-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_11324409-11515508

-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_35434-T1
Valid prediction for GlimmerHMM_glimmerT_35451-T1
Valid prediction for snap_scaffold_14-snap.2330-T1
Valid prediction for snap_scaffold_14-snap.2325-T1
Couldn't classify 167357, 167547
Couldn't classify 168886, 168926
Sorry, prediction pasa_asmbl_12362.p1 fails validation.
(AGA)	 CC	167357-167547	GT	AAG
(TAA)	 AG	168260-168340	GT	AGG
(ATC)	 AG	168605-168717	GT	AGG
(ATG)	 AG	168886-168926	AC	ACA
-recovered pasa_asmbl_12362.p1, internal, 168260, 168340
-recovered pasa_asmbl_12362.p1, internal, 168605, 168717
Valid prediction for HiQ_model.g23839.t1
Valid prediction for HiQ_model.g23841.t1
Valid prediction for GeneMark_model.60788_t
Valid prediction for snap_scaffold_14-snap.2328-T1
Valid prediction for pasa_asmbl_12353.p1
Valid prediction for GlimmerHMM_glimmerT_35442-T1
Valid prediction for CodingQuarry_transcript_15788-T1
Valid prediction for snap_scaffold_14-snap.2346-T1
Valid prediction for snap_scaffold_14-snap.2352-T1
Valid prediction for GlimmerHMM_glimmerT_35447-T1
Valid prediction for GeneMark_model.60804_t
Valid prediction for GeneMark_model.60808_t
Valid prediction for snap_scaffold_14-snap.2342-T1
Valid prediction for Augustus_model.g23853.t1
Couldn't classify 70396, 70777
Sorry, prediction pasa_asmbl_12356.p1 fails validation.
(AGC)	 TC	70396-70777	GT	AGG
(GCC)	 AG	70914-71154	GT	AAG
(GGC)	 AG	71271-71378	GT	AAG
(GTT)	 AG	71506-71647	GT	AGG
(GCC)	 AG	71740-72159	GA	GAG
-recovered pasa_asmbl_12356.p1, terminal, 71740, 72159
-recovered pasa_asmbl_12356.p1, internal, 70914, 71154
-recovered pasa_asmbl_12356.p1, internal, 71271, 71378
-recovered pasa_asmbl_12356.p1, internal, 71506, 71647
Valid prediction for GlimmerHMM_glimmerT_35450-T1
Valid prediction for snap_scaffold_14-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_35445-T1
Valid prediction for GeneMark_model.60799_t
Valid prediction for GeneMark_model.60812_t
Valid prediction for GeneMark_model.60810_t
Valid prediction for GeneMark_model.60793_t
Valid prediction for snap_scaffold_14-snap.2337-T1
Valid prediction for pasa_asmbl_12358.p1
Valid prediction for snap_scaffold_14-snap.2344-T1
Valid prediction for snap_scaffold_14-snap.2329-T1
Valid prediction for snap_scaffold_14-snap.2333-T1
Couldn't classify 69412, 70095
Sorry, prediction pasa_asmbl_12355.p1 fails validation.
(ATG)	 AA	69412-70095	AC	CCA
Valid prediction for GeneMark_model.60801_t
Valid prediction for Augustus_model.g23854.t1
Couldn't classify 160515, 161156
Sorry, prediction pasa_asmbl_12360.p1 fails validation.
(CTA)	 CT	160515-161156	CG	CCC
Valid prediction for snap_scaffold_14-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_35432-T1
Valid prediction for GeneMark_model.60796_t
Valid prediction for snap_scaffold_14-snap.2350-T1
Valid prediction for snap_scaffold_14-snap.2321-T1
Valid prediction for GlimmerHMM_glimmerT_35436-T1
Valid prediction for snap_scaffold_14-snap.2347-T1
Valid prediction for HiQ_model.g23843.t1
Valid prediction for Augustus_model.g23838.t1
Valid prediction for Augustus_model.g23837.t1
Valid prediction for snap_scaffold_14-snap.2355-T1
Valid prediction for GlimmerHMM_glimmerT_35439-T1
Valid prediction for snap_scaffold_14-snap.2335-T1
Valid prediction for GeneMark_model.60803_t
Valid prediction for snap_scaffold_14-snap.2353-T1
Couldn't classify 43589, 43630
Sorry, prediction pasa_asmbl_12350.p1 fails validation.
