-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_3783562-3928760

-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.892-T1
Valid prediction for snap_scaffold_2-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_3592-T1
Valid prediction for GlimmerHMM_glimmerT_3599-T1
Valid prediction for Augustus_model.g2394.t1
Valid prediction for snap_scaffold_2-snap.905-T1
Valid prediction for pasa_asmbl_24315.p1
Valid prediction for HiQ_model.g2395.t1
Valid prediction for CodingQuarry_transcript_28512-T1
Valid prediction for HiQ_model.g2409.t1
Valid prediction for snap_scaffold_2-snap.911-T1
Valid prediction for snap_scaffold_2-snap.913-T1
Valid prediction for snap_scaffold_2-snap.910-T1
Valid prediction for pasa_asmbl_24319.p1
Valid prediction for GlimmerHMM_glimmerT_3596-T1
Valid prediction for snap_scaffold_2-snap.917-T1
Valid prediction for snap_scaffold_2-snap.902-T1
Valid prediction for snap_scaffold_2-snap.907-T1
Valid prediction for GlimmerHMM_glimmerT_3580-T1
Valid prediction for snap_scaffold_2-snap.888-T1
Valid prediction for snap_scaffold_2-snap.920-T1
Valid prediction for snap_scaffold_2-snap.899-T1
Valid prediction for snap_scaffold_2-snap.922-T1
Valid prediction for CodingQuarry_transcript_28507-T1
Valid prediction for snap_scaffold_2-snap.916-T1
Valid prediction for snap_scaffold_2-snap.923-T1
Valid prediction for snap_scaffold_2-snap.903-T1
Valid prediction for snap_scaffold_2-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_3588-T1
Valid prediction for GlimmerHMM_glimmerT_3590-T1
Valid prediction for snap_scaffold_2-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_3579-T1
Valid prediction for HiQ_model.g2402.t1
Valid prediction for GlimmerHMM_glimmerT_3586-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_2-snap.912-T1
Valid prediction for HiQ_model.g2404.t1
Couldn't classify 24982, 25086
Sorry, prediction pasa_asmbl_23016.p1 fails validation.
(CTG)	 CC	24982-25086	GT	AGG
(GAC)	 AG	25188-25262	GT	AGG
(CGC)	 AG	25388-25548	GT	AGG
(GAG)	 AG	25683-25779	GT	AGG
(GGT)	 AG	25967-26164	TC	GAT
-recovered pasa_asmbl_23016.p1, terminal, 25967, 26164
-recovered pasa_asmbl_23016.p1, internal, 25188, 25262
-recovered pasa_asmbl_23016.p1, internal, 25388, 25548
-recovered pasa_asmbl_23016.p1, internal, 25683, 25779
Couldn't classify 46887, 47023
Sorry, prediction pasa_asmbl_23010.p1 fails validation.
(ATG)	 TC	44762-44831	GT	AGG
(TGG)	 AG	45289-45445	GT	CTG
(GAA)	 AG	45576-45697	GT	GAG
(TGG)	 AG	46887-47023	AG	ACA
-recovered pasa_asmbl_23010.p1, initial, 44762, 44831
-recovered pasa_asmbl_23010.p1, internal, 45289, 45445
-recovered pasa_asmbl_23010.p1, internal, 45576, 45697
Valid prediction for Augustus_model.g2403.t1
Valid prediction for GlimmerHMM_glimmerT_3600-T1
Valid prediction for Augustus_model.g2410.t1
Valid prediction for GlimmerHMM_glimmerT_3591-T1
Valid prediction for Augustus_model.g2401.t1
Valid prediction for GlimmerHMM_glimmerT_3594-T1
Valid prediction for GlimmerHMM_glimmerT_3601-T1
Couldn't classify 52865, 52947
Couldn't classify 56877, 57096
Sorry, prediction pasa_asmbl_23009.p1 fails validation.
(ACA)	 GA	52865-52947	GT	AGG
(GAC)	 AG	54265-54404	GT	AGG
(GTA)	 AG	54861-55101	GT	GGG
(CTG)	 AG	55504-55593	GT	GGG
(CTG)	 AG	56877-57096	CC	ACC
-recovered pasa_asmbl_23009.p1, internal, 54265, 54404
-recovered pasa_asmbl_23009.p1, internal, 54861, 55101
-recovered pasa_asmbl_23009.p1, internal, 55504, 55593
Valid prediction for snap_scaffold_2-snap.895-T1
Valid prediction for snap_scaffold_2-snap.921-T1
Valid prediction for GlimmerHMM_glimmerT_3582-T1
Couldn't classify 22537, 22631
Sorry, prediction pasa_asmbl_23019.p2 fails validation.
