-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_4788084-4962692

-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_2-snap.1101-T1
Valid prediction for HiQ_model.g2499.t1
Valid prediction for snap_scaffold_2-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_3720-T1
Valid prediction for GlimmerHMM_glimmerT_3734-T1
Valid prediction for snap_scaffold_2-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_3717-T1
Valid prediction for snap_scaffold_2-snap.1112-T1
Couldn't classify 97457, 97507
Couldn't classify 98979, 98986
Sorry, prediction pasa_asmbl_24385.p1 fails validation.
(AAC)	 GG	97457-97507	GT	CGG
(GTG)	 AG	97712-97852	GT	AGG
(ACT)	 AG	98108-98212	GT	AGG
(TCT)	 AG	98473-98559	GT	AGG
(ATC)	 AG	98753-98888	GT	AGG
(TAC)	 AG	98979-98986	TA	GCT
-recovered pasa_asmbl_24385.p1, internal, 97712, 97852
-recovered pasa_asmbl_24385.p1, internal, 98108, 98212
-recovered pasa_asmbl_24385.p1, internal, 98473, 98559
-recovered pasa_asmbl_24385.p1, internal, 98753, 98888
Valid prediction for GlimmerHMM_glimmerT_3742-T1
Valid prediction for snap_scaffold_2-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_3723-T1
Valid prediction for snap_scaffold_2-snap.1089-T1
Valid prediction for snap_scaffold_2-snap.1115-T1
Valid prediction for GlimmerHMM_glimmerT_3735-T1
Valid prediction for Augustus_model.g2493.t1
Valid prediction for GlimmerHMM_glimmerT_3746-T1
Valid prediction for snap_scaffold_2-snap.1102-T1
Valid prediction for snap_scaffold_2-snap.1117-T1
Valid prediction for snap_scaffold_2-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_3739-T1
Valid prediction for snap_scaffold_2-snap.1087-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1104-T1
Valid prediction for snap_scaffold_2-snap.1103-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 99505, 99656
Sorry, prediction pasa_asmbl_24386.p1 fails validation.
(CTG)	 TA	99505-99656	GT	AGG
(CAC)	 AG	99815-99947	GT	GAG
(GTG)	 AG	100349-100468	GT	AGG
(ATC)	 AG	100563-100700	GT	AGG
(GTG)	 AG	101166-101278	GT	ATG
(GAA)	 AG	101479-101627	GT	AGG
(TGG)	 AG	101750-101856	GG	GAG
-recovered pasa_asmbl_24386.p1, terminal, 101750, 101856
-recovered pasa_asmbl_24386.p1, internal, 99815, 99947
-recovered pasa_asmbl_24386.p1, internal, 100349, 100468
-recovered pasa_asmbl_24386.p1, internal, 100563, 100700
-recovered pasa_asmbl_24386.p1, internal, 101166, 101278
-recovered pasa_asmbl_24386.p1, internal, 101479, 101627
Valid prediction for snap_scaffold_2-snap.1097-T1
Valid prediction for snap_scaffold_2-snap.1105-T1
Valid prediction for snap_scaffold_2-snap.1100-T1
Valid prediction for GlimmerHMM_glimmerT_3733-T1
Valid prediction for Augustus_model.g2500.t1
Valid prediction for GlimmerHMM_glimmerT_3725-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 Augustus_model.g2492.t1
Valid prediction for snap_scaffold_2-snap.1094-T1
Couldn't classify 61318, 61432
Sorry, prediction pasa_asmbl_23112.p1 fails validation.
