-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_10754136-10931394

-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 GlimmerHMM_glimmerT_44802-T1
Valid prediction for snap_scaffold_19-snap.2092-T1
Couldn't classify 66516, 66552
Sorry, prediction pasa_asmbl_21660.p1 fails validation.
(CAA)	 CT	66516-66552	GT	AGG
(CCT)	 AG	67136-67319	GT	CAG
(GGC)	 AG	67422-67546	GT	AGG
(ACC)	 AG	67753-67781	AT	AAA
-recovered pasa_asmbl_21660.p1, terminal, 67753, 67781
-recovered pasa_asmbl_21660.p1, internal, 67136, 67319
-recovered pasa_asmbl_21660.p1, internal, 67422, 67546
Valid prediction for GlimmerHMM_glimmerT_44803-T1
Valid prediction for pasa_asmbl_21655.p1
Valid prediction for snap_scaffold_19-snap.2084-T1
Valid prediction for Augustus_model.g29703.t1
Valid prediction for GlimmerHMM_glimmerT_44817-T1
Valid prediction for Augustus_model.g29713.t1
Valid prediction for snap_scaffold_19-snap.2093-T1
Valid prediction for snap_scaffold_19-snap.2087-T1
Valid prediction for CodingQuarry_transcript_25786-T1
Valid prediction for snap_scaffold_19-snap.2072-T1
Valid prediction for HiQ_model.g29707.t1
Valid prediction for GlimmerHMM_glimmerT_44814-T1
Valid prediction for snap_scaffold_19-snap.2080-T1
Valid prediction for snap_scaffold_19-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_44815-T1
Valid prediction for GlimmerHMM_glimmerT_44795-T1
Valid prediction for GlimmerHMM_glimmerT_44818-T1
Valid prediction for snap_scaffold_19-snap.2086-T1
Valid prediction for snap_scaffold_19-snap.2069-T1
Valid prediction for snap_scaffold_19-snap.2059-T1
Valid prediction for Augustus_model.g29705.t1
Valid prediction for GlimmerHMM_glimmerT_44793-T1
Valid prediction for snap_scaffold_19-snap.2089-T1
Couldn't classify 8967, 9076
Sorry, prediction pasa_asmbl_21649.p2 fails validation.
(ATG)	 CC	8614-8827	GT	AGG
(GTG)	 AG	8967-9076	AG	GGA
-recovered pasa_asmbl_21649.p2, initial, 8614, 8827
Valid prediction for Augustus_model.g29715.t1
Valid prediction for snap_scaffold_19-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_44797-T1
Valid prediction for CodingQuarry_transcript_25787-T1
Valid prediction for snap_scaffold_19-snap.2065-T1
Valid prediction for GlimmerHMM_glimmerT_44794-T1
Valid prediction for snap_scaffold_19-snap.2062-T1
Valid prediction for snap_scaffold_19-snap.2057-T1
Valid prediction for Augustus_model.g29716.t1
Valid prediction for GlimmerHMM_glimmerT_44801-T1
Valid prediction for snap_scaffold_19-snap.2063-T1
Valid prediction for Augustus_model.g29706.t1
Valid prediction for pasa_asmbl_21659.p2
Valid prediction for snap_scaffold_19-snap.2070-T1
Valid prediction for snap_scaffold_19-snap.2079-T1
Couldn't classify 10857, 10880
Sorry, prediction pasa_asmbl_21650.p1 fails validation.
