-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_11196807-11417086

-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_32371-T1
Valid prediction for GlimmerHMM_glimmerT_32380-T1
Valid prediction for pasa_asmbl_11266.p1
Valid prediction for Augustus_model.g21614.t1
Couldn't classify 24465, 24648
Sorry, prediction pasa_asmbl_11255.p1 fails validation.
(ATG)	 CC	21676-21750	GT	AGG
(GTG)	 AG	21948-22792	GT	AGG
(GTC)	 AG	24465-24648	GG	CAG
-recovered pasa_asmbl_11255.p1, initial, 21676, 21750
-recovered pasa_asmbl_11255.p1, internal, 21948, 22792
Valid prediction for snap_scaffold_13-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_32358-T1
Valid prediction for Augustus_model.g21607.t1
Valid prediction for Augustus_model.g21626.t1
Valid prediction for snap_scaffold_13-snap.2104-T1
Valid prediction for snap_scaffold_13-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_32363-T1
Valid prediction for HiQ_model.g21618.t1
Valid prediction for snap_scaffold_13-snap.2102-T1
Valid prediction for CodingQuarry_transcript_13242-T1
Valid prediction for Augustus_model.g21611.t1
Valid prediction for snap_scaffold_13-snap.2071-T1
Valid prediction for snap_scaffold_13-snap.2068-T1
Valid prediction for snap_scaffold_13-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_32384-T1
Valid prediction for GlimmerHMM_glimmerT_32386-T1
Valid prediction for snap_scaffold_13-snap.2097-T1
Valid prediction for HiQ_model.g21623.t1
Valid prediction for snap_scaffold_13-snap.2108-T1
Valid prediction for snap_scaffold_13-snap.2069-T1
Valid prediction for Augustus_model.g21604.t1
Valid prediction for GlimmerHMM_glimmerT_32360-T1
Valid prediction for GlimmerHMM_glimmerT_32372-T1
Couldn't classify 147323, 147399
Couldn't classify 147606, 147750
Sorry, prediction pasa_asmbl_11261.p1 fails validation.
(ATG)	 AA	144859-145039	GT	ATG
(ATA)	 AG	145437-145536	GT	GTG
(GTA)	 AG	145717-145864	GT	AGG
(GTT)	 AG	146045-146205	GC	AGG
(TTT)	 AG	146516-146636	GT	AGG
(CTG)	 AG	146941-147146	GT	AGG
(GCC)	 AG	147323-147399	AT	TCA
(AGA)	 AC	147606-147750	GT	AGG
(GGT)	 AG	148008-148185	GC	GAG
-recovered pasa_asmbl_11261.p1, initial, 144859, 145039
add_exon() Sorry, pasa_asmbl_11261.p1 146045-146205-terminal-2 is invalid.
-recovered pasa_asmbl_11261.p1, terminal, 146045, 146205
-recovered pasa_asmbl_11261.p1, terminal, 148008, 148185
-recovered pasa_asmbl_11261.p1, internal, 145437, 145536
-recovered pasa_asmbl_11261.p1, internal, 145717, 145864
-recovered pasa_asmbl_11261.p1, internal, 146045, 146205
-recovered pasa_asmbl_11261.p1, internal, 146516, 146636
-recovered pasa_asmbl_11261.p1, internal, 146941, 147146
-recovered pasa_asmbl_11261.p1, internal, 148008, 148185
Valid prediction for pasa_asmbl_11263.p1
Valid prediction for GlimmerHMM_glimmerT_32355-T1
Valid prediction for GlimmerHMM_glimmerT_32356-T1
Valid prediction for CodingQuarry_transcript_13241-T1
Valid prediction for snap_scaffold_13-snap.2099-T1
Valid prediction for snap_scaffold_13-snap.2072-T1
Valid prediction for snap_scaffold_13-snap.2110-T1
Valid prediction for snap_scaffold_13-snap.2080-T1
Valid prediction for snap_scaffold_13-snap.2073-T1
Valid prediction for Augustus_model.g21606.t1
Valid prediction for GlimmerHMM_glimmerT_32357-T1
Valid prediction for snap_scaffold_13-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_32354-T1
Valid prediction for snap_scaffold_13-snap.2114-T1
Valid prediction for pasa_asmbl_11253.p2
Valid prediction for GlimmerHMM_glimmerT_32361-T1
Valid prediction for snap_scaffold_13-snap.2087-T1
Valid prediction for Augustus_model.g21608.t1
Valid prediction for snap_scaffold_13-snap.2094-T1
Valid prediction for Augustus_model.g21624.t1
Valid prediction for snap_scaffold_13-snap.2100-T1
Valid prediction for snap_scaffold_13-snap.2083-T1
Valid prediction for snap_scaffold_13-snap.2109-T1
Valid prediction for HiQ_model.g21622.t1
Valid prediction for GlimmerHMM_glimmerT_32390-T1
Valid prediction for GlimmerHMM_glimmerT_32367-T1
Valid prediction for GlimmerHMM_glimmerT_32387-T1
Valid prediction for GlimmerHMM_glimmerT_32379-T1
Valid prediction for GlimmerHMM_glimmerT_32376-T1
Valid prediction for Augustus_model.g21605.t1
Valid prediction for GlimmerHMM_glimmerT_32369-T1
Valid prediction for HiQ_model.g21603.t1
Couldn't classify 11938, 11973
Sorry, prediction pasa_asmbl_11254.p1 fails validation.
