-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_11015834-11156751

-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_4-snap.2401-T1
Valid prediction for Augustus_model.g6834.t1
Valid prediction for Augustus_model.g6817.t1
Valid prediction for GlimmerHMM_glimmerT_10411-T1
Valid prediction for GeneMark_model.16965_t
Valid prediction for GeneMark_model.16996_t
Valid prediction for GeneMark_model.16970_t
Valid prediction for GeneMark_model.16987_t
Valid prediction for GeneMark_model.16961_t
Valid prediction for GeneMark_model.16958_t
Valid prediction for snap_scaffold_4-snap.2411-T1
Valid prediction for snap_scaffold_4-snap.2381-T1
Valid prediction for snap_scaffold_4-snap.2383-T1
Valid prediction for snap_scaffold_4-snap.2386-T1
Valid prediction for GeneMark_model.16951_t
Valid prediction for GeneMark_model.16978_t
Valid prediction for Augustus_model.g6826.t1
Valid prediction for snap_scaffold_4-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_10418-T1
Valid prediction for Augustus_model.g6816.t1
Valid prediction for GeneMark_model.16980_t
Valid prediction for GeneMark_model.16988_t
Valid prediction for Augustus_model.g6831.t1
Valid prediction for snap_scaffold_4-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_10408-T1
Valid prediction for snap_scaffold_4-snap.2392-T1
Valid prediction for snap_scaffold_4-snap.2403-T1
Valid prediction for GeneMark_model.16991_t
Valid prediction for GlimmerHMM_glimmerT_10419-T1
Valid prediction for snap_scaffold_4-snap.2395-T1
Valid prediction for GlimmerHMM_glimmerT_10415-T1
Valid prediction for GeneMark_model.16960_t
Valid prediction for GeneMark_model.16950_t
Valid prediction for snap_scaffold_4-snap.2405-T1
Valid prediction for snap_scaffold_4-snap.2410-T1
Valid prediction for GeneMark_model.16976_t
Valid prediction for GeneMark_model.16998_t
Valid prediction for GlimmerHMM_glimmerT_10396-T1
Valid prediction for CodingQuarry_transcript_49027-T1
Valid prediction for GlimmerHMM_glimmerT_10399-T1
Valid prediction for GlimmerHMM_glimmerT_10404-T1
Valid prediction for GlimmerHMM_glimmerT_10421-T1
Valid prediction for snap_scaffold_4-snap.2391-T1
Valid prediction for snap_scaffold_4-snap.2384-T1
Valid prediction for snap_scaffold_4-snap.2400-T1
Valid prediction for GeneMark_model.16989_t
Valid prediction for snap_scaffold_4-snap.2408-T1
Valid prediction for GeneMark_model.16984_t
Valid prediction for GeneMark_model.16963_t
Valid prediction for HiQ_model.g6822.t1
Valid prediction for snap_scaffold_4-snap.2390-T1
Valid prediction for CodingQuarry_transcript_49026-T1
Valid prediction for Augustus_model.g6828.t1
Valid prediction for snap_scaffold_4-snap.2412-T1
Valid prediction for snap_scaffold_4-snap.2397-T1
Valid prediction for snap_scaffold_4-snap.2379-T1
Valid prediction for CodingQuarry_transcript_49028-T1
Valid prediction for Augustus_model.g6833.t1
Valid prediction for GeneMark_model.16969_t
Valid prediction for Augustus_model.g6823.t1
Valid prediction for Augustus_model.g6827.t1
Valid prediction for GlimmerHMM_glimmerT_10400-T1
Valid prediction for GeneMark_model.16954_t
Valid prediction for GeneMark_model.16974_t
Valid prediction for snap_scaffold_4-snap.2375-T1
Valid prediction for Augustus_model.g6818.t1
Valid prediction for Augustus_model.g6819.t1
Valid prediction for GeneMark_model.16956_t
Valid prediction for GlimmerHMM_glimmerT_10409-T1
Valid prediction for GlimmerHMM_glimmerT_10422-T1
Valid prediction for snap_scaffold_4-snap.2389-T1
Valid prediction for snap_scaffold_4-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_10394-T1
Valid prediction for GlimmerHMM_glimmerT_10406-T1
Valid prediction for Augustus_model.g6820.t1
Valid prediction for GlimmerHMM_glimmerT_10412-T1
Valid prediction for snap_scaffold_4-snap.2377-T1
Valid prediction for snap_scaffold_4-snap.2406-T1
Valid prediction for GeneMark_model.16967_t
Valid prediction for GlimmerHMM_glimmerT_10407-T1
Valid prediction for GlimmerHMM_glimmerT_10402-T1
Valid prediction for GeneMark_model.16972_t
Valid prediction for pasa_asmbl_43032.p1
Valid prediction for GlimmerHMM_glimmerT_10414-T1
Valid prediction for snap_scaffold_4-snap.2398-T1
Valid prediction for GeneMark_model.16948_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.16982_t
Valid prediction for GeneMark_model.16953_t
Valid prediction for GlimmerHMM_glimmerT_10420-T1
Valid prediction for snap_scaffold_4-snap.2388-T1
Valid prediction for GeneMark_model.16973_t
Valid prediction for GlimmerHMM_glimmerT_10413-T1
Valid prediction for snap_scaffold_4-snap.2380-T1
Valid prediction for GeneMark_model.16981_t
Valid prediction for GeneMark_model.16975_t
Valid prediction for GeneMark_model.16952_t
Valid prediction for snap_scaffold_4-snap.2402-T1
Valid prediction for GeneMark_model.17000_t
Valid prediction for GeneMark_model.16957_t
Valid prediction for snap_scaffold_4-snap.2376-T1
Valid prediction for snap_scaffold_4-snap.2378-T1
Valid prediction for snap_scaffold_4-snap.2407-T1
Valid prediction for Augustus_model.g6832.t1
Valid prediction for snap_scaffold_4-snap.2382-T1
Valid prediction for GeneMark_model.16986_t
Valid prediction for GeneMark_model.16955_t
Valid prediction for Augustus_model.g6824.t1
Valid prediction for GeneMark_model.16959_t
Valid prediction for GeneMark_model.16966_t
Valid prediction for snap_scaffold_4-snap.2387-T1
Valid prediction for GeneMark_model.16949_t
Valid prediction for snap_scaffold_4-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_10397-T1