(ATG)	 CA	21265-21359	GT	AGG
(GTC)	 AG	21607-21643	GT	GGG
(AAC)	 AG	21733-21882	GT	AGG
(GTC)	 AG	22325-22433	GT	AGG
(ATG)	 AG	22537-22631	CA	CCC
-recovered pasa_asmbl_23019.p2, initial, 21265, 21359
-recovered pasa_asmbl_23019.p2, internal, 21607, 21643
-recovered pasa_asmbl_23019.p2, internal, 21733, 21882
-recovered pasa_asmbl_23019.p2, internal, 22325, 22433
Valid prediction for GlimmerHMM_glimmerT_3597-T1
Valid prediction for CodingQuarry_transcript_28506-T1
Valid prediction for GlimmerHMM_glimmerT_3593-T1
Valid prediction for HiQ_model.g2393.t1
Valid prediction for pasa_asmbl_23013.p1
Valid prediction for HiQ_model.g2408.t1
Couldn't classify 113970, 114127
Couldn't classify 114819, 115023
Sorry, prediction pasa_asmbl_24033.p1 fails validation.
(GAC)	 CC	113970-114127	GT	AGG
(ACT)	 AG	114819-115023	GT	AGG
-recovered pasa_asmbl_24033.p1, internal, 114819, 115023
Valid prediction for CodingQuarry_transcript_28508-T1
Valid prediction for snap_scaffold_2-snap.906-T1
Valid prediction for snap_scaffold_2-snap.918-T1
Couldn't classify 22953, 23185
Couldn't classify 24714, 24797
Sorry, prediction pasa_asmbl_23018.p1 fails validation.
(CAG)	 TC	22953-23185	GT	AGG
(TGT)	 AG	23454-23634	GT	CAG
(TGG)	 AG	23821-23948	GT	AGG
(TAG)	 AG	24063-24204	GT	CAG
(GTT)	 AG	24351-24434	GT	AGG
(GTG)	 AG	24545-24592	GT	AGG
(GTT)	 AG	24714-24797	GA	GAG
-recovered pasa_asmbl_23018.p1, internal, 23454, 23634
-recovered pasa_asmbl_23018.p1, internal, 23821, 23948
-recovered pasa_asmbl_23018.p1, internal, 24063, 24204
-recovered pasa_asmbl_23018.p1, internal, 24351, 24434
-recovered pasa_asmbl_23018.p1, internal, 24545, 24592
Valid prediction for GlimmerHMM_glimmerT_3578-T1
Valid prediction for snap_scaffold_2-snap.909-T1
Valid prediction for snap_scaffold_2-snap.915-T1
Valid prediction for snap_scaffold_2-snap.904-T1
Valid prediction for Augustus_model.g2406.t1
Valid prediction for snap_scaffold_2-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_3584-T1
Valid prediction for GlimmerHMM_glimmerT_3581-T1
Valid prediction for Augustus_model.g2392.t1
Valid prediction for snap_scaffold_2-snap.887-T1
Valid prediction for CodingQuarry_transcript_28511-T1
Valid prediction for CodingQuarry_transcript_28513-T1
Couldn't classify 116549, 116639
Sorry, prediction pasa_asmbl_23003.p1 fails validation.
(GTG)	 CA	116549-116639	GT	CGG
(GTT)	 AG	117255-117445	GT	TGG
(GTG)	 AG	117786-117878	AG	GAA
-recovered pasa_asmbl_23003.p1, terminal, 117786, 117878
-recovered pasa_asmbl_23003.p1, internal, 117255, 117445
Valid prediction for Augustus_model.g2405.t1
Valid prediction for GlimmerHMM_glimmerT_3585-T1
Valid prediction for Augustus_model.g2412.t1
Valid prediction for CodingQuarry_transcript_28510-T1
Valid prediction for HiQ_model.g2396.t1
Valid prediction for GlimmerHMM_glimmerT_3583-T1
Valid prediction for Augustus_model.g2397.t1
Couldn't classify 63683, 63765
Sorry, prediction pasa_asmbl_23008.p1 fails validation.
