-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_12466898-12640981

-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_9-snap.2503-T1
Valid prediction for GlimmerHMM_glimmerT_23559-T1
Valid prediction for snap_scaffold_9-snap.2489-T1
Valid prediction for HiQ_model.g15815.t1
Valid prediction for snap_scaffold_9-snap.2493-T1
Valid prediction for GeneMark_model.40271_t
Valid prediction for GeneMark_model.40274_t
Valid prediction for snap_scaffold_9-snap.2507-T1
Valid prediction for snap_scaffold_9-snap.2498-T1
Couldn't classify 3963, 4159
Sorry, prediction CodingQuarry_transcript_62206-T1 fails validation.
(ATG)	 AC	3538-3556	GT	AAG
(CAT)	 TT	3963-4159	GC	AGG
(GCT)	 AG	6171-6497	GT	AGG
(ATC)	 AG	7498-7664	GT	AGG
(TTT)	 AG	7823-7914	GT	AAG
(CGG)	 AG	8112-8243	GT	GAG
(AGG)	 AG	8551-8655	GT	AGG
(ATG)	 AG	8763-8978	GT	AGG
(ATC)	 AG	9222-9293	GT	AGG
(CTC)	 AG	9436-9950	GA	GAG
-recovered CodingQuarry_transcript_62206-T1, initial, 3538, 3556
add_exon() Sorry, CodingQuarry_transcript_62206-T1 8763-8978-initial-1 is invalid.
-recovered CodingQuarry_transcript_62206-T1, initial, 8763, 8978
-recovered CodingQuarry_transcript_62206-T1, terminal, 9436, 9950
-recovered CodingQuarry_transcript_62206-T1, internal, 6171, 6497
-recovered CodingQuarry_transcript_62206-T1, internal, 7498, 7664
-recovered CodingQuarry_transcript_62206-T1, internal, 7823, 7914
-recovered CodingQuarry_transcript_62206-T1, internal, 8112, 8243
-recovered CodingQuarry_transcript_62206-T1, internal, 8551, 8655
-recovered CodingQuarry_transcript_62206-T1, internal, 8763, 8978
-recovered CodingQuarry_transcript_62206-T1, internal, 9222, 9293
Valid prediction for Augustus_model.g15814.t1
Valid prediction for snap_scaffold_9-snap.2477-T1
Valid prediction for snap_scaffold_9-snap.2491-T1
Valid prediction for snap_scaffold_9-snap.2494-T1
Valid prediction for snap_scaffold_9-snap.2468-T1
Valid prediction for snap_scaffold_9-snap.2483-T1
Valid prediction for GeneMark_model.40288_t
Valid prediction for GlimmerHMM_glimmerT_23563-T1
Valid prediction for snap_scaffold_9-snap.2481-T1
Valid prediction for CodingQuarry_transcript_62212-T1
Valid prediction for GeneMark_model.40293_t
Valid prediction for GeneMark_model.40298_t
Valid prediction for GeneMark_model.40296_t
Valid prediction for GeneMark_model.40291_t
Valid prediction for GlimmerHMM_glimmerT_23574-T1
Valid prediction for Augustus_model.g15807.t1
Valid prediction for GlimmerHMM_glimmerT_23554-T1
Valid prediction for GlimmerHMM_glimmerT_23564-T1
Valid prediction for snap_scaffold_9-snap.2495-T1
Valid prediction for Augustus_model.g15808.t1
Valid prediction for GlimmerHMM_glimmerT_23561-T1
Valid prediction for snap_scaffold_9-snap.2469-T1
Valid prediction for GeneMark_model.40286_t
Valid prediction for snap_scaffold_9-snap.2497-T1
Valid prediction for Augustus_model.g15801.t1
Valid prediction for GlimmerHMM_glimmerT_23565-T1
Valid prediction for GeneMark_model.40278_t
Valid prediction for GeneMark_model.40290_t
Couldn't classify 98798, 98843
Sorry, prediction pasa_asmbl_54422.p1 fails validation.
