-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_309570-522955

-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_27-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_56536-T1
Valid prediction for snap_scaffold_27-snap.89-T1
Valid prediction for GlimmerHMM_glimmerT_56526-T1
Valid prediction for snap_scaffold_27-snap.95-T1
Valid prediction for snap_scaffold_27-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_56535-T1
Valid prediction for snap_scaffold_27-snap.123-T1
Couldn't classify 86028, 86555
Sorry, prediction pasa_asmbl_36690.p1 fails validation.
(ATG)	 TA	86028-86555	AC	GCA
Valid prediction for GlimmerHMM_glimmerT_56531-T1
Valid prediction for snap_scaffold_27-snap.101-T1
Valid prediction for snap_scaffold_27-snap.96-T1
Valid prediction for Augustus_model.g37464.t1
Valid prediction for snap_scaffold_27-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_56529-T1
Valid prediction for snap_scaffold_27-snap.106-T1
Valid prediction for snap_scaffold_27-snap.120-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.113-T1
Valid prediction for snap_scaffold_27-snap.108-T1
Valid prediction for snap_scaffold_27-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_56525-T1
Valid prediction for snap_scaffold_27-snap.116-T1
Valid prediction for snap_scaffold_27-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_56538-T1
Valid prediction for snap_scaffold_27-snap.110-T1
Valid prediction for snap_scaffold_27-snap.78-T1
Valid prediction for snap_scaffold_27-snap.83-T1
Valid prediction for Augustus_model.g37463.t1
Valid prediction for snap_scaffold_27-snap.99-T1
Valid prediction for Augustus_model.g37458.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_36666.p1
Valid prediction for snap_scaffold_27-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_56523-T1
Valid prediction for HiQ_model.g37461.t1
Valid prediction for CodingQuarry_transcript_41740-T1
Valid prediction for GlimmerHMM_glimmerT_56524-T1
Couldn't classify 181384, 181636
Sorry, prediction pasa_asmbl_36674.p1 fails validation.
(TCC)	 TG	181384-181636	GT	TGG
(GTG)	 AG	181787-181927	GT	TGG
(GAG)	 AG	182090-182520	GT	AGG
(GAG)	 AG	182948-183184	CT	GAC
-recovered pasa_asmbl_36674.p1, terminal, 182948, 183184
-recovered pasa_asmbl_36674.p1, internal, 181787, 181927
-recovered pasa_asmbl_36674.p1, internal, 182090, 182520
Couldn't classify 188954, 189025
Couldn't classify 190691, 190784
Sorry, prediction pasa_asmbl_36670.p1 fails validation.
(CAC)	 CA	188954-189025	GT	AGG
(CCC)	 AG	189181-189306	GT	TGG
(GAC)	 AG	190438-190598	GT	AGG
(GTA)	 AG	190691-190784	GT	AGG
-recovered pasa_asmbl_36670.p1, internal, 189181, 189306
-recovered pasa_asmbl_36670.p1, internal, 190438, 190598
-recovered pasa_asmbl_36670.p1, internal, 190691, 190784
Valid prediction for GlimmerHMM_glimmerT_56542-T1
Valid prediction for snap_scaffold_27-snap.111-T1
Valid prediction for snap_scaffold_27-snap.119-T1
Valid prediction for pasa_asmbl_36675.p1
Valid prediction for GlimmerHMM_glimmerT_56520-T1
Valid prediction for GlimmerHMM_glimmerT_56530-T1
Valid prediction for snap_scaffold_27-snap.102-T1
Valid prediction for snap_scaffold_27-snap.90-T1
Valid prediction for snap_scaffold_27-snap.87-T1
Couldn't classify 138135, 138216
Sorry, prediction pasa_asmbl_36684.p1 fails validation.
