-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_7945336-8132998

-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.35077_t
Valid prediction for GlimmerHMM_glimmerT_20519-T1
Valid prediction for GlimmerHMM_glimmerT_20542-T1
Valid prediction for Augustus_model.g13729.t1
Valid prediction for GeneMark_model.35111_t
Valid prediction for GeneMark_model.35080_t
Valid prediction for GeneMark_model.35067_t
Valid prediction for GeneMark_model.35109_t
Valid prediction for snap_scaffold_8-snap.1554-T1
Valid prediction for GeneMark_model.35097_t
Valid prediction for GeneMark_model.35064_t
Valid prediction for snap_scaffold_8-snap.1575-T1
Valid prediction for GeneMark_model.35073_t
Valid prediction for GeneMark_model.35105_t
Valid prediction for GeneMark_model.35102_t
Valid prediction for GeneMark_model.35106_t
Valid prediction for GeneMark_model.35074_t
Valid prediction for snap_scaffold_8-snap.1583-T1
Valid prediction for GeneMark_model.35104_t
Valid prediction for GeneMark_model.35090_t
Valid prediction for Augustus_model.g13724.t1
Valid prediction for snap_scaffold_8-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_20535-T1
Valid prediction for GeneMark_model.35100_t
Valid prediction for GeneMark_model.35108_t
Valid prediction for Augustus_model.g13738.t1
Valid prediction for snap_scaffold_8-snap.1569-T1
Valid prediction for snap_scaffold_8-snap.1581-T1
Valid prediction for snap_scaffold_8-snap.1590-T1
Valid prediction for GlimmerHMM_glimmerT_20533-T1
Valid prediction for snap_scaffold_8-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_20532-T1
Valid prediction for Augustus_model.g13737.t1
Valid prediction for GlimmerHMM_glimmerT_20530-T1
Valid prediction for GeneMark_model.35094_t
Valid prediction for snap_scaffold_8-snap.1556-T1
Valid prediction for snap_scaffold_8-snap.1563-T1
Valid prediction for GeneMark_model.35096_t
Valid prediction for GlimmerHMM_glimmerT_20537-T1
Valid prediction for GeneMark_model.35086_t
Valid prediction for GeneMark_model.35092_t
Valid prediction for GeneMark_model.35118_t
Valid prediction for GeneMark_model.35113_t
Valid prediction for snap_scaffold_8-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_20541-T1
Valid prediction for snap_scaffold_8-snap.1587-T1
Valid prediction for snap_scaffold_8-snap.1588-T1
Valid prediction for snap_scaffold_8-snap.1570-T1
Valid prediction for Augustus_model.g13735.t1
Valid prediction for snap_scaffold_8-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_20528-T1
Valid prediction for GeneMark_model.35115_t
Valid prediction for snap_scaffold_8-snap.1552-T1
Valid prediction for GeneMark_model.35079_t
Valid prediction for snap_scaffold_8-snap.1592-T1
Valid prediction for GeneMark_model.35061_t
Valid prediction for snap_scaffold_8-snap.1572-T1
Valid prediction for GeneMark_model.35059_t
Valid prediction for GeneMark_model.35099_t
Valid prediction for snap_scaffold_8-snap.1586-T1
Valid prediction for Augustus_model.g13722.t1
Valid prediction for Augustus_model.g13733.t1
Valid prediction for GlimmerHMM_glimmerT_20536-T1
Valid prediction for GlimmerHMM_glimmerT_20524-T1
Valid prediction for GeneMark_model.35084_t
Valid prediction for snap_scaffold_8-snap.1574-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_8-snap.1593-T1
Valid prediction for GeneMark_model.35117_t
Valid prediction for CodingQuarry_transcript_59553-T1
Valid prediction for GeneMark_model.35101_t
Couldn't classify 152983, 153621
Sorry, prediction GeneMark_model.35069_t fails validation.
(CCC)	 AG	152983-153621	GT	AGG
(CCA)	 AG	154238-154263	GT	CTG
(ACA)	 AG	154316-154330	GT	AGG
(GGC)	 AG	154357-154426	GT	AGG
(TTG)	 AG	155256-155263	GT	GGG
(GGG)	 AG	155305-155316	GT	TTG
(GGG)	 AG	155458-155469	GT	GAG
(GGG)	 AG	156743-156771	GT	ATG
(TGT)	 AG	156875-157003	GT	GCG
(GGG)	 AG	157153-157169	AC	AGA
-recovered GeneMark_model.35069_t, terminal, 157153, 157169
-recovered GeneMark_model.35069_t, internal, 152983, 153621
-recovered GeneMark_model.35069_t, internal, 154238, 154263
-recovered GeneMark_model.35069_t, internal, 154316, 154330
-recovered GeneMark_model.35069_t, internal, 154357, 154426
-recovered GeneMark_model.35069_t, internal, 155256, 155263
-recovered GeneMark_model.35069_t, internal, 155305, 155316
-recovered GeneMark_model.35069_t, internal, 155458, 155469
-recovered GeneMark_model.35069_t, internal, 156743, 156771
-recovered GeneMark_model.35069_t, internal, 156875, 157003
Valid prediction for snap_scaffold_8-snap.1553-T1
Valid prediction for HiQ_model.g13727.t1
Valid prediction for Augustus_model.g13739.t1
Valid prediction for GlimmerHMM_glimmerT_20520-T1
Valid prediction for GeneMark_model.35068_t
Valid prediction for GeneMark_model.35063_t
Valid prediction for Augustus_model.g13731.t1
Valid prediction for GeneMark_model.35114_t
Valid prediction for GeneMark_model.35082_t
Valid prediction for pasa_asmbl_52929.p1
Valid prediction for GeneMark_model.35110_t
Valid prediction for Augustus_model.g13723.t1
Valid prediction for Augustus_model.g13734.t1
Valid prediction for snap_scaffold_8-snap.1578-T1
Valid prediction for HiQ_model.g13726.t1
Valid prediction for snap_scaffold_8-snap.1559-T1
Valid prediction for snap_scaffold_8-snap.1584-T1
Valid prediction for GeneMark_model.35098_t
Valid prediction for GeneMark_model.35078_t
Valid prediction for GeneMark_model.35095_t
Valid prediction for snap_scaffold_8-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_20527-T1
Valid prediction for GeneMark_model.35091_t
Valid prediction for snap_scaffold_8-snap.1562-T1
Valid prediction for GeneMark_model.35103_t
Valid prediction for Augustus_model.g13728.t1
Valid prediction for GeneMark_model.35088_t
Valid prediction for GeneMark_model.35058_t
Valid prediction for Augustus_model.g13732.t1