(CGG)	 GA	11938-11973	GT	AGG
(CTT)	 AG	12198-12618	GT	AGG
(GGA)	 AG	12708-12892	GT	AGG
(TAT)	 AG	13268-13645	GG	GAG
-recovered pasa_asmbl_11254.p1, terminal, 13268, 13645
-recovered pasa_asmbl_11254.p1, internal, 12198, 12618
-recovered pasa_asmbl_11254.p1, internal, 12708, 12892
Valid prediction for HiQ_model.g21621.t1
Valid prediction for snap_scaffold_13-snap.2112-T1
Valid prediction for snap_scaffold_13-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_32362-T1
Valid prediction for snap_scaffold_13-snap.2070-T1
Valid prediction for Augustus_model.g21602.t1
Couldn't classify 61048, 61117
Sorry, prediction pasa_asmbl_11259.p1 fails validation.
(CCT)	 AC	61048-61117	GT	TGG
(AGT)	 AG	62883-63118	GT	AGG
(ATT)	 AG	63643-63717	GT	AGG
(GCG)	 AG	64008-64081	GT	AGG
(GGT)	 AG	64354-64474	GC	GAG
-recovered pasa_asmbl_11259.p1, terminal, 64354, 64474
-recovered pasa_asmbl_11259.p1, internal, 62883, 63118
-recovered pasa_asmbl_11259.p1, internal, 63643, 63717
-recovered pasa_asmbl_11259.p1, internal, 64008, 64081
-recovered pasa_asmbl_11259.p1, internal, 64354, 64474
Valid prediction for GlimmerHMM_glimmerT_32385-T1
Valid prediction for snap_scaffold_13-snap.2074-T1
Couldn't classify 33337, 33525
Sorry, prediction pasa_asmbl_11256.p1 fails validation.
(GTT)	 AG	33337-33525	GT	AGG
(GTT)	 AG	34657-34845	GT	AGG
(GAG)	 AG	35079-35279	CA	GAC
-recovered pasa_asmbl_11256.p1, terminal, 35079, 35279
-recovered pasa_asmbl_11256.p1, internal, 33337, 33525
-recovered pasa_asmbl_11256.p1, internal, 34657, 34845
Valid prediction for snap_scaffold_13-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_32359-T1
Valid prediction for snap_scaffold_13-snap.2086-T1
Valid prediction for HiQ_model.g21617.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.2111-T1
Valid prediction for Augustus_model.g21610.t1
Valid prediction for snap_scaffold_13-snap.2089-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2090-T1
Valid prediction for GlimmerHMM_glimmerT_32389-T1
Couldn't classify 142492, 142632
Sorry, prediction pasa_asmbl_10078.p1 fails validation.
