovered pasa_asmbl_5909.p1, internal, 266141, 266278
-recovered pasa_asmbl_5909.p1, internal, 266762, 266998
-recovered pasa_asmbl_5909.p1, internal, 267198, 267351
-recovered pasa_asmbl_5909.p1, internal, 267603, 267760
-recovered pasa_asmbl_5909.p1, internal, 268006, 268237
-recovered pasa_asmbl_5909.p1, internal, 268419, 268636
-recovered pasa_asmbl_5909.p1, internal, 268838, 269089
-recovered pasa_asmbl_5909.p1, internal, 269393, 269596
-recovered pasa_asmbl_5909.p1, internal, 269913, 270107
-recovered pasa_asmbl_5909.p1, internal, 270360, 270494
-recovered pasa_asmbl_5909.p1, internal, 270793, 270958
Valid prediction for GlimmerHMM_glimmerT_28379-T1
Valid prediction for GlimmerHMM_glimmerT_28381-T1
Valid prediction for pasa_asmbl_5888.p1
Valid prediction for GeneMark_model.49001_t
Valid prediction for GlimmerHMM_glimmerT_28380-T1
Valid prediction for snap_scaffold_11-snap.2314-T1
Valid prediction for snap_scaffold_11-snap.2321-T1
Couldn't classify 170962, 170994
Sorry, prediction pasa_asmbl_5898.p1 fails validation.
(AAG)	 TC	170962-170994	GT	AAG
(GTT)	 AG	171751-171852	GT	AGG
(ATA)	 AG	172110-172251	GT	AGG
(GAG)	 AG	172461-172548	GT	TGG
(GGC)	 AG	173361-173580	GT	AAG
(GTA)	 AG	173694-173954	GT	TGG
(AGA)	 AG	174054-174186	GT	AGG
(GCT)	 AG	174312-174450	GT	TGG
(CAT)	 AG	174617-174650	GG	AAG
-recovered pasa_asmbl_5898.p1, terminal, 174617, 174650
-recovered pasa_asmbl_5898.p1, internal, 171751, 171852
-recovered pasa_asmbl_5898.p1, internal, 172110, 172251
-recovered pasa_asmbl_5898.p1, internal, 172461, 172548
-recovered pasa_asmbl_5898.p1, internal, 173361, 173580
-recovered pasa_asmbl_5898.p1, internal, 173694, 173954
-recovered pasa_asmbl_5898.p1, internal, 174054, 174186
-recovered pasa_asmbl_5898.p1, internal, 174312, 174450
Valid prediction for Augustus_model.g18933.t1
Couldn't classify 254842, 254959
Couldn't classify 256531, 256554
Sorry, prediction pasa_asmbl_6294.p1 fails validation.
(CGT)	 CT	254842-254959	GT	AGG
(CCG)	 AG	255161-255372	GT	AGG
(GCC)	 AG	256531-256554	AC	ACA
-recovered pasa_asmbl_6294.p1, internal, 255161, 255372
Valid prediction for GlimmerHMM_glimmerT_28386-T1
Valid prediction for snap_scaffold_11-snap.2297-T1
Valid prediction for snap_scaffold_11-snap.2308-T1
Valid prediction for snap_scaffold_11-snap.2313-T1
Valid prediction for snap_scaffold_11-snap.2330-T1
Valid prediction for GeneMark_model.49009_t
Valid prediction for pasa_asmbl_5902.p1
Valid prediction for CodingQuarry_transcript_8200-T1
Valid prediction for GeneMark_model.49010_t
Valid prediction for GeneMark_model.48998_t
Valid prediction for GlimmerHMM_glimmerT_28388-T1
Couldn't classify 262888, 263027
Couldn't classify 263979, 264055
Sorry, prediction pasa_asmbl_5904.p1 fails validation.