(CTT)	 AT	98798-98843	GT	AGG
(TGT)	 AG	98949-99259	TA	GAT
-recovered pasa_asmbl_54422.p1, terminal, 98949, 99259
Valid prediction for GlimmerHMM_glimmerT_23552-T1
Valid prediction for CodingQuarry_transcript_62207-T1
Valid prediction for GlimmerHMM_glimmerT_23575-T1
Valid prediction for GeneMark_model.40300_t
Valid prediction for snap_scaffold_9-snap.2473-T1
Valid prediction for CodingQuarry_transcript_62211-T1
Valid prediction for GeneMark_model.40280_t
Valid prediction for pasa_asmbl_54429.p1
Valid prediction for snap_scaffold_9-snap.2501-T1
Valid prediction for Augustus_model.g15809.t1
Valid prediction for GlimmerHMM_glimmerT_23571-T1
Valid prediction for GeneMark_model.40294_t
Valid prediction for snap_scaffold_9-snap.2475-T1
Valid prediction for GeneMark_model.40305_t
Valid prediction for GeneMark_model.40283_t
Valid prediction for snap_scaffold_9-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_23553-T1
Valid prediction for snap_scaffold_9-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_23562-T1
Valid prediction for CodingQuarry_transcript_62213-T1
Valid prediction for GlimmerHMM_glimmerT_23566-T1
Valid prediction for GeneMark_model.40303_t
Valid prediction for pasa_asmbl_54420.p1
Valid prediction for snap_scaffold_9-snap.2487-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 GeneMark_model.40289_t
Valid prediction for snap_scaffold_9-snap.2504-T1
Valid prediction for GeneMark_model.40302_t
Valid prediction for GeneMark_model.40285_t
Valid prediction for snap_scaffold_9-snap.2474-T1
Valid prediction for snap_scaffold_9-snap.2502-T1
Valid prediction for GeneMark_model.40276_t
Valid prediction for GeneMark_model.40275_t
Valid prediction for snap_scaffold_9-snap.2484-T1
Valid prediction for snap_scaffold_9-snap.2499-T1
Couldn't classify 144724, 145155
Sorry, prediction pasa_asmbl_55346.p1 fails validation.
(GTG)	 AG	144724-145155	CC	CCC
Valid prediction for GeneMark_model.40295_t
Valid prediction for snap_scaffold_9-snap.2509-T1
Valid prediction for Augustus_model.g15805.t1
Couldn't classify 18995, 19090
Sorry, prediction pasa_asmbl_55359.p1 fails validation.
(GAG)	 AG	18995-19090	GT	AGG
(GTG)	 AG	19221-19439	GT	AGG
(GGC)	 AG	20390-20507	GT	GGG
(AGA)	 AG	20678-20792	GT	AAG
(GAG)	 AG	20971-21034	GT	TGG
(GAT)	 AG	21259-21288	CT	AAC
-recovered pasa_asmbl_55359.p1, terminal, 21259, 21288
-recovered pasa_asmbl_55359.p1, internal, 18995, 19090
-recovered pasa_asmbl_55359.p1, internal, 19221, 19439
-recovered pasa_asmbl_55359.p1, internal, 20390, 20507
-recovered pasa_asmbl_55359.p1, internal, 20678, 20792
-recovered pasa_asmbl_55359.p1, internal, 20971, 21034
Valid prediction for GeneMark_model.40279_t
Valid prediction for GeneMark_model.40277_t
Valid prediction for snap_scaffold_9-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_23570-T1
Valid prediction for CodingQuarry_transcript_62208-T1
Couldn't classify 145939, 146977
Sorry, prediction pasa_asmbl_55343.p1 fails validation.
(GAG)	 GG	145939-146977	GT	CAG
(AAC)	 AG	147119-147192	GG	AAG
-recovered pasa_asmbl_55343.p1, terminal, 147119, 147192
Valid prediction for snap_scaffold_9-snap.2478-T1
Valid prediction for Augustus_model.g15804.t1
Valid prediction for Augustus_model.g15811.t1
Couldn't classify 126159, 126890
Sorry, prediction pasa_asmbl_55348.p1 fails validation.
(ATG)	 CC	126159-126890	TG	CCT
Valid prediction for snap_scaffold_9-snap.2485-T1
Valid prediction for snap_scaffold_9-snap.2506-T1
Valid prediction for GeneMark_model.40281_t
Valid prediction for GlimmerHMM_glimmerT_23560-T1
Valid prediction for GlimmerHMM_glimmerT_23567-T1
Valid prediction for GeneMark_model.40304_t
Valid prediction for GlimmerHMM_glimmerT_23573-T1
Valid prediction for GlimmerHMM_glimmerT_23568-T1
Valid prediction for GlimmerHMM_glimmerT_23556-T1
Valid prediction for GeneMark_model.40292_t
Valid prediction for GlimmerHMM_glimmerT_23569-T1
Couldn't classify 35183, 36040
Sorry, prediction pasa_asmbl_55355.p1 fails validation.
(ATG)	 CC	35183-36040	CT	TGC
Valid prediction for snap_scaffold_9-snap.2480-T1
Couldn't classify 145180, 145767
Sorry, prediction pasa_asmbl_55345.p1 fails validation.
