-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_6452889-6626787

-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_52690-T1
Valid prediction for snap_scaffold_24-snap.1309-T1
Valid prediction for snap_scaffold_24-snap.1284-T1
Valid prediction for snap_scaffold_24-snap.1315-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g35080.t1
Valid prediction for pasa_asmbl_32321.p1
Valid prediction for GlimmerHMM_glimmerT_52684-T1
Valid prediction for Augustus_model.g35094.t1
Valid prediction for Augustus_model.g35086.t1
Couldn't classify 61567, 61770
Couldn't classify 63261, 63386
Sorry, prediction pasa_asmbl_32600.p1 fails validation.
(CTC)	 AT	61567-61770	GT	AGG
(CTG)	 AG	63261-63386	GT	ACG
-recovered pasa_asmbl_32600.p1, internal, 63261, 63386
Valid prediction for GlimmerHMM_glimmerT_52660-T1
Valid prediction for snap_scaffold_24-snap.1298-T1
Valid prediction for Augustus_model.g35090.t1
Valid prediction for GlimmerHMM_glimmerT_52693-T1
Valid prediction for GlimmerHMM_glimmerT_52662-T1
Valid prediction for GlimmerHMM_glimmerT_52679-T1
Valid prediction for GlimmerHMM_glimmerT_52689-T1
Valid prediction for snap_scaffold_24-snap.1295-T1
Valid prediction for GlimmerHMM_glimmerT_52686-T1
Valid prediction for HiQ_model.g35089.t1
Valid prediction for snap_scaffold_24-snap.1320-T1
Valid prediction for GlimmerHMM_glimmerT_52688-T1
Valid prediction for snap_scaffold_24-snap.1303-T1
Valid prediction for snap_scaffold_24-snap.1286-T1
Couldn't classify 74026, 74159
Sorry, prediction pasa_asmbl_32328.p2 fails validation.
(GCT)	 AG	74026-74159	GT	AGG
(AGG)	 AG	74252-74369	GT	AGG
(GTG)	 AG	74715-74785	GT	CTG
(GAA)	 AG	75032-75107	GT	AGG
(TAC)	 AG	75791-75853	GT	AGG
(GCG)	 AG	76189-76258	GT	AGG
(AAA)	 AG	77932-78014	GG	AAG
-recovered pasa_asmbl_32328.p2, terminal, 77932, 78014
-recovered pasa_asmbl_32328.p2, internal, 74026, 74159
-recovered pasa_asmbl_32328.p2, internal, 74252, 74369
-recovered pasa_asmbl_32328.p2, internal, 74715, 74785
-recovered pasa_asmbl_32328.p2, internal, 75032, 75107
-recovered pasa_asmbl_32328.p2, internal, 75791, 75853
-recovered pasa_asmbl_32328.p2, internal, 76189, 76258
Valid prediction for GlimmerHMM_glimmerT_52678-T1
Valid prediction for Augustus_model.g35082.t1
Valid prediction for snap_scaffold_24-snap.1322-T1
Valid prediction for snap_scaffold_24-snap.1304-T1
Couldn't classify 18999, 19242
Sorry, prediction pasa_asmbl_32326.p1 fails validation.
(GCC)	 CA	18999-19242	GT	AGG
(TCT)	 AG	19472-19592	GT	CTG
(AAA)	 AG	19857-20072	GT	AAG
(GAT)	 AG	20261-20353	GT	AGG
(GAT)	 AG	20457-20478	CT	AAC
-recovered pasa_asmbl_32326.p1, terminal, 20457, 20478
-recovered pasa_asmbl_32326.p1, internal, 19472, 19592
-recovered pasa_asmbl_32326.p1, internal, 19857, 20072
-recovered pasa_asmbl_32326.p1, internal, 20261, 20353
Valid prediction for snap_scaffold_24-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_52672-T1
Valid prediction for Augustus_model.g35100.t1
Couldn't classify 17373, 17420
Couldn't classify 18506, 18558
Sorry, prediction pasa_asmbl_32325.p2 fails validation.
(TCC)	 CC	17373-17420	GT	CGG
(GTG)	 AG	17844-18023	GT	AGG
(GAG)	 AG	18183-18294	GT	AGG
(GTC)	 AG	18506-18558	AG	TGA
-recovered pasa_asmbl_32325.p2, internal, 17844, 18023
-recovered pasa_asmbl_32325.p2, internal, 18183, 18294
Valid prediction for snap_scaffold_24-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_52659-T1
Valid prediction for snap_scaffold_24-snap.1291-T1
Valid prediction for snap_scaffold_24-snap.1299-T1
Valid prediction for GlimmerHMM_glimmerT_52666-T1
Valid prediction for HiQ_model.g35077.t1
Valid prediction for Augustus_model.g35096.t1
Valid prediction for snap_scaffold_24-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_52657-T1
Valid prediction for Augustus_model.g35079.t1
Valid prediction for GlimmerHMM_glimmerT_52674-T1
Valid prediction for Augustus_model.g35087.t1
Valid prediction for snap_scaffold_24-snap.1306-T1
Valid prediction for snap_scaffold_24-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_52691-T1
Valid prediction for CodingQuarry_transcript_37338-T1
Valid prediction for GlimmerHMM_glimmerT_52668-T1
Valid prediction for GlimmerHMM_glimmerT_52669-T1
Valid prediction for GlimmerHMM_glimmerT_52677-T1
Valid prediction for snap_scaffold_24-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_52675-T1
Valid prediction for snap_scaffold_24-snap.1302-T1
Valid prediction for GlimmerHMM_glimmerT_52685-T1
Valid prediction for pasa_asmbl_32331.p1
Valid prediction for snap_scaffold_24-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_52673-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_24-snap.1301-T1
Valid prediction for Augustus_model.g35088.t1
Valid prediction for Augustus_model.g35098.t1
Valid prediction for snap_scaffold_24-snap.1314-T1
Valid prediction for Augustus_model.g35085.t1
Valid prediction for Augustus_model.g35091.t1
Valid prediction for GlimmerHMM_glimmerT_52661-T1
Valid prediction for snap_scaffold_24-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_52658-T1
Valid prediction for snap_scaffold_24-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_52683-T1
Valid prediction for Augustus_model.g35093.t1
Valid prediction for GlimmerHMM_glimmerT_52692-T1
Valid prediction for Augustus_model.g35078.t1
Valid prediction for GlimmerHMM_glimmerT_52671-T1
Valid prediction for GlimmerHMM_glimmerT_52665-T1
Valid prediction for Augustus_model.g35099.t1
Valid prediction for snap_scaffold_24-snap.1292-T1
Couldn't classify 93075, 93272
Couldn't classify 94364, 94476
Sorry, prediction pasa_asmbl_32961.p1 fails validation.
(CGG)	 AA	93075-93272	GT	CGG
(CTG)	 AG	93728-93836	GT	AGG
(GCT)	 AG	94364-94476	GA	GTG
-recovered pasa_asmbl_32961.p1, internal, 93728, 93836
Valid prediction for Augustus_model.g35097.t1
Valid prediction for GlimmerHMM_glimmerT_52687-T1
Valid prediction for Augustus_model.g35092.t1
Valid prediction for snap_scaffold_24-snap.1289-T1
Valid prediction for snap_scaffold_24-snap.1300-T1
Valid prediction for Augustus_model.g35083.t1
Valid prediction for snap_scaffold_24-snap.1319-T1
