-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_12416489-12617876

-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_14-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_35616-T1
Valid prediction for GeneMark_model.61060_t
Valid prediction for GeneMark_model.61069_t
Valid prediction for GeneMark_model.61070_t
Valid prediction for GlimmerHMM_glimmerT_35620-T1
Valid prediction for GlimmerHMM_glimmerT_35601-T1
Valid prediction for Augustus_model.g23973.t1
Valid prediction for snap_scaffold_14-snap.2590-T1
Valid prediction for GlimmerHMM_glimmerT_35608-T1
Valid prediction for Augustus_model.g23985.t1
Valid prediction for GeneMark_model.61033_t
Valid prediction for Augustus_model.g23976.t1
Valid prediction for GeneMark_model.61047_t
Valid prediction for GeneMark_model.61029_t
Valid prediction for GeneMark_model.61044_t
Valid prediction for GeneMark_model.61065_t
Valid prediction for GeneMark_model.61036_t
Valid prediction for GlimmerHMM_glimmerT_35606-T1
Valid prediction for GeneMark_model.61075_t
Valid prediction for GeneMark_model.61034_t
Valid prediction for snap_scaffold_14-snap.2575-T1
Valid prediction for GeneMark_model.61049_t
Valid prediction for GeneMark_model.61051_t
Valid prediction for snap_scaffold_14-snap.2581-T1
Valid prediction for snap_scaffold_14-snap.2584-T1
Valid prediction for Augustus_model.g23981.t1
Valid prediction for GlimmerHMM_glimmerT_35611-T1
Valid prediction for GeneMark_model.61077_t
Valid prediction for GeneMark_model.61056_t
Valid prediction for snap_scaffold_14-snap.2593-T1
Valid prediction for snap_scaffold_14-snap.2572-T1
Valid prediction for Augustus_model.g23978.t1
Valid prediction for GlimmerHMM_glimmerT_35629-T1
Valid prediction for snap_scaffold_14-snap.2561-T1
Valid prediction for snap_scaffold_14-snap.2564-T1
Valid prediction for CodingQuarry_transcript_15834-T1
Valid prediction for snap_scaffold_14-snap.2595-T1
Valid prediction for GlimmerHMM_glimmerT_35627-T1
Valid prediction for snap_scaffold_14-snap.2580-T1
Valid prediction for snap_scaffold_14-snap.2565-T1
Valid prediction for GeneMark_model.61067_t
Valid prediction for GlimmerHMM_glimmerT_35602-T1
Valid prediction for GeneMark_model.61031_t
Valid prediction for GlimmerHMM_glimmerT_35607-T1
Valid prediction for Augustus_model.g23970.t1
Valid prediction for GlimmerHMM_glimmerT_35619-T1
Valid prediction for snap_scaffold_14-snap.2585-T1
Valid prediction for GeneMark_model.61053_t
Valid prediction for snap_scaffold_14-snap.2566-T1
Valid prediction for GeneMark_model.61030_t
Valid prediction for snap_scaffold_14-snap.2588-T1
Valid prediction for HiQ_model.g23987.t1
Valid prediction for snap_scaffold_14-snap.2567-T1
Valid prediction for snap_scaffold_14-snap.2562-T1
Valid prediction for pasa_asmbl_12414.p1
Valid prediction for GlimmerHMM_glimmerT_35615-T1
Valid prediction for snap_scaffold_14-snap.2578-T1
Valid prediction for Augustus_model.g23966.t1
Valid prediction for snap_scaffold_14-snap.2594-T1
Valid prediction for Augustus_model.g23977.t1
Valid prediction for GlimmerHMM_glimmerT_35604-T1
Valid prediction for snap_scaffold_14-snap.2596-T1
Valid prediction for snap_scaffold_14-snap.2598-T1
Valid prediction for snap_scaffold_14-snap.2579-T1
Valid prediction for GeneMark_model.61041_t
Valid prediction for GlimmerHMM_glimmerT_35630-T1
Valid prediction for GeneMark_model.61039_t
Valid prediction for GeneMark_model.61073_t
Valid prediction for Augustus_model.g23967.t1
Valid prediction for GlimmerHMM_glimmerT_35628-T1
Valid prediction for GlimmerHMM_glimmerT_35625-T1
Valid prediction for GeneMark_model.61037_t
Valid prediction for CodingQuarry_transcript_15832-T1
Valid prediction for GlimmerHMM_glimmerT_35618-T1
Valid prediction for CodingQuarry_transcript_15833-T1
Valid prediction for Augustus_model.g23986.t1
Valid prediction for Augustus_model.g23969.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: -)Couldn't classify 144702, 144820
Couldn't classify 145669, 145738
Sorry, prediction pasa_asmbl_13828.p1 fails validation.
(ATC)	 GC	144702-144820	GT	AGG
(AAT)	 AG	144998-145096	GT	AGG
(ATA)	 AG	145418-145540	GT	GGG
(CGA)	 AG	145669-145738	AT	GCA
-recovered pasa_asmbl_13828.p1, internal, 144998, 145096
-recovered pasa_asmbl_13828.p1, internal, 145418, 145540
Valid prediction for GlimmerHMM_glimmerT_35623-T1
Valid prediction for GeneMark_model.61062_t
Valid prediction for Augustus_model.g23971.t1
Valid prediction for GeneMark_model.61027_t
Valid prediction for GeneMark_model.61046_t
Valid prediction for Augustus_model.g23968.t1
Valid prediction for GeneMark_model.61076_t
Valid prediction for Augustus_model.g23979.t1
Couldn't classify 104991, 105455
Sorry, prediction pasa_asmbl_12409.p1 fails validation.
