-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_8622024-8822485

-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: +)Couldn't classify 104320, 104462
Sorry, prediction pasa_asmbl_11146.p1 fails validation.
(ACT)	 AA	104320-104462	GT	AGG
(GGA)	 AG	104900-104959	GT	AGG
(GCA)	 AG	105356-105451	GT	AGG
(GGG)	 AG	105624-105704	GT	AGG
(GAG)	 AG	106176-106299	GT	ACG
(GAC)	 AG	106467-106766	GG	AAG
-recovered pasa_asmbl_11146.p1, terminal, 106467, 106766
-recovered pasa_asmbl_11146.p1, internal, 104900, 104959
-recovered pasa_asmbl_11146.p1, internal, 105356, 105451
-recovered pasa_asmbl_11146.p1, internal, 105624, 105704
-recovered pasa_asmbl_11146.p1, internal, 106176, 106299
Valid prediction for Augustus_model.g21353.t1
Valid prediction for snap_scaffold_13-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_32029-T1
Valid prediction for GlimmerHMM_glimmerT_32031-T1
Valid prediction for HiQ_model.g21361.t1
Valid prediction for CodingQuarry_transcript_13172-T1
Couldn't classify 66562, 66720
Sorry, prediction pasa_asmbl_11600.p1 fails validation.
(CGG)	 TG	66562-66720	GT	AGG
(GGC)	 AG	66848-66989	GT	TGG
(CGG)	 AG	67197-67736	GT	AGG
(AGC)	 AG	67837-67958	GT	AGG
(CCT)	 AG	68062-68194	GT	AGG
(GCT)	 AG	68742-68849	GT	TGG
(GTT)	 AG	68984-69094	GT	TGG
(ACC)	 AG	69238-69350	GT	TGG
(ATG)	 AG	69468-69629	AA	AGA
add_exon() Sorry, pasa_asmbl_11600.p1 67197-67736-terminal-1 is invalid.
-recovered pasa_asmbl_11600.p1, terminal, 67197, 67736
-recovered pasa_asmbl_11600.p1, terminal, 69468, 69629
-recovered pasa_asmbl_11600.p1, internal, 66848, 66989
-recovered pasa_asmbl_11600.p1, internal, 67197, 67736
-recovered pasa_asmbl_11600.p1, internal, 67837, 67958
-recovered pasa_asmbl_11600.p1, internal, 68062, 68194
-recovered pasa_asmbl_11600.p1, internal, 68742, 68849
-recovered pasa_asmbl_11600.p1, internal, 68984, 69094
-recovered pasa_asmbl_11600.p1, internal, 69238, 69350
Valid prediction for HiQ_model.g21366.t1
Valid prediction for snap_scaffold_13-snap.1589-T1
Valid prediction for snap_scaffold_13-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_32028-T1
Valid prediction for Augustus_model.g21355.t1
Valid prediction for GlimmerHMM_glimmerT_32026-T1
Valid prediction for snap_scaffold_13-snap.1582-T1
Valid prediction for GlimmerHMM_glimmerT_32044-T1
Valid prediction for GlimmerHMM_glimmerT_32030-T1
Valid prediction for snap_scaffold_13-snap.1587-T1
Valid prediction for snap_scaffold_13-snap.1567-T1
Valid prediction for snap_scaffold_13-snap.1588-T1
Valid prediction for snap_scaffold_13-snap.1570-T1
Valid prediction for GlimmerHMM_glimmerT_32042-T1
Couldn't classify 90652, 90780
Couldn't classify 91240, 91337
Sorry, prediction pasa_asmbl_11603.p1 fails validation.
