-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_1844668-2086063

-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_17-snap.398-T1
Valid prediction for snap_scaffold_17-snap.402-T1
Valid prediction for snap_scaffold_17-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_39815-T1
Valid prediction for GlimmerHMM_glimmerT_39838-T1
Valid prediction for Augustus_model.g26530.t1
Valid prediction for GlimmerHMM_glimmerT_39823-T1
Valid prediction for GlimmerHMM_glimmerT_39826-T1
Valid prediction for GlimmerHMM_glimmerT_39831-T1
Valid prediction for snap_scaffold_17-snap.409-T1
Valid prediction for snap_scaffold_17-snap.390-T1
Valid prediction for snap_scaffold_17-snap.423-T1
Valid prediction for snap_scaffold_17-snap.415-T1
Valid prediction for snap_scaffold_17-snap.428-T1
Valid prediction for snap_scaffold_17-snap.389-T1
Valid prediction for snap_scaffold_17-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_39818-T1
Valid prediction for GlimmerHMM_glimmerT_39827-T1
Valid prediction for snap_scaffold_17-snap.427-T1
Valid prediction for snap_scaffold_17-snap.433-T1
Valid prediction for snap_scaffold_17-snap.387-T1
Valid prediction for snap_scaffold_17-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_39834-T1
Valid prediction for snap_scaffold_17-snap.421-T1
Valid prediction for snap_scaffold_17-snap.407-T1
Valid prediction for snap_scaffold_17-snap.431-T1
Valid prediction for snap_scaffold_17-snap.393-T1
Valid prediction for snap_scaffold_17-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_39837-T1
Valid prediction for snap_scaffold_17-snap.420-T1
Valid prediction for snap_scaffold_17-snap.404-T1
Valid prediction for snap_scaffold_17-snap.412-T1
Valid prediction for snap_scaffold_17-snap.424-T1
Valid prediction for snap_scaffold_17-snap.417-T1
Valid prediction for snap_scaffold_17-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_39832-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_21875-T1
Valid prediction for snap_scaffold_17-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_39825-T1
Valid prediction for snap_scaffold_17-snap.385-T1
Valid prediction for snap_scaffold_17-snap.432-T1
Valid prediction for GlimmerHMM_glimmerT_39828-T1
Valid prediction for GlimmerHMM_glimmerT_39829-T1
Valid prediction for Augustus_model.g26529.t1
Valid prediction for snap_scaffold_17-snap.425-T1
Valid prediction for Augustus_model.g26533.t1
Valid prediction for snap_scaffold_17-snap.414-T1
Valid prediction for Augustus_model.g26522.t1
Valid prediction for Augustus_model.g26536.t1
Couldn't classify 140646, 140732
Sorry, prediction Augustus_model.g26528.t1 fails validation.
(TGC)	 AG	140646-140732	GT	AGG
(ATC)	 AG	141292-141448	GT	CAG
(GTA)	 AG	141577-141609	GT	AGG
(GTT)	 AG	142436-142627	GT	AGG
(CTG)	 AG	144793-144919	GT	AGG
(TCT)	 AG	146319-146521	GT	CAG
(GTT)	 AG	146625-146816	GT	AGG
(CTC)	 AG	147119-147257	GT	AGG
(CTT)	 AG	151346-151533	GT	AGG
(CCA)	 AG	151652-151846	GT	GGG
(CTC)	 AG	152401-152517	GT	TGG
(GTC)	 AG	152872-152936	AA	AGA
add_exon() Sorry, Augustus_model.g26528.t1 142436-142627-terminal-1 is invalid.
-recovered Augustus_model.g26528.t1, terminal, 142436, 142627
add_exon() Sorry, Augustus_model.g26528.t1 146625-146816-terminal-1 is invalid.