(ACC)	 CC	262888-263027	GT	AGG
(GAG)	 AG	263294-263474	GT	AGG
(CTC)	 AG	263628-263808	GT	AGG
(CCA)	 AG	263979-264055	AT	AGA
-recovered pasa_asmbl_5904.p1, internal, 263294, 263474
-recovered pasa_asmbl_5904.p1, internal, 263628, 263808
Valid prediction for snap_scaffold_11-snap.2326-T1
Valid prediction for Augustus_model.g18941.t1
Valid prediction for Augustus_model.g18936.t1
Valid prediction for snap_scaffold_11-snap.2303-T1
Valid prediction for snap_scaffold_11-snap.2328-T1
Valid prediction for GlimmerHMM_glimmerT_28392-T1
Valid prediction for GeneMark_model.48994_t
Valid prediction for snap_scaffold_11-snap.2302-T1
Valid prediction for snap_scaffold_11-snap.2300-T1
Valid prediction for snap_scaffold_11-snap.2322-T1
Valid prediction for Augustus_model.g18940.t1
Valid prediction for snap_scaffold_11-snap.2333-T1
Valid prediction for snap_scaffold_11-snap.2334-T1
Valid prediction for CodingQuarry_transcript_8193-T1
Valid prediction for GlimmerHMM_glimmerT_28395-T1
Valid prediction for snap_scaffold_11-snap.2331-T1
Valid prediction for snap_scaffold_11-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_28375-T1
Valid prediction for snap_scaffold_11-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_28391-T1
Valid prediction for Augustus_model.g18952.t1
Valid prediction for HiQ_model.g18948.t1
Valid prediction for GlimmerHMM_glimmerT_28396-T1
Valid prediction for GeneMark_model.49020_t
Valid prediction for GlimmerHMM_glimmerT_28371-T1
Couldn't classify 189227, 189253
Sorry, prediction pasa_asmbl_5899.p1 fails validation.
(AAA)	 AG	189227-189253	GT	CGG
(GAT)	 AG	190064-190167	GT	AGG
(ATG)	 AG	191092-191187	GT	GCG
(CCT)	 AG	191426-191489	GT	AGG
(GAT)	 AG	191609-191722	GT	CGG
(CTG)	 AG	191809-191948	GT	GGG
(GAG)	 AG	192747-192861	AA	GAA
add_exon() Sorry, pasa_asmbl_5899.p1 191092-191187-initial-1 is invalid.
-recovered pasa_asmbl_5899.p1, initial, 191092, 191187
-recovered pasa_asmbl_5899.p1, terminal, 192747, 192861
-recovered pasa_asmbl_5899.p1, internal, 189227, 189253
-recovered pasa_asmbl_5899.p1, internal, 190064, 190167
-recovered pasa_asmbl_5899.p1, internal, 191092, 191187
-recovered pasa_asmbl_5899.p1, internal, 191426, 191489
-recovered pasa_asmbl_5899.p1, internal, 191609, 191722
-recovered pasa_asmbl_5899.p1, internal, 191809, 191948
Valid prediction for GeneMark_model.48996_t
Valid prediction for snap_scaffold_11-snap.2332-T1
Couldn't classify 37564, 37671
Sorry, prediction pasa_asmbl_5886.p1 fails validation.
(ATG)	 AC	35864-37234	GT	AGG
(GGT)	 AG	37564-37671	CA	AGC
-recovered pasa_asmbl_5886.p1, initial, 35864, 37234
Valid prediction for GeneMark_model.48991_t
Valid prediction for GeneMark_model.49003_t
Valid prediction for pasa_asmbl_5889.p1
Valid prediction for HiQ_model.g18951.t1
Valid prediction for CodingQuarry_transcript_8199-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_11-snap.2310-T1
Valid prediction for Augustus_model.g18938.t1
Valid prediction for snap_scaffold_11-snap.2335-T1
Valid prediction for CodingQuarry_transcript_8195-T1
Valid prediction for GeneMark_model.49025_t
Valid prediction for GeneMark_model.48995_t
Valid prediction for snap_scaffold_11-snap.2338-T1
Valid prediction for GlimmerHMM_glimmerT_28377-T1
Valid prediction for GlimmerHMM_glimmerT_28373-T1
Valid prediction for GeneMark_model.49008_t
Valid prediction for snap_scaffold_11-snap.2315-T1
Valid prediction for GeneMark_model.48997_t
Valid prediction for snap_scaffold_11-snap.2337-T1
Valid prediction for GlimmerHMM_glimmerT_28389-T1
Valid prediction for GeneMark_model.49002_t
Valid prediction for snap_scaffold_11-snap.2320-T1
Valid prediction for snap_scaffold_11-snap.2323-T1
Valid prediction for CodingQuarry_transcript_8192-T1
Valid prediction for GeneMark_model.48992_t
Valid prediction for Augustus_model.g18946.t1
Valid prediction for Augustus_model.g18956.t1
Valid prediction for Augustus_model.g18932.t1
Valid prediction for snap_scaffold_11-snap.2306-T1
Valid prediction for snap_scaffold_11-snap.2304-T1
Valid prediction for GeneMark_model.49022_t
Valid prediction for pasa_asmbl_6973.p1
Valid prediction for GlimmerHMM_glimmerT_28387-T1
Valid prediction for GlimmerHMM_glimmerT_28374-T1
Valid prediction for GlimmerHMM_glimmerT_28383-T1
Valid prediction for Augustus_model.g18957.t1
Valid prediction for snap_scaffold_11-snap.2318-T1
Valid prediction for CodingQuarry_transcript_8198-T1
Valid prediction for snap_scaffold_11-snap.2309-T1
Valid prediction for snap_scaffold_11-snap.2319-T1
Valid prediction for pasa_asmbl_6970.p1
Couldn't classify 290419, 290588
Couldn't classify 293301, 293439
Sorry, prediction pasa_asmbl_6964.p1 fails validation.