(GAG)	 CA	63683-63765	GT	GGG
(CTC)	 AG	66632-66710	GT	ATG
(TCG)	 AG	66813-66884	GT	AGG
(ATT)	 AG	67133-67221	GT	AGG
(GGA)	 AG	68521-68680	GT	TGG
(GCT)	 AG	70011-70144	GT	AAG
(GGA)	 AG	70306-70446	GT	AGG
(TCT)	 AG	70562-70682	GT	AGG
(CTG)	 AG	70792-70896	GT	AGG
(GTA)	 AG	71315-71411	GT	AGG
(GGA)	 AG	71722-71794	GT	TGG
(CTT)	 AG	71951-72050	GG	GAG
add_exon() Sorry, pasa_asmbl_23008.p1 71315-71411-terminal-3 is invalid.
-recovered pasa_asmbl_23008.p1, terminal, 71315, 71411
-recovered pasa_asmbl_23008.p1, terminal, 71951, 72050
-recovered pasa_asmbl_23008.p1, internal, 66632, 66710
-recovered pasa_asmbl_23008.p1, internal, 66813, 66884
-recovered pasa_asmbl_23008.p1, internal, 67133, 67221
-recovered pasa_asmbl_23008.p1, internal, 68521, 68680
-recovered pasa_asmbl_23008.p1, internal, 70011, 70144
-recovered pasa_asmbl_23008.p1, internal, 70306, 70446
-recovered pasa_asmbl_23008.p1, internal, 70562, 70682
-recovered pasa_asmbl_23008.p1, internal, 70792, 70896
-recovered pasa_asmbl_23008.p1, internal, 71315, 71411
-recovered pasa_asmbl_23008.p1, internal, 71722, 71794
Valid prediction for GlimmerHMM_glimmerT_3598-T1
Valid prediction for GlimmerHMM_glimmerT_3577-T1
Valid prediction for Augustus_model.g2400.t1
Valid prediction for snap_scaffold_2-snap.894-T1
Valid prediction for Augustus_model.g2398.t1
Valid prediction for GlimmerHMM_glimmerT_3595-T1
Valid prediction for CodingQuarry_transcript_28509-T1
Valid prediction for HiQ_model.g2407.t1
Valid prediction for snap_scaffold_2-snap.891-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3587-T1
Valid prediction for snap_scaffold_2-snap.919-T1
Valid prediction for snap_scaffold_2-snap.898-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.893-T1
Valid prediction for snap_scaffold_2-snap.901-T1
Valid prediction for snap_scaffold_2-snap.897-T1
Valid prediction for Augustus_model.g2399.t1
Valid prediction for HiQ_model.g2411.t1
Valid prediction for snap_scaffold_2-snap.908-T1
Valid prediction for pasa_asmbl_23012.p1
Valid prediction for snap_scaffold_2-snap.914-T1
Valid prediction for snap_scaffold_2-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_3589-T1
Valid prediction for pasa_asmbl_23001.p1
Valid prediction for pasa_asmbl_23020.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11792, rend_intergenic: 7744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20350, rend_intergenic: 18667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24502, rend_intergenic: 21955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36397, rend_intergenic: 29604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48714, rend_intergenic: 38741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69333, rend_intergenic: 65724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75900, rend_intergenic: 73150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78653, rend_intergenic: 76349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83718, rend_intergenic: 78669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100438, rend_intergenic: 83833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106450, rend_intergenic: 103957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114688, rend_intergenic: 111387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130519, rend_intergenic: 126360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142535, rend_intergenic: 133513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145199
-exon list size: 474


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11792, rend_intergenic: 7744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20350, rend_intergenic: 18667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24502, rend_intergenic: 21955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36397, rend_intergenic: 29604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48714, rend_intergenic: 38741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69333, rend_intergenic: 65724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75900, rend_intergenic: 73150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78653, rend_intergenic: 76349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83718, rend_intergenic: 78669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100438, rend_intergenic: 83833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106450, rend_intergenic: 103957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114688, rend_intergenic: 111387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130519, rend_intergenic: 126360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142535, rend_intergenic: 133513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support