-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_8258972-8467749

-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_55991-T1
Valid prediction for Augustus_model.g37329.t1
Valid prediction for GeneMark_model.97575_t
Valid prediction for snap_scaffold_25-snap.1867-T1
Valid prediction for snap_scaffold_25-snap.1848-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for HiQ_model.g37322.t1
Valid prediction for snap_scaffold_25-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_55984-T1
Valid prediction for snap_scaffold_25-snap.1843-T1
Valid prediction for snap_scaffold_25-snap.1864-T1
Valid prediction for GeneMark_model.97574_t
Valid prediction for GeneMark_model.97561_t
Valid prediction for snap_scaffold_25-snap.1866-T1
Valid prediction for Augustus_model.g37340.t1
Valid prediction for GlimmerHMM_glimmerT_55974-T1
Couldn't classify 44824, 44942
Sorry, prediction GeneMark_model.97568_t fails validation.
(TTG)	 AG	44824-44942	GT	AGG
(AGC)	 AG	44965-44974	GT	AAG
(GTC)	 AG	45351-45493	GT	AAG
(GCA)	 AG	46578-46818	AA	GAA
-recovered GeneMark_model.97568_t, terminal, 46578, 46818
-recovered GeneMark_model.97568_t, internal, 44824, 44942
-recovered GeneMark_model.97568_t, internal, 44965, 44974
-recovered GeneMark_model.97568_t, internal, 45351, 45493
Valid prediction for snap_scaffold_25-snap.1878-T1
Valid prediction for snap_scaffold_25-snap.1845-T1
Valid prediction for Augustus_model.g37321.t1
Valid prediction for snap_scaffold_25-snap.1861-T1
Valid prediction for GeneMark_model.97590_t
Valid prediction for GeneMark_model.97569_t
Valid prediction for GlimmerHMM_glimmerT_55990-T1
Valid prediction for GeneMark_model.97579_t
Valid prediction for snap_scaffold_25-snap.1851-T1
Valid prediction for GeneMark_model.97565_t
Valid prediction for GeneMark_model.97581_t
Valid prediction for Augustus_model.g37342.t1
Valid prediction for GlimmerHMM_glimmerT_55975-T1
Valid prediction for snap_scaffold_25-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_55986-T1
Valid prediction for GlimmerHMM_glimmerT_55971-T1
Valid prediction for snap_scaffold_25-snap.1853-T1
Valid prediction for snap_scaffold_25-snap.1882-T1
Valid prediction for snap_scaffold_25-snap.1881-T1
Valid prediction for snap_scaffold_25-snap.1883-T1
Valid prediction for CodingQuarry_transcript_38718-T1
Valid prediction for Augustus_model.g37323.t1
Valid prediction for snap_scaffold_25-snap.1869-T1
Valid prediction for Augustus_model.g37341.t1
Valid prediction for Augustus_model.g37331.t1
Valid prediction for snap_scaffold_25-snap.1847-T1
Valid prediction for GlimmerHMM_glimmerT_55992-T1
Valid prediction for Augustus_model.g37318.t1
Valid prediction for pasa_asmbl_33726.p1
Valid prediction for snap_scaffold_25-snap.1884-T1
Valid prediction for GeneMark_model.97588_t
Valid prediction for GlimmerHMM_glimmerT_55972-T1
Valid prediction for snap_scaffold_25-snap.1862-T1
Valid prediction for snap_scaffold_25-snap.1863-T1
Valid prediction for Augustus_model.g37332.t1
Valid prediction for GlimmerHMM_glimmerT_55980-T1
Valid prediction for GeneMark_model.97580_t
Valid prediction for GlimmerHMM_glimmerT_55982-T1
Valid prediction for GeneMark_model.97589_t

-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 GeneMark_model.97564_t
Valid prediction for GlimmerHMM_glimmerT_55970-T1
Valid prediction for snap_scaffold_25-snap.1857-T1
Valid prediction for Augustus_model.g37328.t1
Valid prediction for GeneMark_model.97586_t
Valid prediction for CodingQuarry_transcript_38719-T1
Valid prediction for snap_scaffold_25-snap.1859-T1
Valid prediction for GlimmerHMM_glimmerT_55979-T1
Valid prediction for Augustus_model.g37326.t1
Valid prediction for snap_scaffold_25-snap.1860-T1
Valid prediction for snap_scaffold_25-snap.1879-T1
Valid prediction for Augustus_model.g37336.t1
Couldn't classify 55570, 56700
Couldn't classify 59625, 59750
Sorry, prediction pasa_asmbl_34412.p1 fails validation.
(CCC)	 GT	55570-56700	GT	AGG
(GTT)	 AG	59625-59750	GG	CAG
Valid prediction for snap_scaffold_25-snap.1873-T1
Valid prediction for snap_scaffold_25-snap.1872-T1
Valid prediction for snap_scaffold_25-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_55987-T1
Valid prediction for GeneMark_model.97567_t
Valid prediction for GeneMark_model.97560_t
Valid prediction for GeneMark_model.97566_t
Couldn't classify 70759, 71103
Sorry, prediction pasa_asmbl_34411.p1 fails validation.
