-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_8652426-8819349

-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 HiQ_model.g21972.t1
Valid prediction for pasa_asmbl_11129.p1
Valid prediction for GeneMark_model.55900_t
Valid prediction for Augustus_model.g21974.t1
Valid prediction for CodingQuarry_transcript_13142-T1
Valid prediction for GeneMark_model.55902_t
Valid prediction for GlimmerHMM_glimmerT_32760-T1
Valid prediction for snap_scaffold_13-snap.1585-T1
Valid prediction for HiQ_model.g21976.t1
Valid prediction for GlimmerHMM_glimmerT_32745-T1
Valid prediction for snap_scaffold_13-snap.1595-T1
Valid prediction for GeneMark_model.55910_t
Valid prediction for GeneMark_model.55915_t
Valid prediction for Augustus_model.g21983.t1
Valid prediction for GlimmerHMM_glimmerT_32747-T1
Valid prediction for GeneMark_model.55914_t
Valid prediction for GlimmerHMM_glimmerT_32749-T1
Valid prediction for GeneMark_model.55903_t
Valid prediction for snap_scaffold_13-snap.1578-T1
Valid prediction for Augustus_model.g21977.t1
Valid prediction for Augustus_model.g21980.t1
Valid prediction for GlimmerHMM_glimmerT_32746-T1
Valid prediction for GeneMark_model.55899_t
Valid prediction for HiQ_model.g21981.t1
Valid prediction for snap_scaffold_13-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_32743-T1
Valid prediction for GlimmerHMM_glimmerT_32744-T1
Valid prediction for GeneMark_model.55895_t
Valid prediction for snap_scaffold_13-snap.1592-T1
Valid prediction for snap_scaffold_13-snap.1581-T1
Valid prediction for GeneMark_model.55924_t
Valid prediction for GeneMark_model.55896_t
Valid prediction for CodingQuarry_transcript_13141-T1
Valid prediction for CodingQuarry_transcript_13143-T1
Valid prediction for snap_scaffold_13-snap.1596-T1
Valid prediction for CodingQuarry_transcript_13139-T1
Valid prediction for snap_scaffold_13-snap.1582-T1
Valid prediction for GeneMark_model.55898_t
Valid prediction for GeneMark_model.55917_t
Valid prediction for GeneMark_model.55907_t
Valid prediction for pasa_asmbl_11126.p1
Valid prediction for snap_scaffold_13-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_32762-T1
Valid prediction for GeneMark_model.55922_t
Couldn't classify 60250, 60378
Couldn't classify 60838, 60935
Sorry, prediction pasa_asmbl_11599.p1 fails validation.
(GCC)	 GT	60250-60378	GT	CTG
(TGC)	 AG	60531-60753	GT	AGG
(TGG)	 AG	60838-60935	AA	TCA
-recovered pasa_asmbl_11599.p1, internal, 60531, 60753
Couldn't classify 36160, 36318
Sorry, prediction pasa_asmbl_11667.p1 fails validation.
(CGG)	 TG	36160-36318	GT	AGG
(GGC)	 AG	36446-36587	GT	TGG
(CGG)	 AG	36795-37334	GT	AGG
(AGC)	 AG	37435-37556	GT	AGG
(CCT)	 AG	37660-37792	GT	AGG
(GCT)	 AG	38340-38447	GT	TGG
(GTT)	 AG	38582-38692	GT	TGG
(ACC)	 AG	38836-38948	GT	TGG
(ATG)	 AG	39066-39227	AA	AGA
add_exon() Sorry, pasa_asmbl_11667.p1 36795-37334-terminal-1 is invalid.
-recovered pasa_asmbl_11667.p1, terminal, 36795, 37334
-recovered pasa_asmbl_11667.p1, terminal, 39066, 39227
-recovered pasa_asmbl_11667.p1, internal, 36446, 36587
-recovered pasa_asmbl_11667.p1, internal, 36795, 37334
-recovered pasa_asmbl_11667.p1, internal, 37435, 37556
-recovered pasa_asmbl_11667.p1, internal, 37660, 37792
-recovered pasa_asmbl_11667.p1, internal, 38340, 38447
-recovered pasa_asmbl_11667.p1, internal, 38582, 38692
-recovered pasa_asmbl_11667.p1, internal, 38836, 38948
Valid prediction for GeneMark_model.55893_t
Valid prediction for Augustus_model.g21971.t1
Valid prediction for snap_scaffold_13-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_32748-T1
Valid prediction for pasa_asmbl_11132.p1
Valid prediction for snap_scaffold_13-snap.1574-T1
Couldn't classify 73918, 74060
Sorry, prediction pasa_asmbl_11131.p1 fails validation.