(AGG)	 CC	61318-61432	GT	AGG
(GCT)	 AG	61539-61672	GT	AGG
(ATG)	 AG	61864-61947	GT	TGG
(GAT)	 AG	62047-62129	GT	ATG
(ATA)	 AG	62318-62361	GT	AGG
(GAG)	 AG	62459-62505	GT	AGG
(TGG)	 AG	62615-62673	GT	CGG
(GTC)	 AG	63537-63609	GT	AGG
(GTG)	 AG	63971-64060	AC	GAA
-recovered pasa_asmbl_23112.p1, initial, 61864, 61947
-recovered pasa_asmbl_23112.p1, terminal, 63971, 64060
-recovered pasa_asmbl_23112.p1, internal, 61539, 61672
-recovered pasa_asmbl_23112.p1, internal, 61864, 61947
-recovered pasa_asmbl_23112.p1, internal, 62047, 62129
-recovered pasa_asmbl_23112.p1, internal, 62318, 62361
-recovered pasa_asmbl_23112.p1, internal, 62459, 62505
-recovered pasa_asmbl_23112.p1, internal, 62615, 62673
-recovered pasa_asmbl_23112.p1, internal, 63537, 63609
Valid prediction for snap_scaffold_2-snap.1099-T1
Valid prediction for Augustus_model.g2502.t1
Valid prediction for Augustus_model.g2497.t1
Valid prediction for GlimmerHMM_glimmerT_3745-T1
Valid prediction for GlimmerHMM_glimmerT_3731-T1
Valid prediction for GlimmerHMM_glimmerT_3716-T1
Valid prediction for GlimmerHMM_glimmerT_3741-T1
Valid prediction for snap_scaffold_2-snap.1091-T1
Valid prediction for snap_scaffold_2-snap.1108-T1
Valid prediction for snap_scaffold_2-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_3730-T1
Valid prediction for snap_scaffold_2-snap.1109-T1
Couldn't classify 88843, 88908
Couldn't classify 93336, 93381
Sorry, prediction pasa_asmbl_23988.p1 fails validation.
(CAG)	 TC	88843-88908	GT	GGG
(ACG)	 AG	90233-90361	GT	AGG
(CCC)	 AG	91697-91771	GT	AGG
(ATC)	 AG	92876-92968	GT	AGG
(AAC)	 AG	93101-93240	GT	AGG
(CTA)	 AG	93336-93381	GC	AGG
-recovered pasa_asmbl_23988.p1, internal, 90233, 90361
-recovered pasa_asmbl_23988.p1, internal, 91697, 91771
-recovered pasa_asmbl_23988.p1, internal, 92876, 92968
-recovered pasa_asmbl_23988.p1, internal, 93101, 93240
-recovered pasa_asmbl_23988.p1, internal, 93336, 93381
Valid prediction for CodingQuarry_transcript_28544-T1
Valid prediction for pasa_asmbl_23105.p1
Valid prediction for GlimmerHMM_glimmerT_3729-T1
Valid prediction for GlimmerHMM_glimmerT_3722-T1
Valid prediction for Augustus_model.g2504.t1
Valid prediction for GlimmerHMM_glimmerT_3721-T1
Valid prediction for snap_scaffold_2-snap.1090-T1
Valid prediction for snap_scaffold_2-snap.1111-T1
Valid prediction for snap_scaffold_2-snap.1114-T1
Valid prediction for Augustus_model.g2505.t1
Valid prediction for GlimmerHMM_glimmerT_3737-T1
Valid prediction for GlimmerHMM_glimmerT_3727-T1
Valid prediction for GlimmerHMM_glimmerT_3719-T1
Valid prediction for Augustus_model.g2491.t1
Valid prediction for snap_scaffold_2-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_3728-T1
Valid prediction for Augustus_model.g2496.t1
Valid prediction for snap_scaffold_2-snap.1086-T1
Valid prediction for Augustus_model.g2501.t1
Valid prediction for GlimmerHMM_glimmerT_3724-T1
Valid prediction for Augustus_model.g2490.t1
Valid prediction for GlimmerHMM_glimmerT_3732-T1
Valid prediction for snap_scaffold_2-snap.1118-T1
Valid prediction for Augustus_model.g2506.t1
Couldn't classify 59424, 59502
Sorry, prediction pasa_asmbl_23114.p1 fails validation.