Valid prediction for snap_scaffold_24-snap.1310-T1
Valid prediction for Augustus_model.g35084.t1
Valid prediction for GlimmerHMM_glimmerT_52680-T1
Valid prediction for GlimmerHMM_glimmerT_52670-T1
Valid prediction for snap_scaffold_24-snap.1290-T1
Valid prediction for snap_scaffold_24-snap.1311-T1
Valid prediction for snap_scaffold_24-snap.1297-T1
Valid prediction for snap_scaffold_24-snap.1323-T1
Valid prediction for snap_scaffold_24-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_52664-T1
Valid prediction for Augustus_model.g35101.t1
Valid prediction for snap_scaffold_24-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_52663-T1
Valid prediction for GlimmerHMM_glimmerT_52667-T1
Valid prediction for GlimmerHMM_glimmerT_52682-T1
Valid prediction for GlimmerHMM_glimmerT_52681-T1
Valid prediction for snap_scaffold_24-snap.1308-T1
Valid prediction for GlimmerHMM_glimmerT_52676-T1
Valid prediction for snap_scaffold_24-snap.1287-T1
Valid prediction for snap_scaffold_24-snap.1285-T1
Valid prediction for snap_scaffold_24-snap.1313-T1
Valid prediction for snap_scaffold_24-snap.1305-T1
Valid prediction for Augustus_model.g35081.t1
Valid prediction for snap_scaffold_24-snap.1326-T1
Valid prediction for snap_scaffold_24-snap.1317-T1
Valid prediction for Augustus_model.g35095.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20027, rend_intergenic: 17352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44796, rend_intergenic: 44737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47840, rend_intergenic: 44895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51115, rend_intergenic: 49057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58171, rend_intergenic: 51924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61896, rend_intergenic: 60420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65869, rend_intergenic: 63216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78014, rend_intergenic: 67763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99663, rend_intergenic: 94584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107615, rend_intergenic: 104602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116447, rend_intergenic: 111107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122436, rend_intergenic: 116677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131549, rend_intergenic: 122683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133507, rend_intergenic: 131672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139063, rend_intergenic: 134040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149916, rend_intergenic: 139143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152061, rend_intergenic: 150466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154224, rend_intergenic: 152336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164700, rend_intergenic: 160696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169108, rend_intergenic: 167097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173899
-exon list size: 445


building trellis

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28.9    
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29.3    
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30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
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36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
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44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
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45.6    
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46.1    
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47.4    
47.7    
47.9    
48.1    
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49.0    
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49.4    
49.7    
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50.6    
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91.3    
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91.9    
92.2    
92.4    
92.6    
92.8    
93.1    
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93.5    
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94.2    
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96.6    
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97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 20027, rend_intergenic: 17352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44796, rend_intergenic: 44737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47840, rend_intergenic: 44895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51115, rend_intergenic: 49057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58171, rend_intergenic: 51924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61896, rend_intergenic: 60420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65869, rend_intergenic: 63216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78014, rend_intergenic: 67763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99663, rend_intergenic: 94584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107615, rend_intergenic: 104602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116447, rend_intergenic: 111107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122436, rend_intergenic: 116677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131549, rend_intergenic: 122683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133507, rend_intergenic: 131672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139063, rend_intergenic: 134040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149916, rend_intergenic: 139143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152061, rend_intergenic: 150466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154224, rend_intergenic: 152336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164700, rend_intergenic: 160696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169108, rend_intergenic: 167097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support