-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_11405778-11676748 -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_48017-T1 Valid prediction for GeneMark_model.83630_t Valid prediction for HiQ_model.g32098.t1 Couldn't classify 244971, 245321 Sorry, prediction pasa_asmbl_26235.p1 fails validation. (CTC) AC 244971-245321 AA AAA Valid prediction for Augustus_model.g32085.t1 Valid prediction for HiQ_model.g32068.t1 Valid prediction for Augustus_model.g32092.t1 Valid prediction for GeneMark_model.83625_t Valid prediction for GeneMark_model.83629_t Valid prediction for Augustus_model.g32081.t1 Valid prediction for GlimmerHMM_glimmerT_48024-T1 Valid prediction for snap_scaffold_20-snap.2437-T1 Valid prediction for Augustus_model.g32084.t1 Valid prediction for GeneMark_model.83645_t Valid prediction for GlimmerHMM_glimmerT_48010-T1 Valid prediction for CodingQuarry_transcript_30611-T1 Valid prediction for GeneMark_model.83627_t Valid prediction for GeneMark_model.83633_t Valid prediction for snap_scaffold_20-snap.2452-T1 Valid prediction for GeneMark_model.83642_t Valid prediction for GeneMark_model.83638_t Valid prediction for pasa_asmbl_26200.p1 Valid prediction for CodingQuarry_transcript_30606-T1 Valid prediction for Augustus_model.g32076.t1 Valid prediction for pasa_asmbl_26345.p1 Valid prediction for GlimmerHMM_glimmerT_48020-T1 Valid prediction for GlimmerHMM_glimmerT_48022-T1 Valid prediction for snap_scaffold_20-snap.2436-T1 Valid prediction for pasa_asmbl_26196.p1 Valid prediction for snap_scaffold_20-snap.2431-T1 Valid prediction for snap_scaffold_20-snap.2419-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for Augustus_model.g32101.t1 Valid prediction for Augustus_model.g32075.t1 Valid prediction for GlimmerHMM_glimmerT_48040-T1 Valid prediction for GlimmerHMM_glimmerT_48029-T1 Couldn't classify 231809, 231963 Sorry, prediction pasa_asmbl_26233.p1 fails validation. (TTT) GG 231809-231963 GT AAG (GAG) AG 232104-232337 GT CAG (ATA) AG 232546-232850 GT AGG (AAA) AG 233162-233310 GT AGG (CTC) AG 233499-233618 GT CAG (GGT) AG 233864-233959 GT AGG (GAA) AG 235222-235321 GT AGG (GAA) AG 235530-235713 GT AGG (GTA) AG 235870-236025 GT AGG (CGA) AG 236267-236500 GT CAG (CTT) AG 239077-239227 AC AAA -recovered pasa_asmbl_26233.p1, terminal, 239077, 239227 -recovered pasa_asmbl_26233.p1, internal, 232104, 232337 -recovered pasa_asmbl_26233.p1, internal, 232546, 232850 -recovered pasa_asmbl_26233.p1, internal, 233162, 233310 -recovered pasa_asmbl_26233.p1, internal, 233499, 233618 -recovered pasa_asmbl_26233.p1, internal, 233864, 233959 -recovered pasa_asmbl_26233.p1, internal, 235222, 235321 -recovered pasa_asmbl_26233.p1, internal, 235530, 235713 -recovered pasa_asmbl_26233.p1, internal, 235870, 236025 -recovered pasa_asmbl_26233.p1, internal, 236267, 236500 Valid prediction for GlimmerHMM_glimmerT_48032-T1 Valid prediction for Augustus_model.g32074.t1 Valid prediction for snap_scaffold_20-snap.2455-T1 