(TCA)	 AG	138135-138216	GT	AGG
(GTG)	 AG	138467-138541	GT	TGG
(TAG)	 AG	141026-141300	GT	AGG
(AGT)	 AG	141453-141645	GT	AGG
(GCA)	 AG	141845-142152	GA	GAG
-recovered pasa_asmbl_36684.p1, terminal, 141845, 142152
-recovered pasa_asmbl_36684.p1, internal, 138135, 138216
-recovered pasa_asmbl_36684.p1, internal, 138467, 138541
-recovered pasa_asmbl_36684.p1, internal, 141026, 141300
-recovered pasa_asmbl_36684.p1, internal, 141453, 141645
Valid prediction for GlimmerHMM_glimmerT_56527-T1
Valid prediction for snap_scaffold_27-snap.122-T1
Valid prediction for Augustus_model.g37457.t1
Valid prediction for snap_scaffold_27-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_56519-T1
Valid prediction for GlimmerHMM_glimmerT_56539-T1
Valid prediction for snap_scaffold_27-snap.107-T1
Valid prediction for snap_scaffold_27-snap.92-T1
Valid prediction for GlimmerHMM_glimmerT_56534-T1
Valid prediction for CodingQuarry_transcript_41741-T1
Couldn't classify 133395, 133620
Sorry, prediction pasa_asmbl_36685.p1 fails validation.
(ATG)	 TC	128460-128476	GT	AAG
(GTC)	 AG	129003-129208	GT	AGG
(ATG)	 AG	131412-131579	GT	CTG
(CGT)	 AG	132493-132673	GT	AGG
(TGA)	 AG	133395-133620	GT	AGG
-recovered pasa_asmbl_36685.p1, initial, 128460, 128476
add_exon() Sorry, pasa_asmbl_36685.p1 131412-131579-initial-1 is invalid.
-recovered pasa_asmbl_36685.p1, initial, 131412, 131579
add_exon() Sorry, pasa_asmbl_36685.p1 129003-129208-terminal-2 is invalid.
-recovered pasa_asmbl_36685.p1, terminal, 129003, 129208
-recovered pasa_asmbl_36685.p1, internal, 129003, 129208
-recovered pasa_asmbl_36685.p1, internal, 131412, 131579
-recovered pasa_asmbl_36685.p1, internal, 132493, 132673
-recovered pasa_asmbl_36685.p1, internal, 133395, 133620
Valid prediction for CodingQuarry_transcript_41738-T1
Valid prediction for pasa_asmbl_36693.p1
Valid prediction for GlimmerHMM_glimmerT_56541-T1
Valid prediction for snap_scaffold_27-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_56528-T1
Couldn't classify 151089, 151227
Sorry, prediction pasa_asmbl_36677.p1 fails validation.
(GGG)	 GG	151089-151227	GT	CAG
(CTT)	 AG	151510-151749	GT	AGG
(GTG)	 AG	153126-153188	GT	CGG
(GGA)	 AG	155906-156118	GT	AGG
(AAA)	 AG	156229-156332	GT	AGG
(GAG)	 AG	157311-157399	GT	TGG
(GTG)	 AG	158023-158183	GT	GGG
(GTA)	 AG	158325-158400	GT	AAG
(GAA)	 AG	160298-160439	GT	GGG
(GTA)	 AG	160599-160688	GT	AGG
(GTG)	 AG	160806-160924	GT	AGG
(GAC)	 AG	161021-161171	GT	AGG
(GTG)	 AG	163338-163502	GT	AGG
(AGT)	 AG	163585-163767	GT	TGG
(GTG)	 AG	163906-164085	GT	TGG
(ATC)	 AG	164223-164306	GT	GGG
(AAG)	 AG	164536-164636	GT	AGG
(GTC)	 AG	164727-164928	CC	GAC
add_exon() Sorry, pasa_asmbl_36677.p1 160806-160924-terminal-2 is invalid.