(ACT)	 AA	73918-74060	GT	AGG
(GGA)	 AG	74498-74557	GT	AGG
(GCA)	 AG	74954-75049	GT	AGG
(GGG)	 AG	75222-75302	GT	AGG
(GAG)	 AG	75774-75897	GT	ACG
(GAC)	 AG	76065-76364	GG	AAG
-recovered pasa_asmbl_11131.p1, terminal, 76065, 76364
-recovered pasa_asmbl_11131.p1, internal, 74498, 74557
-recovered pasa_asmbl_11131.p1, internal, 74954, 75049
-recovered pasa_asmbl_11131.p1, internal, 75222, 75302
-recovered pasa_asmbl_11131.p1, internal, 75774, 75897
Valid prediction for Augustus_model.g21970.t1
Valid prediction for GeneMark_model.55894_t
Valid prediction for GeneMark_model.55905_t
Valid prediction for GlimmerHMM_glimmerT_32751-T1
Valid prediction for GlimmerHMM_glimmerT_32756-T1
Valid prediction for Augustus_model.g21973.t1
Valid prediction for GeneMark_model.55913_t
Valid prediction for GlimmerHMM_glimmerT_32741-T1
Valid prediction for CodingQuarry_transcript_13140-T1
Valid prediction for snap_scaffold_13-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_32766-T1
Valid prediction for GlimmerHMM_glimmerT_32752-T1
Valid prediction for GlimmerHMM_glimmerT_32759-T1
Valid prediction for snap_scaffold_13-snap.1590-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_13-snap.1598-T1
Couldn't classify 99838, 100148
Sorry, prediction pasa_asmbl_9928.p1 fails validation.
(CAG)	 CC	99838-100148	GT	AGG
(TTC)	 AG	100294-100936	GT	AGG
(GCT)	 AG	101148-101243	GT	AGG
(GTC)	 AG	101335-101480	GT	CGG
(ATC)	 AG	101648-101810	GT	AGG
(GTG)	 AG	101900-102014	GT	AGG
(GTG)	 AG	102154-102346	GT	AAG
(GCT)	 AG	102437-102559	GT	GAG
(AGG)	 AG	102682-103067	GT	AGG
(GGG)	 AG	103246-103736	AA	AGA
add_exon() Sorry, pasa_asmbl_9928.p1 102437-102559-terminal-1 is invalid.
-recovered pasa_asmbl_9928.p1, terminal, 102437, 102559
-recovered pasa_asmbl_9928.p1, terminal, 103246, 103736
-recovered pasa_asmbl_9928.p1, internal, 100294, 100936
-recovered pasa_asmbl_9928.p1, internal, 101148, 101243
-recovered pasa_asmbl_9928.p1, internal, 101335, 101480
-recovered pasa_asmbl_9928.p1, internal, 101648, 101810
-recovered pasa_asmbl_9928.p1, internal, 101900, 102014
-recovered pasa_asmbl_9928.p1, internal, 102154, 102346
-recovered pasa_asmbl_9928.p1, internal, 102437, 102559
-recovered pasa_asmbl_9928.p1, internal, 102682, 103067
Valid prediction for GeneMark_model.55921_t
Valid prediction for snap_scaffold_13-snap.1584-T1
Valid prediction for GeneMark_model.55918_t
Valid prediction for GeneMark_model.55909_t
Valid prediction for GeneMark_model.55912_t
Valid prediction for GeneMark_model.55911_t
Couldn't classify 7013, 7090
Sorry, prediction pasa_asmbl_9941.p1 fails validation.
(GGT)	 TA	7013-7090	GT	GGG
(GGC)	 AG	7299-7365	GT	AGG
(GAA)	 AG	8081-8121	GT	AGG
(CCG)	 AG	8253-8385	GT	GGG
(ATA)	 AG	8829-8938	AG	GAA
-recovered pasa_asmbl_9941.p1, terminal, 8829, 8938
-recovered pasa_asmbl_9941.p1, internal, 7299, 7365
-recovered pasa_asmbl_9941.p1, internal, 8081, 8121
-recovered pasa_asmbl_9941.p1, internal, 8253, 8385
Valid prediction for GeneMark_model.55906_t
Valid prediction for GlimmerHMM_glimmerT_32767-T1
Valid prediction for GlimmerHMM_glimmerT_32755-T1
Valid prediction for snap_scaffold_13-snap.1576-T1
Valid prediction for snap_scaffold_13-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_32740-T1
Valid prediction for GeneMark_model.55923_t
Valid prediction for GeneMark_model.55891_t
Valid prediction for snap_scaffold_13-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_32750-T1
Valid prediction for Augustus_model.g21986.t1
Valid prediction for GeneMark_model.55904_t
Valid prediction for snap_scaffold_13-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_32765-T1
Valid prediction for HiQ_model.g21985.t1
Valid prediction for Augustus_model.g21979.t1
Valid prediction for Augustus_model.g21988.t1
Valid prediction for HiQ_model.g21987.t1
Valid prediction for GeneMark_model.55916_t
Valid prediction for snap_scaffold_13-snap.1597-T1
Valid prediction for HiQ_model.g21982.t1
Valid prediction for GeneMark_model.55908_t
Valid prediction for GlimmerHMM_glimmerT_32764-T1
Valid prediction for snap_scaffold_13-snap.1594-T1
Valid prediction for snap_scaffold_13-snap.1575-T1
Valid prediction for snap_scaffold_13-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_32742-T1
Valid prediction for CodingQuarry_transcript_13145-T1
Valid prediction for GlimmerHMM_glimmerT_32761-T1
Couldn't classify 29084, 29326
Couldn't classify 29424, 29501
Sorry, prediction pasa_asmbl_10287.p1 fails validation.