(ATG)	 AG	142202-142408	GT	AGG
(AGC)	 AG	142492-142632	GA	AGG
-recovered pasa_asmbl_10078.p1, initial, 142202, 142408
-recovered pasa_asmbl_10078.p1, internal, 142202, 142408
Valid prediction for pasa_asmbl_10086.p1
Valid prediction for Augustus_model.g21625.t1
Valid prediction for GlimmerHMM_glimmerT_32388-T1
Valid prediction for snap_scaffold_13-snap.2078-T1
Valid prediction for snap_scaffold_13-snap.2093-T1
Valid prediction for Augustus_model.g21612.t1
Valid prediction for snap_scaffold_13-snap.2116-T1
Valid prediction for snap_scaffold_13-snap.2092-T1
Valid prediction for snap_scaffold_13-snap.2081-T1
Valid prediction for snap_scaffold_13-snap.2101-T1
Valid prediction for snap_scaffold_13-snap.2107-T1
Valid prediction for Augustus_model.g21613.t1
Valid prediction for Augustus_model.g21620.t1
Valid prediction for snap_scaffold_13-snap.2095-T1
Valid prediction for GlimmerHMM_glimmerT_32378-T1
Valid prediction for GlimmerHMM_glimmerT_32366-T1
Valid prediction for Augustus_model.g21609.t1
Valid prediction for snap_scaffold_13-snap.2096-T1
Valid prediction for HiQ_model.g21616.t1
Valid prediction for snap_scaffold_13-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_32374-T1
Valid prediction for CodingQuarry_transcript_13240-T1
Valid prediction for GlimmerHMM_glimmerT_32392-T1
Valid prediction for snap_scaffold_13-snap.2082-T1
Valid prediction for snap_scaffold_13-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_32377-T1
Valid prediction for CodingQuarry_transcript_13243-T1
Valid prediction for CodingQuarry_transcript_13239-T1
Valid prediction for Augustus_model.g21627.t1
Valid prediction for pasa_asmbl_10379.p1
Valid prediction for snap_scaffold_13-snap.2077-T1
Valid prediction for GlimmerHMM_glimmerT_32375-T1
Valid prediction for GlimmerHMM_glimmerT_32391-T1
Valid prediction for snap_scaffold_13-snap.2113-T1
Valid prediction for GlimmerHMM_glimmerT_32365-T1
Valid prediction for snap_scaffold_13-snap.2091-T1
Valid prediction for snap_scaffold_13-snap.2115-T1
Valid prediction for Augustus_model.g21619.t1
Valid prediction for snap_scaffold_13-snap.2106-T1
Valid prediction for snap_scaffold_13-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_32381-T1
Valid prediction for GlimmerHMM_glimmerT_32383-T1
Valid prediction for GlimmerHMM_glimmerT_32368-T1
Valid prediction for GlimmerHMM_glimmerT_32364-T1
Couldn't classify 145163, 145209
Sorry, prediction pasa_asmbl_10076.p1 fails validation.
(TAC)	 GC	145163-145209	GT	GGG
(GTA)	 AG	145417-145516	GT	AGG
(GTA)	 AG	145623-145742	GT	AGG
(GTT)	 AG	145873-145959	GG	GAG
-recovered pasa_asmbl_10076.p1, terminal, 145873, 145959
-recovered pasa_asmbl_10076.p1, internal, 145417, 145516
-recovered pasa_asmbl_10076.p1, internal, 145623, 145742
Valid prediction for GlimmerHMM_glimmerT_32370-T1
Couldn't classify 143852, 143983
Couldn't classify 144627, 144680
Sorry, prediction pasa_asmbl_10435.p1 fails validation.
(GAC)	 AG	143852-143983	GT	AGG
(ACG)	 AG	144219-144298	GT	AGG
(CTA)	 AG	144393-144516	GT	CGG
(GTT)	 AG	144627-144680	AA	GAA
-recovered pasa_asmbl_10435.p1, internal, 143852, 143983
-recovered pasa_asmbl_10435.p1, internal, 144219, 144298
-recovered pasa_asmbl_10435.p1, internal, 144393, 144516
Valid prediction for GlimmerHMM_glimmerT_32373-T1
Valid prediction for snap_scaffold_13-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_32382-T1
Valid prediction for HiQ_model.g21615.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 60405, rend_intergenic: 45338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63099, rend_intergenic: 60856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69895, rend_intergenic: 63534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120660, rend_intergenic: 80739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126874, rend_intergenic: 121398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129407, rend_intergenic: 126937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159532, rend_intergenic: 150665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162309, rend_intergenic: 159720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194227, rend_intergenic: 194037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218162, rend_intergenic: 210601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220280
-exon list size: 532


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 60405, rend_intergenic: 45338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63099, rend_intergenic: 60856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69895, rend_intergenic: 63534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120660, rend_intergenic: 80739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126874, rend_intergenic: 121398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129407, rend_intergenic: 126937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159532, rend_intergenic: 150665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162309, rend_intergenic: 159720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194227, rend_intergenic: 194037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218162, rend_intergenic: 210601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support