Valid prediction for snap_scaffold_4-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_10405-T1
Valid prediction for GeneMark_model.16962_t
Valid prediction for GlimmerHMM_glimmerT_10395-T1
Valid prediction for GeneMark_model.16995_t
Valid prediction for Augustus_model.g6821.t1
Valid prediction for Augustus_model.g6830.t1
Valid prediction for Augustus_model.g6829.t1
Valid prediction for GlimmerHMM_glimmerT_10403-T1
Valid prediction for GlimmerHMM_glimmerT_10417-T1
Valid prediction for GeneMark_model.16983_t
Valid prediction for snap_scaffold_4-snap.2409-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.16990_t
Valid prediction for snap_scaffold_4-snap.2374-T1
Valid prediction for GeneMark_model.16994_t
Valid prediction for GeneMark_model.16979_t
Valid prediction for GlimmerHMM_glimmerT_10401-T1
Valid prediction for GeneMark_model.16985_t
Valid prediction for GlimmerHMM_glimmerT_10416-T1
Valid prediction for GeneMark_model.16964_t
Valid prediction for GeneMark_model.16993_t
Valid prediction for GeneMark_model.16999_t
Valid prediction for GeneMark_model.16971_t
Valid prediction for GeneMark_model.16992_t
Valid prediction for snap_scaffold_4-snap.2371-T1
Valid prediction for Augustus_model.g6825.t1
Valid prediction for snap_scaffold_4-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_10398-T1
Valid prediction for Augustus_model.g6835.t1
Valid prediction for GeneMark_model.16997_t
Valid prediction for GlimmerHMM_glimmerT_10410-T1
Valid prediction for snap_scaffold_4-snap.2394-T1
Valid prediction for snap_scaffold_4-snap.2385-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6779, rend_intergenic: 5830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9341, rend_intergenic: 8938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18759, rend_intergenic: 15398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21188, rend_intergenic: 21025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23586, rend_intergenic: 21384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26702, rend_intergenic: 23831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29076, rend_intergenic: 26724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33996, rend_intergenic: 29752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47050, rend_intergenic: 45887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53086, rend_intergenic: 48739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83867, rend_intergenic: 81828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86314, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89180, rend_intergenic: 86557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99756, rend_intergenic: 91135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108970, rend_intergenic: 108291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113319, rend_intergenic: 109554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116731, rend_intergenic: 113319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122743, rend_intergenic: 116806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126602, rend_intergenic: 123354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127618, rend_intergenic: 127237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129396, rend_intergenic: 127676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136721, rend_intergenic: 129570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140918
-exon list size: 671


building trellis

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99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 6779, rend_intergenic: 5830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9341, rend_intergenic: 8938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18759, rend_intergenic: 15398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21188, rend_intergenic: 21025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23586, rend_intergenic: 21384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26702, rend_intergenic: 23831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29076, rend_intergenic: 26724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33996, rend_intergenic: 29752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47050, rend_intergenic: 45887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53086, rend_intergenic: 48739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83867, rend_intergenic: 81828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86314, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89180, rend_intergenic: 86557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99756, rend_intergenic: 91135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108970, rend_intergenic: 108291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113319, rend_intergenic: 109554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116731, rend_intergenic: 113319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122743, rend_intergenic: 116806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126602, rend_intergenic: 123354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127618, rend_intergenic: 127237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129396, rend_intergenic: 127676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136721, rend_intergenic: 129570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support