Valid prediction for Augustus_model.g32090.t1 Valid prediction for GeneMark_model.83621_t Valid prediction for snap_scaffold_20-snap.2433-T1 Valid prediction for HiQ_model.g32088.t1 Couldn't classify 69731, 69862 Sorry, prediction pasa_asmbl_26204.p1 fails validation. (CTT) TT 69731-69862 GT AGG (TGT) AG 69986-70154 GT GGG (GTA) AG 70304-70432 GT AGG (GGC) AG 70589-70724 GT AAG (ACC) AG 70867-70987 CA AGC -recovered pasa_asmbl_26204.p1, terminal, 70867, 70987 -recovered pasa_asmbl_26204.p1, internal, 69986, 70154 -recovered pasa_asmbl_26204.p1, internal, 70304, 70432 -recovered pasa_asmbl_26204.p1, internal, 70589, 70724 Valid prediction for GeneMark_model.83626_t Valid prediction for snap_scaffold_20-snap.2426-T1 Valid prediction for snap_scaffold_20-snap.2458-T1 Valid prediction for HiQ_model.g32099.t1 Valid prediction for CodingQuarry_transcript_30609-T1 Valid prediction for GeneMark_model.83644_t Valid prediction for snap_scaffold_20-snap.2442-T1 Valid prediction for Augustus_model.g32070.t1 Valid prediction for GeneMark_model.83639_t Valid prediction for Augustus_model.g32095.t1 Valid prediction for Augustus_model.g32073.t1 Valid prediction for GlimmerHMM_glimmerT_48023-T1 Valid prediction for snap_scaffold_20-snap.2421-T1 Valid prediction for HiQ_model.g32087.t1 Valid prediction for HiQ_model.g32093.t1 Valid prediction for Augustus_model.g32102.t1 Valid prediction for CodingQuarry_transcript_30612-T1 Valid prediction for Augustus_model.g32080.t1 Valid prediction for GeneMark_model.83632_t Valid prediction for GlimmerHMM_glimmerT_48041-T1 Valid prediction for GeneMark_model.83636_t Couldn't classify 77683, 78369 Sorry, prediction pasa_asmbl_26207.p1 fails validation. (ATG) AG 76700-76753 GT ATG (GAC) AG 77683-78369 GA CAG -recovered pasa_asmbl_26207.p1, initial, 76700, 76753 -recovered pasa_asmbl_26207.p1, internal, 76700, 76753 Valid prediction for GlimmerHMM_glimmerT_48026-T1 Valid prediction for snap_scaffold_20-snap.2424-T1 Valid prediction for snap_scaffold_20-snap.2432-T1 Valid prediction for GlimmerHMM_glimmerT_48015-T1 Valid prediction for GlimmerHMM_glimmerT_48019-T1 Couldn't classify 111623, 111693 Sorry, prediction pasa_asmbl_26222.p1 fails validation. (ATG) AC 105225-105227 GT TGG (GAG) AG 105345-105534 GT TGG (ACA) AG 108132-108215 GT ATG (ATG) AG 108296-108481 GT AGG (GCT) AG 109007-109139 GT ATG (GTA) AG 109355-109547 GT AGG (GCC) AG 110228-110571 GT AGG (GTT) AG 110757-110926 GT AGG (GAG) AG 111623-111693 TT CCT -recovered pasa_asmbl_26222.p1, initial, 105225, 105227 add_exon() Sorry, pasa_asmbl_26222.p1 108296-108481-initial-1 is invalid. -recovered pasa_asmbl_26222.p1, initial, 108296, 108481 -recovered pasa_asmbl_26222.p1, internal, 105345, 105534 -recovered pasa_asmbl_26222.p1, internal, 108132, 108215 -recovered pasa_asmbl_26222.p1, internal, 108296, 108481 -recovered pasa_asmbl_26222.p1, internal, 109007, 109139 -recovered pasa_asmbl_26222.p1, internal, 109355, 109547 -recovered