(GCC)	 GT	90652-90780	GT	CTG
(TGC)	 AG	90933-91155	GT	AGG
(TGG)	 AG	91240-91337	AA	TCA
-recovered pasa_asmbl_11603.p1, internal, 90933, 91155
Valid prediction for GlimmerHMM_glimmerT_32032-T1
Valid prediction for Augustus_model.g21368.t1
Valid prediction for snap_scaffold_13-snap.1592-T1
Valid prediction for snap_scaffold_13-snap.1593-T1
Valid prediction for CodingQuarry_transcript_13174-T1
Valid prediction for snap_scaffold_13-snap.1584-T1
Valid prediction for pasa_asmbl_11144.p1
Valid prediction for GlimmerHMM_glimmerT_32035-T1
Valid prediction for pasa_asmbl_11140.p1
Valid prediction for Augustus_model.g21356.t1
Valid prediction for HiQ_model.g21357.t1
Valid prediction for snap_scaffold_13-snap.1577-T1
Valid prediction for snap_scaffold_13-snap.1572-T1
Valid prediction for pasa_asmbl_11148.p1
Valid prediction for snap_scaffold_13-snap.1569-T1
Valid prediction for snap_scaffold_13-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_32047-T1
Valid prediction for Augustus_model.g21362.t1
Valid prediction for CodingQuarry_transcript_13176-T1
Valid prediction for Augustus_model.g21365.t1
Valid prediction for Augustus_model.g21359.t1
Valid prediction for CodingQuarry_transcript_13175-T1
Valid prediction for Augustus_model.g21358.t1
Valid prediction for GlimmerHMM_glimmerT_32036-T1
Valid prediction for snap_scaffold_13-snap.1579-T1
Valid prediction for GlimmerHMM_glimmerT_32024-T1
Valid prediction for snap_scaffold_13-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_32040-T1
Valid prediction for CodingQuarry_transcript_13173-T1
Valid prediction for GlimmerHMM_glimmerT_32033-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_13-snap.1581-T1
Valid prediction for snap_scaffold_13-snap.1590-T1
Couldn't classify 26325, 26516
Sorry, prediction pasa_asmbl_9975.p1 fails validation.
(ATG)	 GC	25373-25386	GT	AGG
(TCC)	 AG	26015-26177	GT	AGG
(ATA)	 AG	26325-26516	GA	GAG
-recovered pasa_asmbl_9975.p1, initial, 25373, 25386
-recovered pasa_asmbl_9975.p1, internal, 26015, 26177
Valid prediction for snap_scaffold_13-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_32039-T1
Valid prediction for GlimmerHMM_glimmerT_32041-T1
Valid prediction for CodingQuarry_transcript_13178-T1
Valid prediction for HiQ_model.g21360.t1
Valid prediction for snap_scaffold_13-snap.1578-T1
Valid prediction for snap_scaffold_13-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_32038-T1
Couldn't classify 102974, 103284
Sorry, prediction pasa_asmbl_9968.p1 fails validation.
(CAG)	 CC	102974-103284	GT	AGG
(TTC)	 AG	103430-104072	GT	AGG
(GCT)	 AG	104284-104379	GT	AGG
(GTC)	 AG	104471-104616	GT	CGG
(ATC)	 AG	104784-104946	GT	AGG
(GTG)	 AG	105036-105150	GT	AGG
(GTG)	 AG	105290-105482	GT	AAG
(GCT)	 AG	105573-105695	GT	GAG
(AGG)	 AG	105818-106203	GT	AGG
(GGG)	 AG	106382-106872	AA	AGA
add_exon() Sorry, pasa_asmbl_9968.p1 105573-105695-terminal-1 is invalid.
-recovered pasa_asmbl_9968.p1, terminal, 105573, 105695
-recovered pasa_asmbl_9968.p1, terminal, 106382, 106872
-recovered pasa_asmbl_9968.p1, internal, 103430, 104072
-recovered pasa_asmbl_9968.p1, internal, 104284, 104379
-recovered pasa_asmbl_9968.p1, internal, 104471, 104616
-recovered pasa_asmbl_9968.p1, internal, 104784, 104946
-recovered pasa_asmbl_9968.p1, internal, 105036, 105150
-recovered pasa_asmbl_9968.p1, internal, 105290, 105482
-recovered pasa_asmbl_9968.p1, internal, 105573, 105695
-recovered pasa_asmbl_9968.p1, internal, 105818, 106203
Valid prediction for snap_scaffold_13-snap.1573-T1
Valid prediction for Augustus_model.g21363.t1
Valid prediction for HiQ_model.g21370.t1
Valid prediction for snap_scaffold_13-snap.1571-T1
Couldn't classify 10149, 10226
Sorry, prediction pasa_asmbl_9981.p1 fails validation.
(GGT)	 TA	10149-10226	GT	GGG
(GGC)	 AG	10435-10501	GT	AGG
(GAA)	 AG	11217-11257	GT	AGG
(CCG)	 AG	11389-11521	GT	GGG
(ATA)	 AG	11965-12074	AG	GAA
-recovered pasa_asmbl_9981.p1, terminal, 11965, 12074
-recovered pasa_asmbl_9981.p1, internal, 10435, 10501
-recovered pasa_asmbl_9981.p1, internal, 11217, 11257
-recovered pasa_asmbl_9981.p1, internal, 11389, 11521
Valid prediction for snap_scaffold_13-snap.1575-T1
Valid prediction for Augustus_model.g21371.t1
Valid prediction for snap_scaffold_13-snap.1565-T1
Couldn't classify 32220, 32462
Couldn't classify 32560, 32637
Sorry, prediction pasa_asmbl_10425.p1 fails validation.
