-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_1656404-1855454

-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_6-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_14097-T1
Valid prediction for Augustus_model.g9361.t1
Valid prediction for snap_scaffold_6-snap.425-T1
Valid prediction for Augustus_model.g9357.t1
Valid prediction for Augustus_model.g9355.t1
Valid prediction for snap_scaffold_6-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_14085-T1
Couldn't classify 179363, 179427
Sorry, prediction CodingQuarry_transcript_54934-T1 fails validation.
(ATG)	 AC	179092-179146	GT	AGG
(GAT)	 AG	179363-179427	GG	GAG
(AAG)	 AG	179455-179547	AA	GAA
-recovered CodingQuarry_transcript_54934-T1, initial, 179092, 179146
-recovered CodingQuarry_transcript_54934-T1, terminal, 179455, 179547
Couldn't classify 190041, 190107
Sorry, prediction pasa_asmbl_46747.p1 fails validation.
(ATC)	 CC	190041-190107	GT	AGG
(CCT)	 AG	190201-190335	GT	AAG
(GAG)	 AG	190543-190826	TA	AGT
-recovered pasa_asmbl_46747.p1, terminal, 190543, 190826
-recovered pasa_asmbl_46747.p1, internal, 190201, 190335
Valid prediction for pasa_asmbl_46739.p1
Valid prediction for snap_scaffold_6-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_14092-T1
Valid prediction for GlimmerHMM_glimmerT_14103-T1
Valid prediction for snap_scaffold_6-snap.387-T1
Valid prediction for HiQ_model.g9353.t1
Valid prediction for GlimmerHMM_glimmerT_14090-T1
Valid prediction for GlimmerHMM_glimmerT_14087-T1
Valid prediction for GlimmerHMM_glimmerT_14078-T1
Valid prediction for GlimmerHMM_glimmerT_14104-T1
Valid prediction for snap_scaffold_6-snap.430-T1
Valid prediction for Augustus_model.g9366.t1
Valid prediction for snap_scaffold_6-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_14083-T1
Valid prediction for snap_scaffold_6-snap.431-T1
Valid prediction for snap_scaffold_6-snap.401-T1
Valid prediction for Augustus_model.g9360.t1
Valid prediction for snap_scaffold_6-snap.396-T1
Valid prediction for snap_scaffold_6-snap.417-T1
Valid prediction for snap_scaffold_6-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_14094-T1
Valid prediction for GlimmerHMM_glimmerT_14093-T1
Couldn't classify 179865, 180225
Sorry, prediction pasa_asmbl_46745.p1 fails validation.
(TCC)	 CC	179865-180225	GT	TGG
(TGG)	 AG	181349-181409	GT	AGG
(GGA)	 AG	181939-182052	GT	AGG
(CTT)	 AG	182384-182534	CC	GAC
-recovered pasa_asmbl_46745.p1, terminal, 182384, 182534
-recovered pasa_asmbl_46745.p1, internal, 181349, 181409
-recovered pasa_asmbl_46745.p1, internal, 181939, 182052
Valid prediction for GlimmerHMM_glimmerT_14107-T1
Valid prediction for snap_scaffold_6-snap.394-T1
Valid prediction for CodingQuarry_transcript_54935-T1
Valid prediction for snap_scaffold_6-snap.400-T1
Valid prediction for snap_scaffold_6-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_14101-T1
Valid prediction for snap_scaffold_6-snap.403-T1
Valid prediction for snap_scaffold_6-snap.384-T1
Valid prediction for CodingQuarry_transcript_54933-T1
Valid prediction for snap_scaffold_6-snap.422-T1
Valid prediction for snap_scaffold_6-snap.404-T1
Couldn't classify 179363, 179780
Sorry, prediction pasa_asmbl_48003.p1 fails validation.