(AAG)	 GG	10857-10880	GT	AGG
(GTG)	 AG	11115-11249	GT	AGG
(GTG)	 AG	11393-11496	GT	AAG
(GGA)	 AG	11731-11855	GT	AGG
(GCC)	 AG	11984-12096	GT	AGG
(TTT)	 AG	12203-12340	GT	CGG
(GGG)	 AG	12486-12588	GT	CGG
(GTC)	 AG	13685-13785	GT	CAG
(GGG)	 AG	14195-14365	GT	AGG
(CGC)	 AG	14444-14572	AG	AGA
-recovered pasa_asmbl_21650.p1, terminal, 14444, 14572
-recovered pasa_asmbl_21650.p1, internal, 11115, 11249
-recovered pasa_asmbl_21650.p1, internal, 11393, 11496
-recovered pasa_asmbl_21650.p1, internal, 11731, 11855
-recovered pasa_asmbl_21650.p1, internal, 11984, 12096
-recovered pasa_asmbl_21650.p1, internal, 12203, 12340
-recovered pasa_asmbl_21650.p1, internal, 12486, 12588
-recovered pasa_asmbl_21650.p1, internal, 13685, 13785
-recovered pasa_asmbl_21650.p1, internal, 14195, 14365
Valid prediction for GlimmerHMM_glimmerT_44816-T1
Valid prediction for snap_scaffold_19-snap.2067-T1
Valid prediction for CodingQuarry_transcript_25788-T1
Valid prediction for Augustus_model.g29714.t1
Valid prediction for Augustus_model.g29701.t1
Valid prediction for Augustus_model.g29717.t1
Couldn't classify 27275, 27458
Couldn't classify 28396, 28810
Sorry, prediction pasa_asmbl_21653.p1 fails validation.
(GCG)	 AG	27275-27458	GT	TGG
(CGA)	 AG	27670-27845	GT	GGG
(GTG)	 AG	28092-28267	GC	AGG
(TAA)	 AG	28396-28810	AC	GGA
-recovered pasa_asmbl_21653.p1, internal, 27275, 27458
-recovered pasa_asmbl_21653.p1, internal, 27670, 27845
-recovered pasa_asmbl_21653.p1, internal, 28092, 28267
Valid prediction for GlimmerHMM_glimmerT_44799-T1
Valid prediction for GlimmerHMM_glimmerT_44798-T1
Valid prediction for HiQ_model.g29704.t1
Valid prediction for snap_scaffold_19-snap.2077-T1
Valid prediction for GlimmerHMM_glimmerT_44807-T1
Valid prediction for GlimmerHMM_glimmerT_44812-T1
Valid prediction for Augustus_model.g29700.t1
Couldn't classify 19368, 19715
Sorry, prediction pasa_asmbl_21652.p1 fails validation.
(ATG)	 TG	19368-19715	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_44806-T1
Valid prediction for Augustus_model.g29711.t1
Valid prediction for snap_scaffold_19-snap.2083-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_19-snap.2082-T1
Valid prediction for Augustus_model.g29710.t1
Valid prediction for GlimmerHMM_glimmerT_44804-T1
Valid prediction for snap_scaffold_19-snap.2090-T1
Valid prediction for Augustus_model.g29719.t1
Valid prediction for GlimmerHMM_glimmerT_44800-T1
Valid prediction for snap_scaffold_19-snap.2073-T1
Valid prediction for snap_scaffold_19-snap.2078-T1
Valid prediction for snap_scaffold_19-snap.2081-T1
Valid prediction for snap_scaffold_19-snap.2094-T1
Valid prediction for Augustus_model.g29712.t1
Valid prediction for GlimmerHMM_glimmerT_44819-T1
Valid prediction for Augustus_model.g29702.t1
Valid prediction for GlimmerHMM_glimmerT_44805-T1
Valid prediction for snap_scaffold_19-snap.2076-T1
Valid prediction for snap_scaffold_19-snap.2064-T1
Valid prediction for GlimmerHMM_glimmerT_44811-T1
Couldn't classify 72787, 72951
Couldn't classify 74184, 74444
Sorry, prediction pasa_asmbl_22365.p1 fails validation.
(GGT)	 AG	72787-72951	GT	TGG
(CAG)	 AG	73318-73518	GT	AGG
(GTG)	 AG	74184-74444	AG	TGA
-recovered pasa_asmbl_22365.p1, internal, 72787, 72951
-recovered pasa_asmbl_22365.p1, internal, 73318, 73518
Couldn't classify 105436, 105499
Couldn't classify 108603, 108611
Sorry, prediction pasa_asmbl_22355.p1 fails validation.
(CCG)	 GT	105436-105499	GT	AGG
(ATG)	 AG	105823-105933	GT	AGG
(GAA)	 AG	106124-106273	GT	GGG
(TGC)	 AG	106602-106789	GT	TGG
(GAG)	 AG	106882-106984	GT	AGG
(ATG)	 AG	107085-107189	GT	CAG
(GAC)	 AG	107373-107385	GT	CGG
(GCC)	 AG	108337-108370	GT	ATG
(CCT)	 AG	108603-108611	TT	ACT
add_exon() Sorry, pasa_asmbl_22355.p1 105823-105933-initial-1 is invalid.