(AGT)	 TC	290419-290588	GT	TGG
(GGT)	 AG	291776-291943	GT	AAG
(GAG)	 AG	293301-293439	GT	GGG
-recovered pasa_asmbl_6964.p1, internal, 291776, 291943
-recovered pasa_asmbl_6964.p1, internal, 293301, 293439
Valid prediction for HiQ_model.g18950.t1
Valid prediction for Augustus_model.g18939.t1
Valid prediction for snap_scaffold_11-snap.2311-T1
Valid prediction for snap_scaffold_11-snap.2307-T1
Couldn't classify 276996, 277125
Couldn't classify 278692, 278713
Sorry, prediction pasa_asmbl_6966.p1 fails validation.
(CAC)	 TC	276996-277125	GT	AAG
(CCA)	 AG	278265-278421	GT	TGG
(GAC)	 AG	278692-278713	CT	GGC
-recovered pasa_asmbl_6966.p1, internal, 278265, 278421
Valid prediction for Augustus_model.g18947.t1
Valid prediction for GeneMark_model.48990_t
Valid prediction for snap_scaffold_11-snap.2312-T1
Valid prediction for Augustus_model.g18931.t1
Valid prediction for snap_scaffold_11-snap.2301-T1
Valid prediction for pasa_asmbl_6972.p1
Valid prediction for GeneMark_model.49024_t
Valid prediction for CodingQuarry_transcript_8197-T1
Valid prediction for GeneMark_model.49011_t
Valid prediction for snap_scaffold_11-snap.2336-T1
Valid prediction for Augustus_model.g18945.t1
Valid prediction for Augustus_model.g18935.t1
Valid prediction for HiQ_model.g18942.t1
Valid prediction for GeneMark_model.49015_t
Valid prediction for GlimmerHMM_glimmerT_28385-T1
Valid prediction for Augustus_model.g18944.t1
Valid prediction for snap_scaffold_11-snap.2299-T1
Valid prediction for GeneMark_model.49006_t
Valid prediction for Augustus_model.g18930.t1
Valid prediction for GeneMark_model.48993_t
Valid prediction for CodingQuarry_transcript_8196-T1
Valid prediction for GlimmerHMM_glimmerT_28398-T1
Valid prediction for snap_scaffold_11-snap.2296-T1
Valid prediction for pasa_asmbl_6971.p1
Valid prediction for snap_scaffold_11-snap.2317-T1
Valid prediction for GeneMark_model.49004_t
Valid prediction for snap_scaffold_11-snap.2298-T1
Valid prediction for GeneMark_model.49023_t
Valid prediction for GlimmerHMM_glimmerT_28384-T1
Valid prediction for HiQ_model.g18949.t1
Valid prediction for CodingQuarry_transcript_8194-T1
Valid prediction for GeneMark_model.49013_t
Valid prediction for GlimmerHMM_glimmerT_28382-T1
Valid prediction for GlimmerHMM_glimmerT_28378-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21821, rend_intergenic: 14889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24472, rend_intergenic: 21831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31048, rend_intergenic: 24651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35122, rend_intergenic: 32613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45432, rend_intergenic: 36916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47536, rend_intergenic: 45586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 308363
-exon list size: 621


building trellis

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65.3    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 21821, rend_intergenic: 14889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24472, rend_intergenic: 21831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31048, rend_intergenic: 24651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35122, rend_intergenic: 32613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45432, rend_intergenic: 36916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47536, rend_intergenic: 45586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14063
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12081
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support