(ATG)	 AC	175638-175693	GT	AGG
(CCC)	 AG	175991-176149	GT	CGG
(TGG)	 AG	176804-176867	GT	CTG
(GGG)	 AG	177244-177327	GT	GTG
(GGC)	 AG	177436-177534	GT	AGG
(GTG)	 AG	178779-178831	GT	AGG
(CCC)	 AG	179045-179146	GT	AGG
(GAT)	 AG	179363-179780	CC	TGC
-recovered pasa_asmbl_48003.p1, initial, 175638, 175693
-recovered pasa_asmbl_48003.p1, internal, 175991, 176149
-recovered pasa_asmbl_48003.p1, internal, 176804, 176867
-recovered pasa_asmbl_48003.p1, internal, 177244, 177327
-recovered pasa_asmbl_48003.p1, internal, 177436, 177534
-recovered pasa_asmbl_48003.p1, internal, 178779, 178831
-recovered pasa_asmbl_48003.p1, internal, 179045, 179146
Valid prediction for GlimmerHMM_glimmerT_14096-T1
Valid prediction for Augustus_model.g9356.t1
Valid prediction for snap_scaffold_6-snap.392-T1
Valid prediction for Augustus_model.g9364.t1
Couldn't classify 104356, 104504
Sorry, prediction pasa_asmbl_46742.p1 fails validation.
(AAG)	 AC	104356-104504	GT	AGG
(TAT)	 AG	104796-104931	GT	AGG
(TCC)	 AG	105420-105581	TG	GAT
-recovered pasa_asmbl_46742.p1, terminal, 105420, 105581
-recovered pasa_asmbl_46742.p1, internal, 104796, 104931
Valid prediction for GlimmerHMM_glimmerT_14100-T1
Valid prediction for snap_scaffold_6-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_14095-T1
Valid prediction for snap_scaffold_6-snap.416-T1
Valid prediction for snap_scaffold_6-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_14106-T1
Valid prediction for GlimmerHMM_glimmerT_14098-T1
Valid prediction for snap_scaffold_6-snap.424-T1
Couldn't classify 185208, 185297
Couldn't classify 189501, 189538
Sorry, prediction pasa_asmbl_46746.p1 fails validation.
(CAG)	 AC	185208-185297	GT	TGG
(GAT)	 AG	186376-186420	GT	TGG
(GGG)	 AG	186618-186727	GT	GAG
(TAT)	 AG	189134-189306	GT	CAG
(ATG)	 AG	189501-189538	AA	AGA
-recovered pasa_asmbl_46746.p1, internal, 186376, 186420
-recovered pasa_asmbl_46746.p1, internal, 186618, 186727
-recovered pasa_asmbl_46746.p1, internal, 189134, 189306
Valid prediction for snap_scaffold_6-snap.419-T1
Valid prediction for snap_scaffold_6-snap.402-T1
Valid prediction for CodingQuarry_transcript_54928-T1
Valid prediction for snap_scaffold_6-snap.414-T1
Valid prediction for snap_scaffold_6-snap.407-T1
Valid prediction for Augustus_model.g9365.t1
Valid prediction for snap_scaffold_6-snap.397-T1
Valid prediction for Augustus_model.g9358.t1
Valid prediction for CodingQuarry_transcript_54932-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 CodingQuarry_transcript_54931-T1
Valid prediction for pasa_asmbl_48112.p1
Valid prediction for snap_scaffold_6-snap.405-T1
Valid prediction for Augustus_model.g9350.t1
Valid prediction for CodingQuarry_transcript_54929-T1
Valid prediction for Augustus_model.g9347.t1
Valid prediction for GlimmerHMM_glimmerT_14077-T1
Valid prediction for GlimmerHMM_glimmerT_14080-T1
Valid prediction for Augustus_model.g9363.t1
Valid prediction for snap_scaffold_6-snap.423-T1
Valid prediction for GlimmerHMM_glimmerT_14091-T1
Valid prediction for CodingQuarry_transcript_54927-T1
Valid prediction for snap_scaffold_6-snap.389-T1
Valid prediction for pasa_asmbl_48110.p2
Valid prediction for GlimmerHMM_glimmerT_14079-T1
Valid prediction for GlimmerHMM_glimmerT_14105-T1
Couldn't classify 115732, 116073
Sorry, prediction pasa_asmbl_48111.p1 fails validation.