(ATG)	 AA	58630-58693	GT	AGG
(GGA)	 AG	58848-58930	GT	AGG
(ACG)	 AG	59102-59185	GT	AGG
(GTG)	 AG	59287-59330	GT	TGG
(TGG)	 AG	59424-59502	GG	GAG
-recovered pasa_asmbl_23114.p1, initial, 58630, 58693
-recovered pasa_asmbl_23114.p1, internal, 58848, 58930
-recovered pasa_asmbl_23114.p1, internal, 59102, 59185
-recovered pasa_asmbl_23114.p1, internal, 59287, 59330
Valid prediction for snap_scaffold_2-snap.1106-T1
Couldn't classify 82330, 82447
Sorry, prediction pasa_asmbl_23110.p1 fails validation.
(ATG)	 CC	81823-82001	GT	GCG
(GTC)	 AG	82330-82447	GT	AGG
-recovered pasa_asmbl_23110.p1, initial, 81823, 82001
-recovered pasa_asmbl_23110.p1, internal, 82330, 82447
Valid prediction for GlimmerHMM_glimmerT_3738-T1
Valid prediction for GlimmerHMM_glimmerT_3736-T1
Valid prediction for CodingQuarry_transcript_28545-T1
Valid prediction for snap_scaffold_2-snap.1119-T1
Valid prediction for snap_scaffold_2-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_3718-T1
Valid prediction for GlimmerHMM_glimmerT_3743-T1
Couldn't classify 48460, 48534
Sorry, prediction pasa_asmbl_23992.p1 fails validation.
(AAC)	 GA	48460-48534	GT	GTG
(GTT)	 AG	49731-49847	GT	AGG
(CAT)	 AG	50743-50838	GT	AGG
(GAC)	 AG	51238-51267	TG	GAT
-recovered pasa_asmbl_23992.p1, terminal, 51238, 51267
-recovered pasa_asmbl_23992.p1, internal, 49731, 49847
-recovered pasa_asmbl_23992.p1, internal, 50743, 50838
Valid prediction for HiQ_model.g2494.t1
Couldn't classify 40310, 40480
Sorry, prediction pasa_asmbl_23116.p1 fails validation.
(ATG)	 AG	37790-37867	GT	AGG
(ATA)	 AG	38411-38497	GT	TAG
(GCC)	 AG	40310-40480	CT	GTC
-recovered pasa_asmbl_23116.p1, initial, 37790, 37867
-recovered pasa_asmbl_23116.p1, internal, 37790, 37867
-recovered pasa_asmbl_23116.p1, internal, 38411, 38497
Valid prediction for CodingQuarry_transcript_28547-T1
Valid prediction for Augustus_model.g2498.t1
Valid prediction for GlimmerHMM_glimmerT_3740-T1
Valid prediction for snap_scaffold_2-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_3744-T1
Valid prediction for GlimmerHMM_glimmerT_3726-T1
Valid prediction for Augustus_model.g2503.t1
Valid prediction for snap_scaffold_2-snap.1092-T1
Valid prediction for pasa_asmbl_23103.p1
Valid prediction for snap_scaffold_2-snap.1096-T1
Valid prediction for HiQ_model.g2495.t1
Valid prediction for GlimmerHMM_glimmerT_3715-T1
Valid prediction for pasa_asmbl_23108.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7557, rend_intergenic: 2921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18460, rend_intergenic: 10910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35490, rend_intergenic: 23242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57670, rend_intergenic: 55124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90398, rend_intergenic: 74717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113489, rend_intergenic: 110909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116115, rend_intergenic: 114377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128836, rend_intergenic: 120290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129572, rend_intergenic: 128852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136820, rend_intergenic: 129597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141885, rend_intergenic: 139467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149054, rend_intergenic: 144709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165327, rend_intergenic: 152459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171832, rend_intergenic: 165363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174609
-exon list size: 469


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 7557, rend_intergenic: 2921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18460, rend_intergenic: 10910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35490, rend_intergenic: 23242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57670, rend_intergenic: 55124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90398, rend_intergenic: 74717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113489, rend_intergenic: 110909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116115, rend_intergenic: 114377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128836, rend_intergenic: 120290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129572, rend_intergenic: 128852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136820, rend_intergenic: 129597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141885, rend_intergenic: 139467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149054, rend_intergenic: 144709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165327, rend_intergenic: 152459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171832, rend_intergenic: 165363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support