-recovered Augustus_model.g26528.t1, terminal, 146625, 146816
-recovered Augustus_model.g26528.t1, terminal, 152872, 152936
-recovered Augustus_model.g26528.t1, internal, 140646, 140732
-recovered Augustus_model.g26528.t1, internal, 141292, 141448
-recovered Augustus_model.g26528.t1, internal, 141577, 141609
-recovered Augustus_model.g26528.t1, internal, 142436, 142627
-recovered Augustus_model.g26528.t1, internal, 144793, 144919
-recovered Augustus_model.g26528.t1, internal, 146319, 146521
-recovered Augustus_model.g26528.t1, internal, 146625, 146816
-recovered Augustus_model.g26528.t1, internal, 147119, 147257
-recovered Augustus_model.g26528.t1, internal, 151346, 151533
-recovered Augustus_model.g26528.t1, internal, 151652, 151846
-recovered Augustus_model.g26528.t1, internal, 152401, 152517
Valid prediction for Augustus_model.g26524.t1
Valid prediction for snap_scaffold_17-snap.429-T1
Valid prediction for snap_scaffold_17-snap.401-T1
Valid prediction for GlimmerHMM_glimmerT_39836-T1
Valid prediction for snap_scaffold_17-snap.386-T1
Valid prediction for Augustus_model.g26531.t1
Valid prediction for Augustus_model.g26526.t1
Valid prediction for snap_scaffold_17-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_39819-T1
Valid prediction for HiQ_model.g26521.t1
Valid prediction for CodingQuarry_transcript_21874-T1
Valid prediction for GlimmerHMM_glimmerT_39822-T1
Valid prediction for snap_scaffold_17-snap.395-T1
Valid prediction for snap_scaffold_17-snap.426-T1
Valid prediction for snap_scaffold_17-snap.408-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.418-T1
Valid prediction for snap_scaffold_17-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_39816-T1
Valid prediction for snap_scaffold_17-snap.403-T1
Valid prediction for snap_scaffold_17-snap.434-T1
Valid prediction for HiQ_model.g26523.t1
Valid prediction for snap_scaffold_17-snap.430-T1
Valid prediction for snap_scaffold_17-snap.399-T1
Valid prediction for Augustus_model.g26525.t1
Valid prediction for snap_scaffold_17-snap.391-T1
Valid prediction for snap_scaffold_17-snap.388-T1
Valid prediction for snap_scaffold_17-snap.416-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39820-T1
Valid prediction for GlimmerHMM_glimmerT_39824-T1
Valid prediction for GlimmerHMM_glimmerT_39830-T1
Valid prediction for Augustus_model.g26534.t1
Valid prediction for pasa_asmbl_17737.p2
Valid prediction for snap_scaffold_17-snap.406-T1
Valid prediction for snap_scaffold_17-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_39817-T1
Valid prediction for Augustus_model.g26527.t1
Valid prediction for snap_scaffold_17-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_39833-T1
Valid prediction for Augustus_model.g26532.t1
Valid prediction for GlimmerHMM_glimmerT_39821-T1
Valid prediction for snap_scaffold_17-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_39835-T1
Valid prediction for Augustus_model.g26535.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12178, rend_intergenic: 10488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16590, rend_intergenic: 12194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20610, rend_intergenic: 16993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 24253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37901, rend_intergenic: 31305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42223, rend_intergenic: 37935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56707, rend_intergenic: 50332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61849, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66068, rend_intergenic: 63566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75957, rend_intergenic: 68068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82560, rend_intergenic: 77672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95632, rend_intergenic: 82582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102266, rend_intergenic: 96484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107322, rend_intergenic: 102894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113806, rend_intergenic: 107347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124500, rend_intergenic: 115417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145747, rend_intergenic: 128313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162229, rend_intergenic: 147294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179748, rend_intergenic: 165293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189814, rend_intergenic: 180571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192898, rend_intergenic: 189934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199756, rend_intergenic: 193021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202636, rend_intergenic: 200021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214568, rend_intergenic: 207718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219309, rend_intergenic: 214748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222517, rend_intergenic: 219437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229922, rend_intergenic: 224237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233113, rend_intergenic: 230143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239919, rend_intergenic: 238001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241396
-exon list size: 446


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 12178, rend_intergenic: 10488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16590, rend_intergenic: 12194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20610, rend_intergenic: 16993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 24253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37901, rend_intergenic: 31305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42223, rend_intergenic: 37935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56707, rend_intergenic: 50332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61849, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66068, rend_intergenic: 63566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75957, rend_intergenic: 68068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82560, rend_intergenic: 77672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95632, rend_intergenic: 82582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102266, rend_intergenic: 96484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107322, rend_intergenic: 102894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113806, rend_intergenic: 107347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124500, rend_intergenic: 115417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145747, rend_intergenic: 128313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162229, rend_intergenic: 147294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179748, rend_intergenic: 165293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189814, rend_intergenic: 180571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192898, rend_intergenic: 189934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199756, rend_intergenic: 193021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202636, rend_intergenic: 200021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214568, rend_intergenic: 207718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219309, rend_intergenic: 214748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222517, rend_intergenic: 219437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229922, rend_intergenic: 224237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233113, rend_intergenic: 230143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239919, rend_intergenic: 238001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support