-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_8234516-8412365

-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_23-snap.1603-T1
Valid prediction for snap_scaffold_23-snap.1594-T1
Valid prediction for Augustus_model.g35431.t1
Valid prediction for GeneMark_model.91366_t
Valid prediction for snap_scaffold_23-snap.1568-T1
Valid prediction for Augustus_model.g35447.t1
Valid prediction for GeneMark_model.91373_t
Valid prediction for GlimmerHMM_glimmerT_52713-T1
Valid prediction for GeneMark_model.91401_t
Valid prediction for CodingQuarry_transcript_35696-T1
Valid prediction for GeneMark_model.91395_t
Valid prediction for GeneMark_model.91387_t
Valid prediction for snap_scaffold_23-snap.1577-T1
Valid prediction for snap_scaffold_23-snap.1572-T1
Valid prediction for GeneMark_model.91371_t
Valid prediction for snap_scaffold_23-snap.1596-T1
Valid prediction for snap_scaffold_23-snap.1571-T1
Valid prediction for GeneMark_model.91399_t
Valid prediction for GlimmerHMM_glimmerT_52711-T1
Valid prediction for GeneMark_model.91379_t
Valid prediction for snap_scaffold_23-snap.1567-T1
Valid prediction for snap_scaffold_23-snap.1602-T1
Valid prediction for GeneMark_model.91368_t
Valid prediction for Augustus_model.g35444.t1
Valid prediction for Augustus_model.g35443.t1
Valid prediction for GeneMark_model.91386_t
Valid prediction for GeneMark_model.91382_t
Valid prediction for GeneMark_model.91384_t
Valid prediction for Augustus_model.g35441.t1
Valid prediction for GeneMark_model.91390_t
Valid prediction for snap_scaffold_23-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_52712-T1
Valid prediction for snap_scaffold_23-snap.1570-T1
Valid prediction for snap_scaffold_23-snap.1590-T1
Valid prediction for snap_scaffold_23-snap.1564-T1
Valid prediction for Augustus_model.g35433.t1
Valid prediction for GeneMark_model.91364_t
Valid prediction for GeneMark_model.91361_t
Valid prediction for GlimmerHMM_glimmerT_52707-T1
Valid prediction for GlimmerHMM_glimmerT_52714-T1
Valid prediction for GeneMark_model.91352_t
Valid prediction for GeneMark_model.91350_t
Valid prediction for GeneMark_model.91394_t
Valid prediction for GeneMark_model.91385_t
Valid prediction for GeneMark_model.91359_t
Valid prediction for snap_scaffold_23-snap.1580-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_52693-T1
Valid prediction for GlimmerHMM_glimmerT_52691-T1
Valid prediction for GeneMark_model.91347_t
Valid prediction for GlimmerHMM_glimmerT_52702-T1
Valid prediction for GeneMark_model.91348_t
Valid prediction for snap_scaffold_23-snap.1576-T1
Valid prediction for snap_scaffold_23-snap.1600-T1
Valid prediction for snap_scaffold_23-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_52695-T1
Valid prediction for GeneMark_model.91355_t
Valid prediction for snap_scaffold_23-snap.1578-T1
Valid prediction for GeneMark_model.91396_t
Valid prediction for GeneMark_model.91400_t
Valid prediction for pasa_asmbl_31067.p1
Valid prediction for GeneMark_model.91360_t
Valid prediction for GeneMark_model.91398_t
Valid prediction for GeneMark_model.91375_t
Valid prediction for snap_scaffold_23-snap.1593-T1
Valid prediction for CodingQuarry_transcript_35695-T1
Valid prediction for GlimmerHMM_glimmerT_52710-T1
Valid prediction for HiQ_model.g35445.t1
Valid prediction for GeneMark_model.91357_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.91377_t
Valid prediction for snap_scaffold_23-snap.1598-T1
Valid prediction for snap_scaffold_23-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_52709-T1
Valid prediction for snap_scaffold_23-snap.1569-T1
Valid prediction for GlimmerHMM_glimmerT_52703-T1
Valid prediction for snap_scaffold_23-snap.1582-T1
Valid prediction for Augustus_model.g35446.t1
Valid prediction for snap_scaffold_23-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_52704-T1
Valid prediction for GlimmerHMM_glimmerT_52698-T1
Valid prediction for GlimmerHMM_glimmerT_52694-T1
Valid prediction for snap_scaffold_23-snap.1583-T1
Valid prediction for GeneMark_model.91392_t
Valid prediction for GeneMark_model.91353_t
Valid prediction for GeneMark_model.91349_t
Valid prediction for Augustus_model.g35435.t1
Valid prediction for GeneMark_model.91389_t
Valid prediction for GeneMark_model.91363_t
Valid prediction for GeneMark_model.91370_t
Valid prediction for GeneMark_model.91376_t
Valid prediction for snap_scaffold_23-snap.1575-T1
Valid prediction for snap_scaffold_23-snap.1599-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52699-T1
Valid prediction for GeneMark_model.91397_t
Valid prediction for snap_scaffold_23-snap.1585-T1
Valid prediction for snap_scaffold_23-snap.1592-T1
Valid prediction for Augustus_model.g35438.t1