(AGG)	 CA	145180-145767	GG	AGG
Valid prediction for snap_scaffold_9-snap.2479-T1
Valid prediction for GeneMark_model.40273_t
Valid prediction for GeneMark_model.40284_t
Valid prediction for Augustus_model.g15810.t1
Valid prediction for pasa_asmbl_55341.p1
Valid prediction for GlimmerHMM_glimmerT_23572-T1
Valid prediction for CodingQuarry_transcript_62209-T1
Valid prediction for Augustus_model.g15806.t1
Valid prediction for GlimmerHMM_glimmerT_23555-T1
Valid prediction for Augustus_model.g15803.t1
Valid prediction for snap_scaffold_9-snap.2488-T1
Valid prediction for GeneMark_model.40297_t
Valid prediction for snap_scaffold_9-snap.2490-T1
Valid prediction for snap_scaffold_9-snap.2492-T1
Valid prediction for GeneMark_model.40272_t
Valid prediction for snap_scaffold_9-snap.2505-T1
Valid prediction for GeneMark_model.40301_t
Valid prediction for GlimmerHMM_glimmerT_23558-T1
Valid prediction for snap_scaffold_9-snap.2470-T1
Valid prediction for snap_scaffold_9-snap.2476-T1
Valid prediction for snap_scaffold_9-snap.2472-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2510-T1
Valid prediction for snap_scaffold_9-snap.2471-T1
Couldn't classify 140160, 140238
Couldn't classify 142764, 142918
Sorry, prediction pasa_asmbl_55347.p1 fails validation.
(CTG)	 GT	140160-140238	GT	AGG
(GGG)	 AG	140379-140479	GT	ATG
(GGT)	 AG	141442-141561	GT	AGG
(ACG)	 AG	142017-142167	GT	GGG
(CCA)	 AG	142458-142613	GT	TGG
(GCT)	 AG	142764-142918	AC	CTA
-recovered pasa_asmbl_55347.p1, internal, 140379, 140479
-recovered pasa_asmbl_55347.p1, internal, 141442, 141561
-recovered pasa_asmbl_55347.p1, internal, 142017, 142167
-recovered pasa_asmbl_55347.p1, internal, 142458, 142613
Valid prediction for GeneMark_model.40287_t
Couldn't classify 25207, 25293
Couldn't classify 25993, 26109
Sorry, prediction pasa_asmbl_55357.p1 fails validation.
(CAT)	 CG	25207-25293	GT	CGG
(TTG)	 AG	25391-25498	GT	AGG
(AAT)	 AG	25742-25795	GT	TGG
(GAT)	 AG	25993-26109	TC	CCT
-recovered pasa_asmbl_55357.p1, internal, 25391, 25498
-recovered pasa_asmbl_55357.p1, internal, 25742, 25795
Valid prediction for Augustus_model.g15813.t1
Valid prediction for Augustus_model.g15812.t1
Valid prediction for GlimmerHMM_glimmerT_23557-T1
Valid prediction for GeneMark_model.40299_t
Valid prediction for snap_scaffold_9-snap.2500-T1
Valid prediction for HiQ_model.g15802.t1
Valid prediction for snap_scaffold_9-snap.2496-T1
Valid prediction for GeneMark_model.40282_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 147685, rend_intergenic: 147682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10383, rend_intergenic: 6091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20053, rend_intergenic: 18200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35052, rend_intergenic: 26893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43553, rend_intergenic: 38882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53268, rend_intergenic: 50716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56847, rend_intergenic: 53274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63635, rend_intergenic: 59463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68544, rend_intergenic: 64683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69986, rend_intergenic: 68888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74040, rend_intergenic: 72056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81820, rend_intergenic: 78077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82785, rend_intergenic: 82350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111715, rend_intergenic: 108441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129971, rend_intergenic: 122798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166259, rend_intergenic: 155841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169743, rend_intergenic: 167082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174084
-exon list size: 547


building trellis

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96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 147685, rend_intergenic: 147682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10383, rend_intergenic: 6091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20053, rend_intergenic: 18200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35052, rend_intergenic: 26893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43553, rend_intergenic: 38882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53268, rend_intergenic: 50716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56847, rend_intergenic: 53274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63635, rend_intergenic: 59463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68544, rend_intergenic: 64683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69986, rend_intergenic: 68888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74040, rend_intergenic: 72056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81820, rend_intergenic: 78077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82785, rend_intergenic: 82350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111715, rend_intergenic: 108441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129971, rend_intergenic: 122798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166259, rend_intergenic: 155841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169743, rend_intergenic: 167082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support