(GAC)	 TC	43589-43630	GT	AGG
(TTT)	 AG	45758-45875	GT	ACG
(AGC)	 AG	46073-46244	GT	TGG
(GGT)	 AG	48380-48473	AA	GAA
-recovered pasa_asmbl_12350.p1, terminal, 48380, 48473
-recovered pasa_asmbl_12350.p1, internal, 45758, 45875
-recovered pasa_asmbl_12350.p1, internal, 46073, 46244
Valid prediction for Augustus_model.g23851.t1
Valid prediction for Augustus_model.g23850.t1
Valid prediction for snap_scaffold_14-snap.2324-T1
Valid prediction for GeneMark_model.60786_t
Valid prediction for CodingQuarry_transcript_15787-T1
Valid prediction for HiQ_model.g23847.t1
Valid prediction for GlimmerHMM_glimmerT_35435-T1
Valid prediction for snap_scaffold_14-snap.2349-T1
Valid prediction for snap_scaffold_14-snap.2331-T1
Couldn't classify 98047, 99033
Sorry, prediction pasa_asmbl_12357.p1 fails validation.
(CTG)	 CC	98047-99033	GT	AGG
(GTC)	 AG	99225-99494	GT	AGG
(GTG)	 AG	100183-100911	CC	AAC
-recovered pasa_asmbl_12357.p1, terminal, 100183, 100911
-recovered pasa_asmbl_12357.p1, internal, 99225, 99494
Valid prediction for GeneMark_model.60790_t
Valid prediction for GeneMark_model.60807_t
Valid prediction for GeneMark_model.60782_t
Valid prediction for GeneMark_model.60794_t
Couldn't classify 161541, 161627
Couldn't classify 162211, 162659
Sorry, prediction pasa_asmbl_12361.p1 fails validation.
(CTT)	 GC	161541-161627	GT	AGG
(ACG)	 AG	161813-161930	GT	AAG
(ATA)	 AG	162211-162659	GA	AGG
-recovered pasa_asmbl_12361.p1, internal, 161813, 161930
Valid prediction for snap_scaffold_14-snap.2326-T1
Valid prediction for CodingQuarry_transcript_15793-T1
Couldn't classify 52708, 52924
Sorry, prediction pasa_asmbl_12351.p1 fails validation.
(AGT)	 GG	52708-52924	GT	AGG
(TGG)	 AG	53276-54483	GT	GAG
-recovered pasa_asmbl_12351.p1, terminal, 53276, 54483
-recovered pasa_asmbl_12351.p1, internal, 53276, 54483
Valid prediction for GeneMark_model.60789_t

-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 GlimmerHMM_glimmerT_35446-T1
Valid prediction for snap_scaffold_14-snap.2338-T1
Valid prediction for Augustus_model.g23848.t1
Valid prediction for GlimmerHMM_glimmerT_35449-T1
Valid prediction for snap_scaffold_14-snap.2345-T1
Valid prediction for snap_scaffold_14-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_35437-T1
Valid prediction for snap_scaffold_14-snap.2332-T1
Valid prediction for CodingQuarry_transcript_15790-T1
Valid prediction for GeneMark_model.60802_t
Valid prediction for GlimmerHMM_glimmerT_35448-T1
Valid prediction for Augustus_model.g23842.t1
Couldn't classify 123819, 123883
Sorry, prediction pasa_asmbl_13460.p1 fails validation.
(TCT)	 TC	123819-123883	GT	AGG
(GAT)	 AG	123997-124157	GT	AGG
(GAA)	 AG	124890-125036	GT	CGG
(GTC)	 AG	125489-125619	GT	AGG
(CTG)	 AG	125776-125932	GT	AGG
(ACT)	 AG	126040-126351	GT	AGG
(GAG)	 AG	126442-126538	GT	GTG
(GGG)	 AG	127001-127204	GT	TAG
(CAT)	 AG	127429-127646	GT	AGG
(ATC)	 AG	127877-128000	GT	TTG
(GTT)	 AG	128130-128282	GT	AGG
(ATG)	 AG	128377-128506	GT	GGG
(AAA)	 AG	128601-128691	GT	ACG
(AAC)	 AG	128815-128955	GT	GGG
(GCT)	 AG	129173-129378	AC	GAA
add_exon() Sorry, pasa_asmbl_13460.p1 128377-128506-initial-1 is invalid.
-recovered pasa_asmbl_13460.p1, initial, 128377, 128506
add_exon() Sorry, pasa_asmbl_13460.p1 125776-125932-terminal-3 is invalid.
-recovered pasa_asmbl_13460.p1, terminal, 125776, 125932
add_exon() Sorry, pasa_asmbl_13460.p1 127429-127646-terminal-2 is invalid.