(CTC)	 TC	104991-105455	GT	GAG
Valid prediction for GeneMark_model.61068_t
Valid prediction for GlimmerHMM_glimmerT_35621-T1
Valid prediction for GeneMark_model.61040_t
Valid prediction for snap_scaffold_14-snap.2577-T1
Valid prediction for GeneMark_model.61078_t
Valid prediction for GlimmerHMM_glimmerT_35622-T1
Valid prediction for GlimmerHMM_glimmerT_35610-T1
Valid prediction for Augustus_model.g23980.t1
Valid prediction for GlimmerHMM_glimmerT_35617-T1
Valid prediction for HiQ_model.g23965.t1
Valid prediction for GeneMark_model.61048_t
Valid prediction for snap_scaffold_14-snap.2586-T1
Valid prediction for Augustus_model.g23988.t1
Couldn't classify 197298, 197358
Sorry, prediction pasa_asmbl_13553.p1 fails validation.
(AAT)	 CG	197298-197358	GT	AGG
(TTA)	 AG	197841-198025	GT	AGG
(GTC)	 AG	198340-198651	CG	AAC
-recovered pasa_asmbl_13553.p1, terminal, 198340, 198651
-recovered pasa_asmbl_13553.p1, internal, 197841, 198025
Couldn't classify 111691, 111768
Sorry, prediction pasa_asmbl_13554.p1 fails validation.
(TGT)	 CC	111691-111768	GT	AGG
(GCG)	 AG	112052-112154	GT	TGG
(GTC)	 AG	113497-113565	GT	AGG
(AGT)	 AG	113681-113842	GT	CTG
(TCA)	 AG	114171-114373	GT	AGG
(GCT)	 AG	114906-115034	GT	CGG
(GAC)	 AG	115285-115461	GA	AAG
-recovered pasa_asmbl_13554.p1, terminal, 115285, 115461
-recovered pasa_asmbl_13554.p1, internal, 112052, 112154
-recovered pasa_asmbl_13554.p1, internal, 113497, 113565
-recovered pasa_asmbl_13554.p1, internal, 113681, 113842
-recovered pasa_asmbl_13554.p1, internal, 114171, 114373
-recovered pasa_asmbl_13554.p1, internal, 114906, 115034
Valid prediction for GlimmerHMM_glimmerT_35603-T1
Valid prediction for GlimmerHMM_glimmerT_35600-T1
Valid prediction for snap_scaffold_14-snap.2560-T1
Valid prediction for GeneMark_model.61054_t
Valid prediction for GeneMark_model.61059_t
Valid prediction for CodingQuarry_transcript_15830-T1
Valid prediction for snap_scaffold_14-snap.2568-T1
Valid prediction for GeneMark_model.61028_t
Valid prediction for GeneMark_model.61042_t
Valid prediction for GlimmerHMM_glimmerT_35613-T1
Valid prediction for Augustus_model.g23974.t1
Valid prediction for GeneMark_model.61074_t
Valid prediction for snap_scaffold_14-snap.2573-T1
Valid prediction for snap_scaffold_14-snap.2571-T1
Valid prediction for Augustus_model.g23984.t1
Valid prediction for snap_scaffold_14-snap.2587-T1
Valid prediction for snap_scaffold_14-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_35632-T1
Valid prediction for Augustus_model.g23972.t1
Valid prediction for GeneMark_model.61035_t
Valid prediction for snap_scaffold_14-snap.2576-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.61061_t
Valid prediction for GlimmerHMM_glimmerT_35626-T1
Valid prediction for GeneMark_model.61032_t
Valid prediction for GeneMark_model.61045_t
Valid prediction for GeneMark_model.61055_t
Valid prediction for GeneMark_model.61050_t
Valid prediction for snap_scaffold_14-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_35631-T1
Valid prediction for GeneMark_model.61072_t
Valid prediction for Augustus_model.g23975.t1
Valid prediction for snap_scaffold_14-snap.2574-T1
Valid prediction for GeneMark_model.61066_t
Valid prediction for GeneMark_model.61043_t
Valid prediction for GeneMark_model.61063_t
Valid prediction for snap_scaffold_14-snap.2583-T1
Valid prediction for snap_scaffold_14-snap.2563-T1
Valid prediction for GeneMark_model.61064_t
Valid prediction for GlimmerHMM_glimmerT_35624-T1
Valid prediction for Augustus_model.g23983.t1
Valid prediction for snap_scaffold_14-snap.2597-T1
Valid prediction for snap_scaffold_14-snap.2591-T1
Valid prediction for snap_scaffold_14-snap.2582-T1
Valid prediction for GeneMark_model.61057_t
Valid prediction for GeneMark_model.61052_t
Valid prediction for Augustus_model.g23982.t1
Valid prediction for GlimmerHMM_glimmerT_35609-T1
Valid prediction for GlimmerHMM_glimmerT_35612-T1
Valid prediction for GlimmerHMM_glimmerT_35614-T1
Valid prediction for GeneMark_model.61071_t
Valid prediction for snap_scaffold_14-snap.2589-T1
Valid prediction for GeneMark_model.61038_t
Valid prediction for GlimmerHMM_glimmerT_35605-T1
Valid prediction for pasa_asmbl_13558.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15805, rend_intergenic: 12930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63654, rend_intergenic: 57942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97773, rend_intergenic: 93884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132999, rend_intergenic: 131539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138587, rend_intergenic: 135111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200964, rend_intergenic: 194950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201388
-exon list size: 608


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 15805, rend_intergenic: 12930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63654, rend_intergenic: 57942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97773, rend_intergenic: 93884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132999, rend_intergenic: 131539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138587, rend_intergenic: 135111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200964, rend_intergenic: 194950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support