(AAG)	 GT	29084-29326	GT	AGG
(GTA)	 AG	29424-29501	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_32754-T1
Couldn't classify 63917, 64476
Sorry, prediction pasa_asmbl_9930.p1 fails validation.
(ATC)	 AA	63917-64476	GT	AGG
(ATT)	 AG	64563-64682	GT	AAG
(GTT)	 AG	64819-64975	GT	AGG
(GCT)	 AG	65145-65250	GT	GGG
(ATA)	 AG	65375-65572	GT	AGG
(GCC)	 AG	65685-65877	GT	AGG
(GTT)	 AG	65987-66074	GT	AGG
(ATC)	 AG	66172-66318	GT	AGG
(GGT)	 AG	66483-66644	TC	AGT
add_exon() Sorry, pasa_asmbl_9930.p1 64563-64682-terminal-1 is invalid.
-recovered pasa_asmbl_9930.p1, terminal, 64563, 64682
-recovered pasa_asmbl_9930.p1, terminal, 66483, 66644
-recovered pasa_asmbl_9930.p1, internal, 64563, 64682
-recovered pasa_asmbl_9930.p1, internal, 64819, 64975
-recovered pasa_asmbl_9930.p1, internal, 65145, 65250
-recovered pasa_asmbl_9930.p1, internal, 65375, 65572
-recovered pasa_asmbl_9930.p1, internal, 65685, 65877
-recovered pasa_asmbl_9930.p1, internal, 65987, 66074
-recovered pasa_asmbl_9930.p1, internal, 66172, 66318
Couldn't classify 23189, 23380
Sorry, prediction pasa_asmbl_9935.p1 fails validation.
(ATG)	 GC	22237-22250	GT	AGG
(TCC)	 AG	22879-23041	GT	AGG
(ATA)	 AG	23189-23380	GA	GAG
-recovered pasa_asmbl_9935.p1, initial, 22237, 22250
-recovered pasa_asmbl_9935.p1, internal, 22879, 23041
Valid prediction for Augustus_model.g21978.t1
Valid prediction for GlimmerHMM_glimmerT_32753-T1
Valid prediction for Augustus_model.g21984.t1
Valid prediction for GlimmerHMM_glimmerT_32763-T1
Valid prediction for snap_scaffold_13-snap.1588-T1
Valid prediction for GlimmerHMM_glimmerT_32758-T1
Valid prediction for GeneMark_model.55897_t
Valid prediction for HiQ_model.g21975.t1
Valid prediction for GeneMark_model.55920_t
Valid prediction for GlimmerHMM_glimmerT_32757-T1
Valid prediction for GeneMark_model.55901_t
Valid prediction for snap_scaffold_13-snap.1601-T1
Valid prediction for GeneMark_model.55919_t
Valid prediction for snap_scaffold_13-snap.1599-T1
Valid prediction for snap_scaffold_13-snap.1600-T1
Valid prediction for CodingQuarry_transcript_13144-T1
Valid prediction for snap_scaffold_13-snap.1579-T1
Valid prediction for snap_scaffold_13-snap.1589-T1
Valid prediction for GeneMark_model.55892_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17134, rend_intergenic: 6201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21365, rend_intergenic: 19085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35369, rend_intergenic: 33191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39227, rend_intergenic: 36277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48230, rend_intergenic: 43151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66660, rend_intergenic: 63480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89406, rend_intergenic: 85493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115835, rend_intergenic: 105337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128855, rend_intergenic: 124483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166924
-exon list size: 556


building trellis

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93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 17134, rend_intergenic: 6201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21365, rend_intergenic: 19085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35369, rend_intergenic: 33191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39227, rend_intergenic: 36277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48230, rend_intergenic: 43151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66660, rend_intergenic: 63480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89406, rend_intergenic: 85493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115835, rend_intergenic: 105337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128855, rend_intergenic: 124483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11616
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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