-recovered pasa_asmbl_36677.p1, terminal, 160806, 160924
-recovered pasa_asmbl_36677.p1, terminal, 164727, 164928
-recovered pasa_asmbl_36677.p1, internal, 151510, 151749
-recovered pasa_asmbl_36677.p1, internal, 153126, 153188
-recovered pasa_asmbl_36677.p1, internal, 155906, 156118
-recovered pasa_asmbl_36677.p1, internal, 156229, 156332
-recovered pasa_asmbl_36677.p1, internal, 157311, 157399
-recovered pasa_asmbl_36677.p1, internal, 158023, 158183
-recovered pasa_asmbl_36677.p1, internal, 158325, 158400
-recovered pasa_asmbl_36677.p1, internal, 160298, 160439
-recovered pasa_asmbl_36677.p1, internal, 160599, 160688
-recovered pasa_asmbl_36677.p1, internal, 160806, 160924
-recovered pasa_asmbl_36677.p1, internal, 161021, 161171
-recovered pasa_asmbl_36677.p1, internal, 163338, 163502
-recovered pasa_asmbl_36677.p1, internal, 163585, 163767
-recovered pasa_asmbl_36677.p1, internal, 163906, 164085
-recovered pasa_asmbl_36677.p1, internal, 164223, 164306
-recovered pasa_asmbl_36677.p1, internal, 164536, 164636
Valid prediction for Augustus_model.g37454.t1
Valid prediction for snap_scaffold_27-snap.86-T1
Valid prediction for Augustus_model.g37459.t1
Valid prediction for Augustus_model.g37466.t1
Valid prediction for GlimmerHMM_glimmerT_56521-T1
Valid prediction for GlimmerHMM_glimmerT_56522-T1
Valid prediction for GlimmerHMM_glimmerT_56537-T1
Valid prediction for GlimmerHMM_glimmerT_56533-T1
Valid prediction for snap_scaffold_27-snap.97-T1
Valid prediction for Augustus_model.g37460.t1
Valid prediction for snap_scaffold_27-snap.79-T1
Valid prediction for CodingQuarry_transcript_41739-T1
Valid prediction for GlimmerHMM_glimmerT_56532-T1
Valid prediction for HiQ_model.g37455.t1
Valid prediction for snap_scaffold_27-snap.80-T1
Valid prediction for snap_scaffold_27-snap.94-T1
Valid prediction for snap_scaffold_27-snap.114-T1
Valid prediction for snap_scaffold_27-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_56543-T1
Valid prediction for GlimmerHMM_glimmerT_56540-T1
Valid prediction for snap_scaffold_27-snap.81-T1
Valid prediction for snap_scaffold_27-snap.84-T1
Valid prediction for HiQ_model.g37453.t1
Valid prediction for snap_scaffold_27-snap.121-T1
Valid prediction for Augustus_model.g37468.t1
Valid prediction for CodingQuarry_transcript_41743-T1
Valid prediction for snap_scaffold_27-snap.112-T1
Valid prediction for snap_scaffold_27-snap.91-T1
Valid prediction for CodingQuarry_transcript_41742-T1
Valid prediction for Augustus_model.g37465.t1
Valid prediction for snap_scaffold_27-snap.98-T1
Valid prediction for CodingQuarry_transcript_41744-T1
Valid prediction for snap_scaffold_27-snap.93-T1
Valid prediction for Augustus_model.g37456.t1
Valid prediction for CodingQuarry_transcript_41736-T1
Valid prediction for Augustus_model.g37462.t1
Valid prediction for snap_scaffold_27-snap.88-T1
Valid prediction for snap_scaffold_27-snap.100-T1
Valid prediction for Augustus_model.g37467.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34122, rend_intergenic: 32564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37608, rend_intergenic: 35207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44269, rend_intergenic: 38150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57877, rend_intergenic: 54919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75578, rend_intergenic: 74117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96016, rend_intergenic: 93417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113640, rend_intergenic: 100990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115623, rend_intergenic: 113811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118988, rend_intergenic: 118461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127525, rend_intergenic: 124910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153450, rend_intergenic: 128076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163655, rend_intergenic: 154209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167937, rend_intergenic: 165476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168973, rend_intergenic: 168090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183077, rend_intergenic: 169001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187460, rend_intergenic: 184115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193686, rend_intergenic: 188303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206104, rend_intergenic: 202239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209835, rend_intergenic: 207530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213386
-exon list size: 405


building trellis

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34.4    
34.6    
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35.9    
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36.4    
36.6    
36.9    
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37.3    
37.6    
37.8    
38.1    
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38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
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43.7    
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44.7    
45.0    
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45.9    
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97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 34122, rend_intergenic: 32564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37608, rend_intergenic: 35207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44269, rend_intergenic: 38150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57877, rend_intergenic: 54919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75578, rend_intergenic: 74117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96016, rend_intergenic: 93417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113640, rend_intergenic: 100990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115623, rend_intergenic: 113811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118988, rend_intergenic: 118461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127525, rend_intergenic: 124910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153450, rend_intergenic: 128076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163655, rend_intergenic: 154209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167937, rend_intergenic: 165476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168973, rend_intergenic: 168090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183077, rend_intergenic: 169001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187460, rend_intergenic: 184115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193686, rend_intergenic: 188303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206104, rend_intergenic: 202239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209835, rend_intergenic: 207530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support