-recovered pasa_asmbl_13460.p1, terminal, 127429, 127646
-recovered pasa_asmbl_13460.p1, terminal, 129173, 129378
-recovered pasa_asmbl_13460.p1, internal, 123997, 124157
-recovered pasa_asmbl_13460.p1, internal, 124890, 125036
-recovered pasa_asmbl_13460.p1, internal, 125489, 125619
-recovered pasa_asmbl_13460.p1, internal, 125776, 125932
-recovered pasa_asmbl_13460.p1, internal, 126040, 126351
-recovered pasa_asmbl_13460.p1, internal, 126442, 126538
-recovered pasa_asmbl_13460.p1, internal, 127001, 127204
-recovered pasa_asmbl_13460.p1, internal, 127429, 127646
-recovered pasa_asmbl_13460.p1, internal, 127877, 128000
-recovered pasa_asmbl_13460.p1, internal, 128130, 128282
-recovered pasa_asmbl_13460.p1, internal, 128377, 128506
-recovered pasa_asmbl_13460.p1, internal, 128601, 128691
-recovered pasa_asmbl_13460.p1, internal, 128815, 128955
Valid prediction for snap_scaffold_14-snap.2348-T1
Valid prediction for GeneMark_model.60780_t
Valid prediction for Augustus_model.g23846.t1
Valid prediction for GeneMark_model.60781_t
Valid prediction for GeneMark_model.60800_t
Valid prediction for GlimmerHMM_glimmerT_35438-T1
Valid prediction for snap_scaffold_14-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_35452-T1
Valid prediction for GeneMark_model.60784_t
Valid prediction for snap_scaffold_14-snap.2319-T1
Valid prediction for HiQ_model.g23835.t1
Valid prediction for GeneMark_model.60811_t
Valid prediction for CodingQuarry_transcript_15791-T1
Valid prediction for HiQ_model.g23834.t1
Valid prediction for GeneMark_model.60783_t
Valid prediction for GlimmerHMM_glimmerT_35428-T1
Valid prediction for snap_scaffold_14-snap.2336-T1
Valid prediction for GeneMark_model.60795_t
Valid prediction for Augustus_model.g23852.t1
Valid prediction for GeneMark_model.60798_t
Valid prediction for GeneMark_model.60809_t
Valid prediction for pasa_asmbl_13459.p1
Valid prediction for GlimmerHMM_glimmerT_35430-T1
Valid prediction for snap_scaffold_14-snap.2351-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35441-T1
Valid prediction for CodingQuarry_transcript_15786-T1
Valid prediction for CodingQuarry_transcript_15785-T1
Valid prediction for snap_scaffold_14-snap.2340-T1
Valid prediction for Augustus_model.g23836.t1
Valid prediction for HiQ_model.g23840.t1
Valid prediction for CodingQuarry_transcript_15783-T1
Valid prediction for pasa_asmbl_13455.p1
Valid prediction for Augustus_model.g23845.t1
Valid prediction for CodingQuarry_transcript_15789-T1
Valid prediction for GlimmerHMM_glimmerT_35431-T1
Valid prediction for snap_scaffold_14-snap.2343-T1
Valid prediction for CodingQuarry_transcript_15784-T1
Valid prediction for Augustus_model.g23844.t1
Valid prediction for GlimmerHMM_glimmerT_35443-T1
Valid prediction for GeneMark_model.60787_t
Valid prediction for GeneMark_model.60797_t
Valid prediction for pasa_asmbl_13453.p1
Valid prediction for CodingQuarry_transcript_15782-T1
Valid prediction for GeneMark_model.60792_t
Valid prediction for pasa_asmbl_13458.p1
Valid prediction for CodingQuarry_transcript_15792-T1
Valid prediction for snap_scaffold_14-snap.2339-T1
Valid prediction for GeneMark_model.60805_t
Valid prediction for GeneMark_model.60785_t
Valid prediction for Augustus_model.g23849.t1
Valid prediction for GlimmerHMM_glimmerT_35429-T1
Valid prediction for GlimmerHMM_glimmerT_35444-T1
Valid prediction for snap_scaffold_14-snap.2354-T1
Valid prediction for snap_scaffold_14-snap.2322-T1
Valid prediction for GeneMark_model.60806_t
Valid prediction for GeneMark_model.60791_t
Valid prediction for GlimmerHMM_glimmerT_35433-T1
Valid prediction for snap_scaffold_14-snap.2334-T1
Valid prediction for HiQ_model.g23833.t1
Valid prediction for snap_scaffold_14-snap.2323-T1
Valid prediction for snap_scaffold_14-snap.2320-T1
Valid prediction for GlimmerHMM_glimmerT_35440-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17461, rend_intergenic: 12974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34171, rend_intergenic: 32202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86699, rend_intergenic: 81839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94811, rend_intergenic: 91025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157678, rend_intergenic: 152400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164583, rend_intergenic: 163286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166772, rend_intergenic: 166210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177291, rend_intergenic: 173363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191100
-exon list size: 482


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17461, rend_intergenic: 12974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34171, rend_intergenic: 32202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86699, rend_intergenic: 81839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94811, rend_intergenic: 91025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157678, rend_intergenic: 152400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164583, rend_intergenic: 163286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166772, rend_intergenic: 166210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177291, rend_intergenic: 173363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support