pasa_asmbl_26222.p1, internal, 110228, 110571 -recovered pasa_asmbl_26222.p1, internal, 110757, 110926 Valid prediction for GeneMark_model.83647_t Valid prediction for CodingQuarry_transcript_30605-T1 Valid prediction for snap_scaffold_20-snap.2425-T1 Valid prediction for snap_scaffold_20-snap.2420-T1 Valid prediction for HiQ_model.g32077.t1 Valid prediction for Augustus_model.g32082.t1 Valid prediction for GlimmerHMM_glimmerT_48011-T1 Valid prediction for snap_scaffold_20-snap.2435-T1 Valid prediction for GeneMark_model.83635_t Valid prediction for GeneMark_model.83622_t Valid prediction for snap_scaffold_20-snap.2459-T1 Couldn't classify 228369, 228544 Sorry, prediction pasa_asmbl_26232.p1 fails validation. (ATG) GG 223793-223855 GT AGG (ATC) AG 225390-225552 GT AGG (AAA) AG 226951-227099 GT GGG (CTT) AG 227521-227640 GT AGG (GCT) AG 227758-227853 GT GGG (GAC) AG 228041-228140 GT AGG (GCA) AG 228369-228544 AA GAA -recovered pasa_asmbl_26232.p1, initial, 223793, 223855 add_exon() Sorry, pasa_asmbl_26232.p1 228041-228140-terminal-3 is invalid. -recovered pasa_asmbl_26232.p1, terminal, 228041, 228140 -recovered pasa_asmbl_26232.p1, internal, 225390, 225552 -recovered pasa_asmbl_26232.p1, internal, 226951, 227099 -recovered pasa_asmbl_26232.p1, internal, 227521, 227640 -recovered pasa_asmbl_26232.p1, internal, 227758, 227853 -recovered pasa_asmbl_26232.p1, internal, 228041, 228140 Valid prediction for GeneMark_model.83618_t Valid prediction for snap_scaffold_20-snap.2449-T1 Valid prediction for Augustus_model.g32078.t1 Valid prediction for GeneMark_model.83634_t Valid prediction for snap_scaffold_20-snap.2454-T1 Valid prediction for Augustus_model.g32083.t1 Valid prediction for Augustus_model.g32086.t1 Valid prediction for snap_scaffold_20-snap.2429-T1 Couldn't classify 78415, 78420 Sorry, prediction pasa_asmbl_26215.p1 fails validation. (ATC) TT 78415-78420 GT AGG (GCA) AG 78767-78982 GT AAG (CTT) AG 79132-79423 GT AGG (GCC) AG 81359-81542 GC AGG (GCC) AG 84115-84308 GT AGG (GAG) AG 84548-84648 AC GAA -recovered pasa_asmbl_26215.p1, terminal, 84548, 84648 -recovered pasa_asmbl_26215.p1, internal, 78767, 78982 -recovered pasa_asmbl_26215.p1, internal, 79132, 79423 -recovered pasa_asmbl_26215.p1, internal, 81359, 81542 -recovered pasa_asmbl_26215.p1, internal, 84115, 84308 Valid prediction for snap_scaffold_20-snap.2440-T1 Valid prediction for CodingQuarry_transcript_30610-T1 Valid prediction for Augustus_model.g32104.t1 Valid prediction for CodingQuarry_transcript_30607-T1 Couldn't classify 115025, 115189 Sorry, prediction pasa_asmbl_26225.p1 fails validation. (CCA) GT 115025-115189 GT AGG (GTA) AG 116668-116921 GT AGG (GTC) AG 117190-117335 GT AGG (GTG) AG 118610-118707 GT ATG (GTT) AG 118801-118913 GT AGG (GGT) AG 119047-119194 AT AAA add_exon() Sorry, pasa_asmbl_26225.p1 117190-117335-terminal-2 is invalid. -recovered pasa_asmbl_26225.p1, terminal, 117190, 117335 -recovered pasa_asmbl_26225.p1, terminal, 119047, 119194 -recovered pasa_asmbl_26225.p1, internal, 116668, 116921 -recovered pasa_asmbl_26225.p1, internal, 117190, 117335 -recovered pasa_asmbl_26225.p1, internal, 118610, 118707 -recovered pasa_asmbl_26225.p1, internal, 118801, 118913 Valid prediction for Augustus_model.g32069.t1 Valid prediction for snap_scaffold_20-snap.2430-T1 Valid prediction for snap_scaffold_20-snap.2438-T1 Valid prediction for GlimmerHMM_glimmerT_48035-T1 Valid prediction for snap_scaffold_20-snap.2451-T1 Valid prediction for snap_scaffold_20-snap.2439-T1 Valid prediction for GeneMark_model.83641_t Valid prediction for GlimmerHMM_glimmerT_48038-T1 Couldn't classify 242766, 242993 Couldn't classify 244461, 244541 Sorry, prediction pasa_asmbl_26234.p1 fails validation. (AGT) CC 242766-242993 GT AGG (GTT) AG 243425-243553 GT AGG (GAG) AG 243903-244040 GT AGG (TTA) AG 244461-244541 GG CAG -recovered pasa_asmbl_26234.p1, internal, 243425, 243553 -recovered pasa_asmbl_26234.p1, internal, 243903, 244040 Valid prediction for snap_scaffold_20-snap.2456-T1 Valid prediction for CodingQuarry_transcript_30608-T1 Valid prediction for GlimmerHMM_glimmerT_48033-T1 Valid prediction for GlimmerHMM_glimmerT_48021-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 GlimmerHMM_glimmerT_48031-T1 Valid prediction for snap_scaffold_20-snap.2450-T1 Valid prediction for snap_scaffold_20-snap.2444-T1 Valid prediction for GlimmerHMM_glimmerT_48027-T1 Valid prediction for GlimmerHMM_glimmerT_48016-T1 Valid prediction for GeneMark_model.83620_t Valid prediction for GlimmerHMM_glimmerT_48014-T1 Valid prediction for snap_scaffold_20-snap.2448-T1 Valid prediction for CodingQuarry_transcript_30618-T1 Valid prediction for GeneMark_model.83637_t Valid prediction for GlimmerHMM_glimmerT_48018-T1 Valid prediction for GlimmerHMM_glimmerT_48037-T1 Valid prediction for GeneMark_model.83619_t Valid prediction for CodingQuarry_transcript_30614-T1 Valid prediction for GlimmerHMM_glimmerT_48039-T1 Valid prediction for snap_scaffold_20-snap.2422-T1 Valid prediction for snap_scaffold_20-snap.2446-T1 Valid prediction for snap_scaffold_20-snap.2441-T1 Couldn't classify 62691, 62770 Sorry, prediction pasa_asmbl_27096.p2 fails validation. (TTT) TA 62691-62770 GT GGG (GAA) AG 64588-64680 GT AGG (GAA) AG 65225-65360 GT AGG (GTT) AG 68181-68335 GT TGG (GTA) AG 68782-68874 GT AGG (GTG) AG 69868-69956 GT AAG (GAC) AG 70094-70138 GT AGG (TGC) AG 70820-70984 GT TGG (ATA) AG 71077-71238 GT AGG (ACG) AG 72207-72348 GT AAG (ATG) AG 72958-73157 GT AGG (TGG) AG 73298-73371 AT AAA add_exon() Sorry, pasa_asmbl_27096.p2 72958-73157-initial-1 is invalid. -recovered pasa_asmbl_27096.p2, initial, 72958, 73157 -recovered pasa_asmbl_27096.p2, terminal, 73298, 73371 -recovered pasa_asmbl_27096.p2, internal, 64588, 64680 -recovered pasa_asmbl_27096.p2, internal, 65225, 65360 -recovered pasa_asmbl_27096.p2, internal, 68181, 68335 -recovered pasa_asmbl_27096.p2, internal, 68782, 68874 -recovered pasa_asmbl_27096.p2, internal, 