-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_7881241-8106462

-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 GeneMark_model.75468_t
Valid prediction for snap_scaffold_18-snap.1666-T1
Valid prediction for Augustus_model.g29312.t1
Valid prediction for GlimmerHMM_glimmerT_43728-T1
Valid prediction for Augustus_model.g29310.t1
Valid prediction for snap_scaffold_18-snap.1674-T1
Valid prediction for snap_scaffold_18-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_43720-T1
Valid prediction for GeneMark_model.75486_t
Valid prediction for GlimmerHMM_glimmerT_43710-T1
Valid prediction for snap_scaffold_18-snap.1662-T1
Valid prediction for HiQ_model.g29313.t1
Valid prediction for Augustus_model.g29302.t1
Valid prediction for GeneMark_model.75480_t
Valid prediction for GeneMark_model.75463_t
Valid prediction for snap_scaffold_18-snap.1680-T1
Valid prediction for GeneMark_model.75470_t
Valid prediction for snap_scaffold_18-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_43723-T1
Valid prediction for GeneMark_model.75447_t
Valid prediction for snap_scaffold_18-snap.1653-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.75484_t
Valid prediction for GeneMark_model.75465_t
Valid prediction for snap_scaffold_18-snap.1691-T1
Valid prediction for GeneMark_model.75457_t
Valid prediction for snap_scaffold_18-snap.1679-T1
Valid prediction for GeneMark_model.75450_t
Valid prediction for GlimmerHMM_glimmerT_43733-T1
Valid prediction for snap_scaffold_18-snap.1663-T1
Valid prediction for GeneMark_model.75453_t
Valid prediction for snap_scaffold_18-snap.1695-T1
Valid prediction for GeneMark_model.75488_t
Valid prediction for Augustus_model.g29298.t1
Valid prediction for Augustus_model.g29305.t1
Valid prediction for snap_scaffold_18-snap.1682-T1
Valid prediction for Augustus_model.g29315.t1
Valid prediction for Augustus_model.g29300.t1
Valid prediction for GlimmerHMM_glimmerT_43713-T1
Valid prediction for GeneMark_model.75456_t
Valid prediction for GlimmerHMM_glimmerT_43716-T1
Valid prediction for GlimmerHMM_glimmerT_43734-T1
Valid prediction for CodingQuarry_transcript_23787-T1
Valid prediction for GeneMark_model.75485_t
Valid prediction for Augustus_model.g29294.t1
Valid prediction for snap_scaffold_18-snap.1677-T1
Valid prediction for snap_scaffold_18-snap.1693-T1
Valid prediction for GeneMark_model.75460_t
Valid prediction for Augustus_model.g29291.t1
Valid prediction for snap_scaffold_18-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_43730-T1
Valid prediction for GeneMark_model.75472_t
Valid prediction for GlimmerHMM_glimmerT_43737-T1
Valid prediction for Augustus_model.g29290.t1
Valid prediction for Augustus_model.g29304.t1
Valid prediction for GlimmerHMM_glimmerT_43717-T1
Valid prediction for GeneMark_model.75482_t
Valid prediction for Augustus_model.g29317.t1
Valid prediction for GlimmerHMM_glimmerT_43732-T1
Valid prediction for GlimmerHMM_glimmerT_43719-T1
Valid prediction for GeneMark_model.75459_t
Valid prediction for GeneMark_model.75492_t
Valid prediction for GeneMark_model.75477_t
Valid prediction for snap_scaffold_18-snap.1690-T1
Valid prediction for snap_scaffold_18-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_43739-T1
Valid prediction for snap_scaffold_18-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_43715-T1
Valid prediction for GlimmerHMM_glimmerT_43726-T1
Valid prediction for GlimmerHMM_glimmerT_43707-T1
Valid prediction for snap_scaffold_18-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_43740-T1
Valid prediction for GeneMark_model.75454_t
Valid prediction for Augustus_model.g29316.t1
Valid prediction for snap_scaffold_18-snap.1678-T1
Valid prediction for Augustus_model.g29297.t1
Valid prediction for GeneMark_model.75452_t
Valid prediction for GeneMark_model.75467_t
Couldn't classify 189576, 189662
Sorry, prediction pasa_asmbl_20844.p1 fails validation.
(TCT)	 TG	189576-189662	GT	TGG
(ATC)	 AG	189955-190014	GT	AGG
(CTG)	 AG	190223-190345	GT	TGG
(TAT)	 AG	190463-190537	GT	AGG
(ATC)	 AG	190807-190893	GT	GGG
(GAC)	 AG	191315-191434	GT	AGG
(ATC)	 AG	191540-191599	GT	AGG
(CCC)	 AG	191707-191790	GT	TGG
(ATT)	 AG	192033-192161	CC	GAC
-recovered pasa_asmbl_20844.p1, terminal, 192033, 192161
-recovered pasa_asmbl_20844.p1, internal, 189955, 190014
-recovered pasa_asmbl_20844.p1, internal, 190223, 190345
-recovered pasa_asmbl_20844.p1, internal, 190463, 190537
-recovered pasa_asmbl_20844.p1, internal, 190807, 190893
-recovered pasa_asmbl_20844.p1, internal, 191315, 191434
-recovered pasa_asmbl_20844.p1, internal, 191540, 191599
-recovered pasa_asmbl_20844.p1, internal, 191707, 191790
Valid prediction for GlimmerHMM_glimmerT_43718-T1
Valid prediction for GeneMark_model.75474_t
Valid prediction for GlimmerHMM_glimmerT_43706-T1
Valid prediction for GeneMark_model.75490_t
Valid prediction for GeneMark_model.75475_t
Valid prediction for snap_scaffold_18-snap.1664-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_18-snap.1676-T1
Valid prediction for GeneMark_model.75473_t
Valid prediction for CodingQuarry_transcript_23788-T1
Valid prediction for GeneMark_model.75481_t
Valid prediction for snap_scaffold_18-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_43708-T1
Valid prediction for snap_scaffold_18-snap.1685-T1
Valid prediction for CodingQuarry_transcript_23786-T1