Valid prediction for GlimmerHMM_glimmerT_52715-T1
Valid prediction for GeneMark_model.91356_t
Valid prediction for GeneMark_model.91381_t
Valid prediction for snap_scaffold_23-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_52701-T1
Valid prediction for GeneMark_model.91365_t
Valid prediction for Augustus_model.g35437.t1
Valid prediction for snap_scaffold_23-snap.1574-T1
Valid prediction for snap_scaffold_23-snap.1604-T1
Valid prediction for Augustus_model.g35434.t1
Valid prediction for GeneMark_model.91374_t
Valid prediction for GlimmerHMM_glimmerT_52700-T1
Valid prediction for GeneMark_model.91369_t
Valid prediction for GeneMark_model.91380_t
Valid prediction for GeneMark_model.91391_t
Valid prediction for GeneMark_model.91393_t
Valid prediction for GeneMark_model.91372_t
Valid prediction for Augustus_model.g35432.t1
Valid prediction for GlimmerHMM_glimmerT_52706-T1
Valid prediction for GlimmerHMM_glimmerT_52697-T1
Valid prediction for snap_scaffold_23-snap.1579-T1
Valid prediction for Augustus_model.g35436.t1
Valid prediction for GeneMark_model.91351_t
Valid prediction for GlimmerHMM_glimmerT_52716-T1
Valid prediction for GlimmerHMM_glimmerT_52696-T1
Valid prediction for snap_scaffold_23-snap.1595-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1591-T1
Valid prediction for snap_scaffold_23-snap.1597-T1
Valid prediction for snap_scaffold_23-snap.1565-T1
Valid prediction for GeneMark_model.91362_t
Valid prediction for snap_scaffold_23-snap.1573-T1
Valid prediction for Augustus_model.g35442.t1
Valid prediction for GlimmerHMM_glimmerT_52692-T1
Valid prediction for Augustus_model.g35430.t1
Valid prediction for snap_scaffold_23-snap.1588-T1
Couldn't classify 125866, 126026
Couldn't classify 126232, 126406
Sorry, prediction pasa_asmbl_31927.p2 fails validation.
(GTG)	 CA	125866-126026	GT	TTG
(TAT)	 AG	126232-126406	GA	ACG
Valid prediction for GlimmerHMM_glimmerT_52705-T1
Valid prediction for GeneMark_model.91367_t
Valid prediction for snap_scaffold_23-snap.1581-T1
Valid prediction for GeneMark_model.91358_t
Valid prediction for GeneMark_model.91383_t
Valid prediction for Augustus_model.g35439.t1
Valid prediction for GlimmerHMM_glimmerT_52708-T1
Valid prediction for Augustus_model.g35440.t1
Valid prediction for snap_scaffold_23-snap.1584-T1
Valid prediction for GeneMark_model.91378_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27771, rend_intergenic: 22857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45420, rend_intergenic: 33294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75248, rend_intergenic: 57222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76172, rend_intergenic: 75426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78770, rend_intergenic: 76241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80614, rend_intergenic: 80122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105088, rend_intergenic: 104227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109125, rend_intergenic: 105401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116751, rend_intergenic: 111499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134050, rend_intergenic: 128013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162145, rend_intergenic: 159253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164486, rend_intergenic: 162963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173730, rend_intergenic: 168958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177850
-exon list size: 776


building trellis

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98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 27771, rend_intergenic: 22857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45420, rend_intergenic: 33294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75248, rend_intergenic: 57222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76172, rend_intergenic: 75426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78770, rend_intergenic: 76241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80614, rend_intergenic: 80122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105088, rend_intergenic: 104227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109125, rend_intergenic: 105401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116751, rend_intergenic: 111499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134050, rend_intergenic: 128013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162145, rend_intergenic: 159253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164486, rend_intergenic: 162963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173730, rend_intergenic: 168958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support