69868, 69956 -recovered pasa_asmbl_27096.p2, internal, 70094, 70138 -recovered pasa_asmbl_27096.p2, internal, 70820, 70984 -recovered pasa_asmbl_27096.p2, internal, 71077, 71238 -recovered pasa_asmbl_27096.p2, internal, 72207, 72348 -recovered pasa_asmbl_27096.p2, internal, 72958, 73157 Valid prediction for snap_scaffold_20-snap.2443-T1 Valid prediction for Augustus_model.g32071.t1 Valid prediction for GeneMark_model.83624_t Valid prediction for CodingQuarry_transcript_30617-T1 Valid prediction for CodingQuarry_transcript_30616-T1 Valid prediction for GlimmerHMM_glimmerT_48013-T1 Valid prediction for snap_scaffold_20-snap.2453-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for snap_scaffold_20-snap.2423-T1 Valid prediction for GlimmerHMM_glimmerT_48034-T1 Valid prediction for HiQ_model.g32096.t1 Valid prediction for GlimmerHMM_glimmerT_48012-T1 Valid prediction for Augustus_model.g32100.t1 Valid prediction for GlimmerHMM_glimmerT_48030-T1 Valid prediction for Augustus_model.g32079.t1 Valid prediction for HiQ_model.g32091.t1 Valid prediction for Augustus_model.g32097.t1 Valid prediction for snap_scaffold_20-snap.2434-T1 Valid prediction for CodingQuarry_transcript_30613-T1 Valid prediction for snap_scaffold_20-snap.2447-T1 Valid prediction for snap_scaffold_20-snap.2427-T1 Valid prediction for snap_scaffold_20-snap.2445-T1 Valid prediction for Augustus_model.g32103.t1 Valid prediction for GlimmerHMM_glimmerT_48025-T1 Valid prediction for snap_scaffold_20-snap.2457-T1 Valid prediction for CodingQuarry_transcript_30615-T1 Valid prediction for HiQ_model.g32094.t1 Valid prediction for GlimmerHMM_glimmerT_48028-T1 Valid prediction for GeneMark_model.83648_t Valid prediction for GeneMark_model.83631_t Valid prediction for Augustus_model.g32089.t1 Valid prediction for snap_scaffold_20-snap.2428-T1 Valid prediction for GeneMark_model.83643_t Couldn't classify 131913, 131977 Sorry, prediction pasa_asmbl_27077.p1 fails validation. (ATG) AA 128763-128862 GT AGG (ACT) AG 128951-129067 GT AGG (TTC) AG 129158-129225 GT AGG (GTG) AG 129355-129599 GT AGG (GAA) AG 129682-129734 GT AGG (GTT) AG 131060-131217 GT TGG (GTC) AG 131746-131791 GT TTG (TTA) AG 131913-131977 TA AGT -recovered pasa_asmbl_27077.p1, initial, 128763, 128862 -recovered pasa_asmbl_27077.p1, internal, 128951, 129067 -recovered pasa_asmbl_27077.p1, internal, 129158, 129225 -recovered pasa_asmbl_27077.p1, internal, 129355, 129599 -recovered pasa_asmbl_27077.p1, internal, 129682, 129734 -recovered pasa_asmbl_27077.p1, internal, 131060, 131217 -recovered pasa_asmbl_27077.p1, internal, 131746, 131791 Valid prediction for GeneMark_model.83640_t Valid prediction for Augustus_model.g32072.t1 Valid prediction for GlimmerHMM_glimmerT_48036-T1 Valid prediction for pasa_asmbl_27083.