(TAC)	 GC	70759-71103	AG	GAA
Couldn't classify 109429, 109541
Sorry, prediction pasa_asmbl_34408.p3 fails validation.
(ATG)	 AT	108716-108899	GT	GGG
(TGG)	 AG	109429-109541	AC	ACA
-recovered pasa_asmbl_34408.p3, initial, 108716, 108899
Valid prediction for pasa_asmbl_34414.p2
Valid prediction for snap_scaffold_25-snap.1868-T1
Valid prediction for GlimmerHMM_glimmerT_55967-T1
Valid prediction for pasa_asmbl_34413.p1
Valid prediction for snap_scaffold_25-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_55985-T1
Valid prediction for Augustus_model.g37339.t1
Valid prediction for GeneMark_model.97578_t
Valid prediction for HiQ_model.g37337.t1
Valid prediction for GeneMark_model.97571_t
Valid prediction for snap_scaffold_25-snap.1865-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1846-T1
Valid prediction for GlimmerHMM_glimmerT_55973-T1
Valid prediction for GlimmerHMM_glimmerT_55976-T1
Valid prediction for Augustus_model.g37333.t1
Valid prediction for GlimmerHMM_glimmerT_55968-T1
Valid prediction for snap_scaffold_25-snap.1871-T1
Couldn't classify 42421, 42957
Sorry, prediction pasa_asmbl_33729.p1 fails validation.
(ATG)	 GG	42421-42957	AC	TCA
Valid prediction for Augustus_model.g37320.t1
Valid prediction for snap_scaffold_25-snap.1874-T1
Valid prediction for GeneMark_model.97559_t
Valid prediction for snap_scaffold_25-snap.1852-T1
Couldn't classify 120007, 120054
Sorry, prediction pasa_asmbl_34405.p1 fails validation.
(TTC)	 CC	120007-120054	GT	AGG
(GTC)	 AG	120238-120408	GT	AGG
(GTG)	 AG	120508-120682	GT	TGG
(CGG)	 AG	120886-121001	GT	TGG
(TCT)	 AG	121162-121239	GT	AAG
(ATC)	 AG	121407-121467	GT	TGG
(CCA)	 AG	121579-121739	GA	AAG
-recovered pasa_asmbl_34405.p1, terminal, 121579, 121739
-recovered pasa_asmbl_34405.p1, internal, 120238, 120408
-recovered pasa_asmbl_34405.p1, internal, 120508, 120682
-recovered pasa_asmbl_34405.p1, internal, 120886, 121001
-recovered pasa_asmbl_34405.p1, internal, 121162, 121239
-recovered pasa_asmbl_34405.p1, internal, 121407, 121467
Valid prediction for Augustus_model.g37319.t1
Valid prediction for snap_scaffold_25-snap.1842-T1
Valid prediction for GeneMark_model.97583_t
Valid prediction for GlimmerHMM_glimmerT_55966-T1
Valid prediction for snap_scaffold_25-snap.1854-T1
Valid prediction for Augustus_model.g37334.t1
Valid prediction for CodingQuarry_transcript_38720-T1
Valid prediction for snap_scaffold_25-snap.1841-T1
Valid prediction for snap_scaffold_25-snap.1850-T1
Couldn't classify 24572, 24671
Sorry, prediction pasa_asmbl_34415.p1 fails validation.
(GCG)	 AG	24572-24671	GT	AGG
(GTA)	 AG	25371-25444	GT	AGG
(GAC)	 AG	26720-26839	GT	AGG
(CCC)	 AG	28735-28791	CA	AAC
-recovered pasa_asmbl_34415.p1, terminal, 28735, 28791
-recovered pasa_asmbl_34415.p1, internal, 24572, 24671
-recovered pasa_asmbl_34415.p1, internal, 25371, 25444
-recovered pasa_asmbl_34415.p1, internal, 26720, 26839
Couldn't classify 117260, 117316
Couldn't classify 119706, 119840
Sorry, prediction pasa_asmbl_34406.p1 fails validation.
