-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_18268741-18451197

-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_1-snap.3344-T1
Valid prediction for GlimmerHMM_glimmerT_2444-T1
Valid prediction for pasa_asmbl_2550.p1
Valid prediction for GlimmerHMM_glimmerT_2458-T1
Couldn't classify 6307, 6516
Sorry, prediction pasa_asmbl_2545.p1 fails validation.
(GTG)	 TG	6307-6516	GT	GTG
(CTT)	 AG	6612-6723	GT	GGG
(ATC)	 AG	6825-6856	GT	AGG
(GAT)	 AG	7057-7150	GT	GGG
(TTT)	 AG	7251-7300	GT	AGG
(GAT)	 AG	7391-7654	CC	GAC
-recovered pasa_asmbl_2545.p1, terminal, 7391, 7654
-recovered pasa_asmbl_2545.p1, internal, 6612, 6723
-recovered pasa_asmbl_2545.p1, internal, 6825, 6856
-recovered pasa_asmbl_2545.p1, internal, 7057, 7150
-recovered pasa_asmbl_2545.p1, internal, 7251, 7300
Valid prediction for snap_scaffold_1-snap.3337-T1
Valid prediction for CodingQuarry_transcript_2998-T1
Valid prediction for snap_scaffold_1-snap.3353-T1
Valid prediction for snap_scaffold_1-snap.3341-T1
Valid prediction for HiQ_model.g1793.t1
Valid prediction for CodingQuarry_transcript_2996-T1
Valid prediction for Augustus_model.g1795.t1
Valid prediction for GlimmerHMM_glimmerT_2467-T1
Valid prediction for snap_scaffold_1-snap.3325-T1
Valid prediction for snap_scaffold_1-snap.3336-T1
Valid prediction for Augustus_model.g1788.t1
Valid prediction for HiQ_model.g1792.t1
Valid prediction for snap_scaffold_1-snap.3355-T1
Valid prediction for CodingQuarry_transcript_2995-T1
Valid prediction for snap_scaffold_1-snap.3334-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3350-T1
Valid prediction for snap_scaffold_1-snap.3326-T1
Valid prediction for CodingQuarry_transcript_2991-T1
Valid prediction for snap_scaffold_1-snap.3357-T1
Valid prediction for GlimmerHMM_glimmerT_2463-T1
Valid prediction for CodingQuarry_transcript_2992-T1
Valid prediction for snap_scaffold_1-snap.3358-T1
Valid prediction for Augustus_model.g1797.t1
Valid prediction for GlimmerHMM_glimmerT_2453-T1
Valid prediction for GlimmerHMM_glimmerT_2448-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_2553.p1
Valid prediction for GlimmerHMM_glimmerT_2451-T1
Valid prediction for snap_scaffold_1-snap.3339-T1
Valid prediction for snap_scaffold_1-snap.3340-T1
Valid prediction for Augustus_model.g1798.t1
Valid prediction for GlimmerHMM_glimmerT_2468-T1
Couldn't classify 68290, 68478
Couldn't classify 68530, 68531
Sorry, prediction CodingQuarry_transcript_2997-T1 fails validation.
(ATG)	 AG	67929-68067	GT	AGG
(GTT)	 AG	68290-68478	CT	TTC
(AGC)	 AC	68530-68531	CA	AGC
-recovered CodingQuarry_transcript_2997-T1, initial, 67929, 68067
-recovered CodingQuarry_transcript_2997-T1, internal, 67929, 68067
Couldn't classify 52524, 52741
Sorry, prediction pasa_asmbl_2549.p1 fails validation.
(GCA)	 GA	52524-52741	GT	TGG
(TCC)	 AG	52833-53019	GG	GAG
-recovered pasa_asmbl_2549.p1, terminal, 52833, 53019
Valid prediction for CodingQuarry_transcript_3000-T1
Valid prediction for GlimmerHMM_glimmerT_2445-T1
Valid prediction for HiQ_model.g1790.t1
Valid prediction for snap_scaffold_1-snap.3338-T1
Valid prediction for GlimmerHMM_glimmerT_2465-T1
Valid prediction for snap_scaffold_1-snap.3348-T1
Valid prediction for Augustus_model.g1784.t1
Couldn't classify 48635, 48775
Sorry, prediction pasa_asmbl_2730.p1 fails validation.
(ATG)	 TC	48045-48293	GT	CAG
(GTA)	 AG	48487-48546	GT	AAG
(GTG)	 AG	48635-48775	GT	AGG
-recovered pasa_asmbl_2730.p1, initial, 48045, 48293
-recovered pasa_asmbl_2730.p1, internal, 48487, 48546
-recovered pasa_asmbl_2730.p1, internal, 48635, 48775
Valid prediction for snap_scaffold_1-snap.3362-T1
Valid prediction for pasa_asmbl_2552.p1
Valid prediction for snap_scaffold_1-snap.3346-T1
Valid prediction for GlimmerHMM_glimmerT_2450-T1
Valid prediction for Augustus_model.g1791.t1
Valid prediction for pasa_asmbl_2563.p1
Valid prediction for GlimmerHMM_glimmerT_2459-T1
Couldn't classify 90927, 91262
Sorry, prediction pasa_asmbl_2561.p1 fails validation.
(CAC)	 GC	90927-91262	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_2452-T1
Valid prediction for snap_scaffold_1-snap.3349-T1
Valid prediction for GlimmerHMM_glimmerT_2461-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_1-snap.3359-T1
Valid prediction for Augustus_model.g1787.t1
Valid prediction for GlimmerHMM_glimmerT_2443-T1
Valid prediction for Augustus_model.g1786.t1
Valid prediction for snap_scaffold_1-snap.3363-T1