(AAG)	 GT	32220-32462	GT	AGG
(GTA)	 AG	32560-32637	CA	CAC
Valid prediction for snap_scaffold_13-snap.1599-T1
Valid prediction for snap_scaffold_13-snap.1568-T1
Valid prediction for snap_scaffold_13-snap.1595-T1
Valid prediction for GlimmerHMM_glimmerT_32027-T1
Valid prediction for snap_scaffold_13-snap.1591-T1
Valid prediction for Augustus_model.g21373.t1
Couldn't classify 67053, 67612
Sorry, prediction pasa_asmbl_9970.p1 fails validation.
(ATC)	 AA	67053-67612	GT	AGG
(ATT)	 AG	67699-67818	GT	AAG
(GTT)	 AG	67955-68111	GT	AGG
(GCT)	 AG	68281-68386	GT	GGG
(ATA)	 AG	68511-68708	GT	AGG
(GCC)	 AG	68821-69013	GT	AGG
(GTT)	 AG	69123-69210	GT	AGG
(ATC)	 AG	69308-69454	GT	AGG
(GGT)	 AG	69619-69780	TC	AGT
add_exon() Sorry, pasa_asmbl_9970.p1 67699-67818-terminal-1 is invalid.
-recovered pasa_asmbl_9970.p1, terminal, 67699, 67818
-recovered pasa_asmbl_9970.p1, terminal, 69619, 69780
-recovered pasa_asmbl_9970.p1, internal, 67699, 67818
-recovered pasa_asmbl_9970.p1, internal, 67955, 68111
-recovered pasa_asmbl_9970.p1, internal, 68281, 68386
-recovered pasa_asmbl_9970.p1, internal, 68511, 68708
-recovered pasa_asmbl_9970.p1, internal, 68821, 69013
-recovered pasa_asmbl_9970.p1, internal, 69123, 69210
-recovered pasa_asmbl_9970.p1, internal, 69308, 69454
Valid prediction for snap_scaffold_13-snap.1600-T1
Valid prediction for snap_scaffold_13-snap.1602-T1
Valid prediction for Augustus_model.g21354.t1
Valid prediction for GlimmerHMM_glimmerT_32025-T1
Valid prediction for HiQ_model.g21372.t1
Valid prediction for GlimmerHMM_glimmerT_32043-T1
Valid prediction for HiQ_model.g21367.t1
Valid prediction for GlimmerHMM_glimmerT_32037-T1
Valid prediction for GlimmerHMM_glimmerT_32045-T1
Valid prediction for GlimmerHMM_glimmerT_32046-T1
Valid prediction for GlimmerHMM_glimmerT_32048-T1
Valid prediction for Augustus_model.g21369.t1
Valid prediction for snap_scaffold_13-snap.1594-T1
Valid prediction for CodingQuarry_transcript_13177-T1
Valid prediction for snap_scaffold_13-snap.1603-T1
Valid prediction for snap_scaffold_13-snap.1566-T1
Valid prediction for snap_scaffold_13-snap.1586-T1
Valid prediction for snap_scaffold_13-snap.1597-T1
Valid prediction for snap_scaffold_13-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_32034-T1
Valid prediction for snap_scaffold_13-snap.1585-T1
Valid prediction for Augustus_model.g21364.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23825, rend_intergenic: 17603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47536, rend_intergenic: 36603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 49487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65771, rend_intergenic: 63593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78250, rend_intergenic: 74220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97062, rend_intergenic: 93882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120308, rend_intergenic: 115895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146237, rend_intergenic: 135739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159257, rend_intergenic: 146911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190923, rend_intergenic: 187039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200462
-exon list size: 463


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 23825, rend_intergenic: 17603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47536, rend_intergenic: 36603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 49487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65771, rend_intergenic: 63593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78250, rend_intergenic: 74220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97062, rend_intergenic: 93882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120308, rend_intergenic: 115895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146237, rend_intergenic: 135739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159257, rend_intergenic: 146911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190923, rend_intergenic: 187039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support