(ATG)	 TC	115732-116073	TT	CCT
Valid prediction for GlimmerHMM_glimmerT_14076-T1
Valid prediction for snap_scaffold_6-snap.409-T1
Valid prediction for Augustus_model.g9349.t1
Valid prediction for Augustus_model.g9362.t1
Valid prediction for snap_scaffold_6-snap.420-T1
Valid prediction for GlimmerHMM_glimmerT_14099-T1
Valid prediction for snap_scaffold_6-snap.412-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.410-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14086-T1
Valid prediction for Augustus_model.g9351.t1
Valid prediction for Augustus_model.g9359.t1
Valid prediction for snap_scaffold_6-snap.426-T1
Valid prediction for snap_scaffold_6-snap.406-T1
Valid prediction for snap_scaffold_6-snap.399-T1
Couldn't classify 129186, 129507
Couldn't classify 131359, 131462
Sorry, prediction pasa_asmbl_49343.p1 fails validation.
(CAG)	 AC	129186-129507	GT	TGG
(ACG)	 AG	131359-131462	AG	AGA
Valid prediction for snap_scaffold_6-snap.391-T1
Valid prediction for CodingQuarry_transcript_54930-T1
Valid prediction for GlimmerHMM_glimmerT_14082-T1
Valid prediction for snap_scaffold_6-snap.386-T1
Valid prediction for HiQ_model.g9354.t1
Valid prediction for snap_scaffold_6-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_14102-T1
Valid prediction for HiQ_model.g9352.t1
Valid prediction for snap_scaffold_6-snap.395-T1
Valid prediction for snap_scaffold_6-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_14088-T1
Valid prediction for snap_scaffold_6-snap.383-T1
Valid prediction for snap_scaffold_6-snap.393-T1
Valid prediction for snap_scaffold_6-snap.415-T1
Valid prediction for snap_scaffold_6-snap.429-T1
Valid prediction for Augustus_model.g9348.t1
Valid prediction for GlimmerHMM_glimmerT_14081-T1
Valid prediction for GlimmerHMM_glimmerT_14084-T1
Valid prediction for GlimmerHMM_glimmerT_14089-T1
Valid prediction for snap_scaffold_6-snap.427-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27903, rend_intergenic: 9359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28549, rend_intergenic: 28093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36006, rend_intergenic: 28606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44795, rend_intergenic: 36047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56015, rend_intergenic: 51145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65628, rend_intergenic: 62327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67406, rend_intergenic: 66810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82196, rend_intergenic: 67477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88841, rend_intergenic: 83268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105581, rend_intergenic: 99353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109857, rend_intergenic: 108965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121677, rend_intergenic: 111996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124037, rend_intergenic: 121959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125513, rend_intergenic: 124219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128646, rend_intergenic: 126543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143803, rend_intergenic: 130152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154112, rend_intergenic: 150996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157461, rend_intergenic: 154770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170299, rend_intergenic: 157552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175337, rend_intergenic: 171135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182534, rend_intergenic: 175966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185287, rend_intergenic: 183137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190826, rend_intergenic: 186560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199051
-exon list size: 466


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 27903, rend_intergenic: 9359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28549, rend_intergenic: 28093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36006, rend_intergenic: 28606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44795, rend_intergenic: 36047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56015, rend_intergenic: 51145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65628, rend_intergenic: 62327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67406, rend_intergenic: 66810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82196, rend_intergenic: 67477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88841, rend_intergenic: 83268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105581, rend_intergenic: 99353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109857, rend_intergenic: 108965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121677, rend_intergenic: 111996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124037, rend_intergenic: 121959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125513, rend_intergenic: 124219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128646, rend_intergenic: 126543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143803, rend_intergenic: 130152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154112, rend_intergenic: 150996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157461, rend_intergenic: 154770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170299, rend_intergenic: 157552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175337, rend_intergenic: 171135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182534, rend_intergenic: 175966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185287, rend_intergenic: 183137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190826, rend_intergenic: 186560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support