Valid prediction for snap_scaffold_1-snap.3352-T1
Valid prediction for pasa_asmbl_1104.p1
Valid prediction for snap_scaffold_1-snap.3332-T1
Valid prediction for Augustus_model.g1796.t1
Valid prediction for GlimmerHMM_glimmerT_2441-T1
Valid prediction for Augustus_model.g1785.t1
Valid prediction for snap_scaffold_1-snap.3335-T1
Valid prediction for snap_scaffold_1-snap.3331-T1
Valid prediction for snap_scaffold_1-snap.3354-T1
Couldn't classify 144488, 146101
Sorry, prediction pasa_asmbl_1101.p1 fails validation.
(CCT)	 TG	144488-146101	CC	AGC
Valid prediction for Augustus_model.g1801.t1
Valid prediction for GlimmerHMM_glimmerT_2466-T1
Valid prediction for Augustus_model.g1802.t1
Valid prediction for GlimmerHMM_glimmerT_2446-T1
Valid prediction for snap_scaffold_1-snap.3343-T1
Valid prediction for snap_scaffold_1-snap.3329-T1
Valid prediction for CodingQuarry_transcript_2999-T1
Valid prediction for Augustus_model.g1800.t1
Valid prediction for snap_scaffold_1-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_2456-T1
Valid prediction for snap_scaffold_1-snap.3364-T1
Valid prediction for GlimmerHMM_glimmerT_2447-T1
Valid prediction for CodingQuarry_transcript_2993-T1
Valid prediction for snap_scaffold_1-snap.3342-T1
Valid prediction for snap_scaffold_1-snap.3361-T1
Valid prediction for snap_scaffold_1-snap.3328-T1
Valid prediction for Augustus_model.g1799.t1
Valid prediction for GlimmerHMM_glimmerT_2460-T1
Valid prediction for snap_scaffold_1-snap.3347-T1
Valid prediction for snap_scaffold_1-snap.3327-T1
Valid prediction for snap_scaffold_1-snap.3351-T1
Valid prediction for Augustus_model.g1783.t1
Valid prediction for snap_scaffold_1-snap.3360-T1
Valid prediction for pasa_asmbl_1103.p1
Valid prediction for CodingQuarry_transcript_2994-T1
Valid prediction for HiQ_model.g1794.t1
Couldn't classify 152788, 154221
Sorry, prediction pasa_asmbl_1100.p1 fails validation.
(CCC)	 AA	152788-154221	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_2464-T1
Valid prediction for GlimmerHMM_glimmerT_2454-T1
Valid prediction for GlimmerHMM_glimmerT_2457-T1
Valid prediction for GlimmerHMM_glimmerT_2455-T1
Valid prediction for GlimmerHMM_glimmerT_2462-T1
Valid prediction for snap_scaffold_1-snap.3345-T1
Valid prediction for GlimmerHMM_glimmerT_2442-T1
Couldn't classify 168202, 168351
Sorry, prediction pasa_asmbl_1097.p2 fails validation.
(CAG)	 CC	168202-168351	GT	GGG
(TTG)	 AG	170614-171032	GT	AGG
(GTG)	 AG	171566-171569	CA	GAC
-recovered pasa_asmbl_1097.p2, terminal, 171566, 171569
-recovered pasa_asmbl_1097.p2, internal, 170614, 171032
Valid prediction for GlimmerHMM_glimmerT_2449-T1
Valid prediction for HiQ_model.g1789.t1
Valid prediction for snap_scaffold_1-snap.3333-T1
Valid prediction for snap_scaffold_1-snap.3356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 81814, rend_intergenic: 80474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83606, rend_intergenic: 82091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121560, rend_intergenic: 118911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128665, rend_intergenic: 128039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135496, rend_intergenic: 128665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139710, rend_intergenic: 137224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142454, rend_intergenic: 139762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170570, rend_intergenic: 165757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182457
-exon list size: 287


building trellis

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99.0    
99.3    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 81814, rend_intergenic: 80474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83606, rend_intergenic: 82091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121560, rend_intergenic: 118911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128665, rend_intergenic: 128039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135496, rend_intergenic: 128665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139710, rend_intergenic: 137224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142454, rend_intergenic: 139762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170570, rend_intergenic: 165757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 170805 - 182457
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support