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -) -building DP trellis -building trellis in range 1 - 270971 -exon list size: 535 building trellis 0.2 0.4 0.6 0.7 0.9 1.1 1.3 1.5 1.7 1.9 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.5 3.7 3.9 4.1 4.3 4.5 4.7 4.8 5.0 5.2 5.4 5.6 5.8 6.0 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.4 7.6 7.8 8.0 8.2 8.4 8.6 8.8 8.9 9.1 9.3 9.5 9.7 9.9 10.1 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.5 11.7 11.9 12.1 12.3 12.5 12.7 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.3 14.5 14.7 14.9 15.1 15.3 15.5 15.6 15.8 16.0 16.2 16.4 16.6 16.8 16.9 17.1 17.3 17.5 17.7 17.9 18.1 18.2 18.4 18.6 18.8 19.0 19.2 19.4 19.6 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.0 21.2 21.4 21.6 21.8 22.0 22.2 22.3 22.5 22.7 22.9 23.1 23.3 23.5 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.0 25.1 25.3 25.5 25.7 25.9 26.1 26.3 26.4 26.6 26.8 27.0 27.2 27.4 27.6 27.7 27.9 28.1 28.3 28.5 28.7 28.9 29.1 29.2 29.4 29.6 29.8 30.0 30.2 30.4 30.5 30.7 30.9 31.1 31.3 31.5 31.7 31.8 32.0 32.2 32.4 32.6 32.8 33.0 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.5 34.6 34.8 35.0 35.2 35.4 35.6 35.8 35.9 36.1 36.3 36.5 36.7 36.9 37.1 37.2 37.4 37.6 37.8 38.0 38.2 38.4 38.5 38.7 38.9 39.1 39.3 39.5 39.7 39.9 40.0 40.2 40.4 40.6 40.8 41.0 41.2 41.3 41.5 41.7 41.9 42.1 42.3 42.5 42.6 42.8 43.0 43.2 43.4 43.6 43.8 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.4 45.6 45.8 46.0 46.2 46.4 46.6 46.7 46.9 47.1 47.3 47.5 47.7 47.9 48.0 48.2 48.4 48.6 48.8 49.0 49.2 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.8 51.0 51.2 51.4 51.6 51.8 52.0 52.1 52.3 52.5 52.7 52.9 53.1 53.3 53.4 53.6 53.8 54.0 54.2 54.4 54.6 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.2 56.4 56.6 56.8 57.0 57.2 57.4 57.5 57.7 57.9 58.1 58.3 58.5 58.7 58.8 59.0 59.2 59.4 59.6 59.8 60.0 60.1 60.3 60.5 60.7 60.9 61.1 61.3 61.5 61.6 61.8 62.0 62.2 62.4 62.6 62.8 62.9 63.1 63.3 63.5 63.7 63.9 64.1 64.2 64.4 64.6 64.8 65.0 65.2 65.4 65.5 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.0 67.2 67.4 67.6 67.8 68.0 68.2 68.3 68.5 68.7 68.9 69.1 69.3 69.5 69.6 69.8 70.0 70.2 70.4 70.6 70.8 70.9 71.1 71.3 71.5 71.7 71.9 72.1 72.3 72.4 72.6 72.8 73.0 73.2 73.4 73.6 73.7 73.9 74.1 74.3 74.5 74.7 74.9 75.0 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.5 76.7 76.9 77.1 77.3 77.5 77.7 77.8 78.0 78.2 78.4 78.6 78.8 79.0 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.4 80.6 80.8 81.0 81.2 81.4 81.6 81.8 81.9 82.1 82.3 82.5 82.7 82.9 83.1 83.2 83.4 83.6 83.8 84.0 84.2 84.4 84.5 84.7 84.9 85.1 85.3 85.5 85.7 85.8 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.3 87.5 87.7 87.9 88.1 88.3 88.5 88.6 88.8 89.0 89.2 89.4 89.6 89.8 89.9 90.1 90.3 90.5 90.7 90.9 91.1 91.2 91.4 91.6 91.8 92.0 92.2 92.4 92.6 92.7 92.9 93.1 93.3 93.5 93.7 93.9 94.0 94.2 94.4 94.6 94.8 95.0 95.2 95.3 95.5 95.7 95.9 96.1 96.3 96.5 96.6 96.8 97.0 97.2 97.4 97.6 97.8 98.0 98.1 98.3 98.5 98.7 98.9 99.1 99.3 99.4 99.6 99.8 -found 42 predictions from path traversal -reporting highest scoring path thru the trellis. -found 40 predictions persist after filtering for low support