Valid prediction for snap_scaffold_18-snap.1673-T1
Valid prediction for GeneMark_model.75469_t
Valid prediction for snap_scaffold_18-snap.1660-T1
Valid prediction for snap_scaffold_18-snap.1675-T1
Valid prediction for HiQ_model.g29306.t1
Valid prediction for GeneMark_model.75491_t
Valid prediction for pasa_asmbl_20027.p1
Valid prediction for snap_scaffold_18-snap.1684-T1
Valid prediction for Augustus_model.g29308.t1
Valid prediction for snap_scaffold_18-snap.1659-T1
Valid prediction for snap_scaffold_18-snap.1696-T1
Valid prediction for Augustus_model.g29293.t1
Valid prediction for GlimmerHMM_glimmerT_43721-T1
Valid prediction for snap_scaffold_18-snap.1654-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1670-T1
Valid prediction for GeneMark_model.75476_t
Valid prediction for GlimmerHMM_glimmerT_43735-T1
Valid prediction for snap_scaffold_18-snap.1686-T1
Valid prediction for Augustus_model.g29303.t1
Valid prediction for pasa_asmbl_20031.p1
Valid prediction for GeneMark_model.75471_t
Valid prediction for GeneMark_model.75479_t
Valid prediction for GlimmerHMM_glimmerT_43722-T1
Valid prediction for GeneMark_model.75461_t
Valid prediction for GeneMark_model.75489_t
Valid prediction for GeneMark_model.75449_t
Valid prediction for GeneMark_model.75462_t
Valid prediction for GeneMark_model.75487_t
Valid prediction for GlimmerHMM_glimmerT_43738-T1
Valid prediction for snap_scaffold_18-snap.1689-T1
Valid prediction for GeneMark_model.75466_t
Valid prediction for snap_scaffold_18-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_43714-T1
Valid prediction for GlimmerHMM_glimmerT_43731-T1
Valid prediction for Augustus_model.g29309.t1
Valid prediction for GlimmerHMM_glimmerT_43711-T1
Valid prediction for GlimmerHMM_glimmerT_43712-T1
Valid prediction for snap_scaffold_18-snap.1656-T1
Valid prediction for GeneMark_model.75483_t
Valid prediction for snap_scaffold_18-snap.1672-T1
Valid prediction for snap_scaffold_18-snap.1669-T1
Valid prediction for CodingQuarry_transcript_23785-T1
Valid prediction for GlimmerHMM_glimmerT_43709-T1
Valid prediction for snap_scaffold_18-snap.1667-T1
Valid prediction for Augustus_model.g29301.t1
Valid prediction for Augustus_model.g29292.t1
Valid prediction for HiQ_model.g29314.t1
Valid prediction for snap_scaffold_18-snap.1681-T1
Valid prediction for GlimmerHMM_glimmerT_43736-T1
Valid prediction for Augustus_model.g29307.t1
Valid prediction for GlimmerHMM_glimmerT_43725-T1
Valid prediction for GeneMark_model.75458_t
Valid prediction for Augustus_model.g29295.t1
Valid prediction for snap_scaffold_18-snap.1657-T1
Valid prediction for Augustus_model.g29296.t1
Valid prediction for snap_scaffold_18-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_43729-T1
Valid prediction for pasa_asmbl_20030.p1
Valid prediction for GlimmerHMM_glimmerT_43724-T1
Valid prediction for Augustus_model.g29311.t1
Valid prediction for snap_scaffold_18-snap.1692-T1
Valid prediction for Augustus_model.g29299.t1
Valid prediction for snap_scaffold_18-snap.1655-T1
Valid prediction for GeneMark_model.75464_t
Valid prediction for snap_scaffold_18-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_43727-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 142324, rend_intergenic: 120535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147236, rend_intergenic: 143619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148582, rend_intergenic: 147593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175713, rend_intergenic: 148926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202459, rend_intergenic: 199853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206865, rend_intergenic: 203253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216832, rend_intergenic: 208056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221703, rend_intergenic: 217259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225222
-exon list size: 636


building trellis

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56.0    
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85.1    
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88.1    
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88.7    
88.9    
89.0    
89.2    
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90.0    
90.1    
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90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
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91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
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97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 142324, rend_intergenic: 120535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147236, rend_intergenic: 143619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148582, rend_intergenic: 147593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175713, rend_intergenic: 148926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202459, rend_intergenic: 199853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206865, rend_intergenic: 203253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216832, rend_intergenic: 208056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221703, rend_intergenic: 217259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support