-recovered pasa_asmbl_22355.p1, initial, 105823, 105933
add_exon() Sorry, pasa_asmbl_22355.p1 107085-107189-initial-1 is invalid.
-recovered pasa_asmbl_22355.p1, initial, 107085, 107189
add_exon() Sorry, pasa_asmbl_22355.p1 106882-106984-terminal-3 is invalid.
-recovered pasa_asmbl_22355.p1, terminal, 106882, 106984
-recovered pasa_asmbl_22355.p1, internal, 105823, 105933
-recovered pasa_asmbl_22355.p1, internal, 106124, 106273
-recovered pasa_asmbl_22355.p1, internal, 106602, 106789
-recovered pasa_asmbl_22355.p1, internal, 106882, 106984
-recovered pasa_asmbl_22355.p1, internal, 107085, 107189
-recovered pasa_asmbl_22355.p1, internal, 107373, 107385
-recovered pasa_asmbl_22355.p1, internal, 108337, 108370
Valid prediction for Augustus_model.g29708.t1
Valid prediction for snap_scaffold_19-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_44820-T1
Valid prediction for snap_scaffold_19-snap.2091-T1
Valid prediction for pasa_asmbl_22357.p1
Valid prediction for CodingQuarry_transcript_25789-T1
Valid prediction for GlimmerHMM_glimmerT_44808-T1
Valid prediction for snap_scaffold_19-snap.2074-T1
Valid prediction for snap_scaffold_19-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_44809-T1
Valid prediction for snap_scaffold_19-snap.2088-T1
Couldn't classify 108244, 108370
Sorry, prediction pasa_asmbl_22354.p1 fails validation.
(TTC)	 GC	108244-108370	GT	ATG
(CCT)	 AG	108603-108793	CC	AGC
-recovered pasa_asmbl_22354.p1, terminal, 108603, 108793
Valid prediction for snap_scaffold_19-snap.2075-T1
Valid prediction for snap_scaffold_19-snap.2058-T1
Valid prediction for HiQ_model.g29709.t1
Valid prediction for GlimmerHMM_glimmerT_44810-T1
Valid prediction for GlimmerHMM_glimmerT_44813-T1
Valid prediction for snap_scaffold_19-snap.2068-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44821-T1
Valid prediction for snap_scaffold_19-snap.2071-T1
Valid prediction for Augustus_model.g29718.t1
Couldn't classify 21086, 21135
Sorry, prediction pasa_asmbl_22369.p1 fails validation.
(CCC)	 TC	21086-21135	GT	GGG
(GTG)	 AG	21228-21322	GT	AGG
(ACC)	 AG	21411-21539	GT	AGG
(GAA)	 AG	21776-21918	GC	GAG
-recovered pasa_asmbl_22369.p1, terminal, 21776, 21918
-recovered pasa_asmbl_22369.p1, internal, 21228, 21322
-recovered pasa_asmbl_22369.p1, internal, 21411, 21539
-recovered pasa_asmbl_22369.p1, internal, 21776, 21918
Valid prediction for GlimmerHMM_glimmerT_44796-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14572, rend_intergenic: 8512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19577, rend_intergenic: 15408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30200, rend_intergenic: 20987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55116, rend_intergenic: 53269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60518, rend_intergenic: 55185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99403, rend_intergenic: 93191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106907, rend_intergenic: 101436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111512, rend_intergenic: 106968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147452, rend_intergenic: 146714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154745, rend_intergenic: 147460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161377, rend_intergenic: 158294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177259
-exon list size: 470


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 14572, rend_intergenic: 8512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19577, rend_intergenic: 15408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30200, rend_intergenic: 20987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55116, rend_intergenic: 53269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60518, rend_intergenic: 55185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99403, rend_intergenic: 93191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106907, rend_intergenic: 101436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111512, rend_intergenic: 106968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147452, rend_intergenic: 146714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154745, rend_intergenic: 147460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161377, rend_intergenic: 158294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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