Valid prediction for GlimmerHMM_glimmerT_20531-T1
Valid prediction for GlimmerHMM_glimmerT_20522-T1
Valid prediction for GeneMark_model.35072_t
Valid prediction for GeneMark_model.35071_t
Valid prediction for GlimmerHMM_glimmerT_20518-T1
Valid prediction for GeneMark_model.35062_t
Valid prediction for snap_scaffold_8-snap.1571-T1
Valid prediction for GeneMark_model.35112_t
Valid prediction for snap_scaffold_8-snap.1560-T1
Valid prediction for Augustus_model.g13730.t1
Valid prediction for snap_scaffold_8-snap.1579-T1
Valid prediction for GlimmerHMM_glimmerT_20534-T1
Valid prediction for snap_scaffold_8-snap.1566-T1
Valid prediction for GeneMark_model.35065_t
Valid prediction for snap_scaffold_8-snap.1558-T1
Valid prediction for GeneMark_model.35119_t
Valid prediction for snap_scaffold_8-snap.1573-T1
Valid prediction for GeneMark_model.35060_t
Valid prediction for GeneMark_model.35066_t
Valid prediction for snap_scaffold_8-snap.1557-T1
Valid prediction for GeneMark_model.35085_t
Valid prediction for GeneMark_model.35087_t
Valid prediction for snap_scaffold_8-snap.1567-T1
Valid prediction for GlimmerHMM_glimmerT_20521-T1
Valid prediction for snap_scaffold_8-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_20525-T1
Valid prediction for Augustus_model.g13725.t1
Valid prediction for GeneMark_model.35075_t
Valid prediction for snap_scaffold_8-snap.1591-T1
Valid prediction for pasa_asmbl_52931.p1
Valid prediction for snap_scaffold_8-snap.1568-T1
Valid prediction for snap_scaffold_8-snap.1577-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_20540-T1
Valid prediction for GeneMark_model.35083_t
Valid prediction for GeneMark_model.35107_t
Valid prediction for Augustus_model.g13721.t1
Valid prediction for snap_scaffold_8-snap.1551-T1
Valid prediction for GlimmerHMM_glimmerT_20526-T1
Valid prediction for CodingQuarry_transcript_59554-T1
Valid prediction for GlimmerHMM_glimmerT_20539-T1
Valid prediction for GlimmerHMM_glimmerT_20523-T1
Valid prediction for Augustus_model.g13736.t1
Valid prediction for GeneMark_model.35081_t
Valid prediction for GeneMark_model.35076_t
Valid prediction for GlimmerHMM_glimmerT_20538-T1
Valid prediction for GeneMark_model.35070_t
Valid prediction for snap_scaffold_8-snap.1589-T1
Valid prediction for snap_scaffold_8-snap.1576-T1
Valid prediction for GeneMark_model.35089_t
Valid prediction for GeneMark_model.35116_t
Valid prediction for GlimmerHMM_glimmerT_20529-T1
Valid prediction for snap_scaffold_8-snap.1582-T1
Valid prediction for GeneMark_model.35093_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8499, rend_intergenic: 5269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9201, rend_intergenic: 9096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13507, rend_intergenic: 10313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20446, rend_intergenic: 13678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51108, rend_intergenic: 50325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62716, rend_intergenic: 60952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98166, rend_intergenic: 87482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104404, rend_intergenic: 101208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105935, rend_intergenic: 105335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110630, rend_intergenic: 106646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126934, rend_intergenic: 116821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136668, rend_intergenic: 132663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142223, rend_intergenic: 139058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151656, rend_intergenic: 142250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165734, rend_intergenic: 162712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175185, rend_intergenic: 168773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183333, rend_intergenic: 175378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 117052, rend_intergenic: 117049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187663
-exon list size: 691


building trellis

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94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 8499, rend_intergenic: 5269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9201, rend_intergenic: 9096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13507, rend_intergenic: 10313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20446, rend_intergenic: 13678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51108, rend_intergenic: 50325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62716, rend_intergenic: 60952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98166, rend_intergenic: 87482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104404, rend_intergenic: 101208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105935, rend_intergenic: 105335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110630, rend_intergenic: 106646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126934, rend_intergenic: 116821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136668, rend_intergenic: 132663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142223, rend_intergenic: 139058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151656, rend_intergenic: 142250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165734, rend_intergenic: 162712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175185, rend_intergenic: 168773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183333, rend_intergenic: 175378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 117052, rend_intergenic: 117049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support