(CAG)	 TC	117260-117316	GT	AGG
(AAA)	 AG	118076-118237	GT	AGG
(GAC)	 AG	118341-118490	GT	ATG
(GTC)	 AG	118670-118756	GT	TGG
(ATC)	 AG	118918-119050	GT	AGG
(GAC)	 AG	119187-119275	GT	AGG
(ATC)	 AG	119405-119620	GT	AGG
(GTC)	 AG	119706-119840	TG	GGT
-recovered pasa_asmbl_34406.p1, internal, 118076, 118237
-recovered pasa_asmbl_34406.p1, internal, 118341, 118490
-recovered pasa_asmbl_34406.p1, internal, 118670, 118756
-recovered pasa_asmbl_34406.p1, internal, 118918, 119050
-recovered pasa_asmbl_34406.p1, internal, 119187, 119275
-recovered pasa_asmbl_34406.p1, internal, 119405, 119620
Valid prediction for snap_scaffold_25-snap.1856-T1
Valid prediction for Augustus_model.g37335.t1
Valid prediction for pasa_asmbl_34404.p1
Valid prediction for GeneMark_model.97562_t
Valid prediction for GeneMark_model.97587_t
Couldn't classify 184595, 184667
Couldn't classify 186757, 186818
Sorry, prediction pasa_asmbl_34568.p2 fails validation.
(AAC)	 AC	184595-184667	GT	CGG
(GGG)	 AG	184771-184947	GT	AGG
(GCT)	 AG	186757-186818	GA	GGG
-recovered pasa_asmbl_34568.p2, internal, 184771, 184947
Valid prediction for Augustus_model.g37330.t1
Couldn't classify 193027, 193080
Couldn't classify 194499, 194750
Sorry, prediction pasa_asmbl_34402.p2 fails validation.
(CAG)	 TC	193027-193080	GT	AGG
(ATA)	 AG	193983-194045	GT	AGG
(ATC)	 AG	194499-194750	GC	GGG
-recovered pasa_asmbl_34402.p2, internal, 193983, 194045
-recovered pasa_asmbl_34402.p2, internal, 194499, 194750
Valid prediction for HiQ_model.g37324.t1
Valid prediction for snap_scaffold_25-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_55978-T1
Valid prediction for GlimmerHMM_glimmerT_55983-T1
Valid prediction for CodingQuarry_transcript_38722-T1
Valid prediction for snap_scaffold_25-snap.1880-T1
Valid prediction for Augustus_model.g37327.t1
Valid prediction for GlimmerHMM_glimmerT_55989-T1
Valid prediction for GeneMark_model.97576_t
Valid prediction for GeneMark_model.97573_t
Valid prediction for Augustus_model.g37325.t1
Couldn't classify 200114, 200114
Sorry, prediction pasa_asmbl_34399.p1 fails validation.
(ATG)	 AC	195191-195253	GT	GGG
(CAC)	 AG	196922-196996	GT	AGG
(ATC)	 AG	197133-197238	GT	AGG
(CGT)	 AG	197384-197494	GT	AGG
(GGT)	 AG	198118-198333	GT	GAG
(TGG)	 AG	198919-198993	GT	AGG
(GTG)	 AG	199820-200009	GT	TGG
(AAA)	 AG	200114-200114	AA	GAA
-recovered pasa_asmbl_34399.p1, initial, 195191, 195253
add_exon() Sorry, pasa_asmbl_34399.p1 197384-197494-terminal-1 is invalid.
-recovered pasa_asmbl_34399.p1, terminal, 197384, 197494
-recovered pasa_asmbl_34399.p1, internal, 196922, 196996
-recovered pasa_asmbl_34399.p1, internal, 197133, 197238
-recovered pasa_asmbl_34399.p1, internal, 197384, 197494
-recovered pasa_asmbl_34399.p1, internal, 198118, 198333
-recovered pasa_asmbl_34399.p1, internal, 198919, 198993
-recovered pasa_asmbl_34399.p1, internal, 199820, 200009
Valid prediction for GlimmerHMM_glimmerT_55981-T1
Valid prediction for CodingQuarry_transcript_38721-T1
Valid prediction for GlimmerHMM_glimmerT_55969-T1
Valid prediction for GeneMark_model.97582_t
Valid prediction for GeneMark_model.97584_t
Valid prediction for HiQ_model.g37338.t1
Valid prediction for GeneMark_model.97577_t
Valid prediction for GlimmerHMM_glimmerT_55977-T1
Valid prediction for GlimmerHMM_glimmerT_55988-T1
Valid prediction for snap_scaffold_25-snap.1858-T1
Valid prediction for snap_scaffold_25-snap.1849-T1
Valid prediction for GeneMark_model.97572_t
Valid prediction for snap_scaffold_25-snap.1844-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11085, rend_intergenic: 10837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14944, rend_intergenic: 11099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19724, rend_intergenic: 17866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24389, rend_intergenic: 19776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32751, rend_intergenic: 26286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34396, rend_intergenic: 32817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67472, rend_intergenic: 62318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107025, rend_intergenic: 103665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184331, rend_intergenic: 175973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208778
-exon list size: 563


building trellis

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89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.0    
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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11085, rend_intergenic: 10837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14944, rend_intergenic: 11099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19724, rend_intergenic: 17866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24389, rend_intergenic: 19776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32751, rend_intergenic: 26286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34396, rend_intergenic: 32817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67472, rend_intergenic: 62318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107025, rend_intergenic: 103665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184331, rend_intergenic: 175973  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