-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_11614492-11828462 -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 Augustus_model.g24663.t1 Valid prediction for snap_scaffold_15-snap.2421-T1 Valid prediction for Augustus_model.g24649.t1 Valid prediction for GlimmerHMM_glimmerT_37031-T1 Valid prediction for GlimmerHMM_glimmerT_37020-T1 Valid prediction for snap_scaffold_15-snap.2405-T1 Valid prediction for GlimmerHMM_glimmerT_37032-T1 Valid prediction for snap_scaffold_15-snap.2397-T1 Couldn't classify 107280, 107471 Couldn't classify 107766, 108176 Sorry, prediction pasa_asmbl_15505.p1 fails validation. (TCT) CG 107280-107471 GT AAG (GCT) AG 107766-108176 TT GGT Valid prediction for GlimmerHMM_glimmerT_37036-T1 Valid prediction for snap_scaffold_15-snap.2415-T1 Valid prediction for snap_scaffold_15-snap.2408-T1 Valid prediction for GlimmerHMM_glimmerT_37029-T1 Valid prediction for snap_scaffold_15-snap.2412-T1 Valid prediction for Augustus_model.g24667.t1 Valid prediction for CodingQuarry_transcript_18152-T1 Valid prediction for snap_scaffold_15-snap.2403-T1 Valid prediction for GlimmerHMM_glimmerT_37037-T1 Valid prediction for GlimmerHMM_glimmerT_37027-T1 Valid prediction for GlimmerHMM_glimmerT_37025-T1 Valid prediction for snap_scaffold_15-snap.2404-T1 Valid prediction for snap_scaffold_15-snap.2395-T1 Valid prediction for snap_scaffold_15-snap.2411-T1 Valid prediction for GlimmerHMM_glimmerT_37044-T1 Valid prediction for GlimmerHMM_glimmerT_37019-T1 Valid prediction for GlimmerHMM_glimmerT_37042-T1 Valid prediction for Augustus_model.g24664.t1 Valid prediction for snap_scaffold_15-snap.2427-T1 Valid prediction for Augustus_model.g24652.t1 Valid prediction for HiQ_model.g24661.t1 Valid prediction for GlimmerHMM_glimmerT_37017-T1 Valid prediction for Augustus_model.g24656.t1 Couldn't classify 109464, 109637 Couldn't classify 113043, 113074 Sorry, prediction pasa_asmbl_15862.p1 fails validation. (ATA) TG 109464-109637 GT GGG (GAT) AG 109742-109898 GT AGG (GTG) AG 110101-110189 GT AAG (CTG) AG 110281-110334 GT AGG (GGA) AG 110449-110551 GT ACG (AAA) AG 110694-110762 GT AGG (TGA) AG 110851-110917 GT CGG (GTT) AG 111091-111197 GT GGG (ATT) AG 111323-111383 GT GGG (CAA) AG 111554-111756 GC AGG (ATC) AG 111893-111937 GT TGG (ACT) AG 112032-112130 GT AGG (GGT) AG 112385-112449 GT AGG (TTC) AG 112571-112652 GT TGG (GGG) AG 113043-113074 GA GGG -recovered pasa_asmbl_15862.p1, terminal, 112032, 112130 -recovered pasa_asmbl_15862.p1, internal, 109742, 109898 -recovered pasa_asmbl_15862.p1, internal, 110101, 110189 -recovered pasa_asmbl_15862.p1, internal, 110281, 110334 -recovered pasa_asmbl_15862.p1, internal, 110449, 110551 -recovered pasa_asmbl_15862.p1, internal, 110694, 110762 -recovered pasa_asmbl_15862.p1, internal, 110851, 110917 -recovered pasa_asmbl_15862.p1, internal, 111091, 111197 -recovered pasa_asmbl_15862.p1, internal, 111323, 111383 -recovered pasa_asmbl_15862.p1, internal, 111554, 111756 -recovered pasa_asmbl_15862.p1, internal, 111893, 111937 -recovered pasa_asmbl_15862.p1, internal, 112032, 112130 -recovered pasa_asmbl_15862.p1, internal, 112385, 112449 -recovered pasa_asmbl_15862.p1, internal, 112571, 112652 Couldn't classify 82905, 83002 Couldn't classify 84075, 84204 Sorry, prediction CodingQuarry_transcript_18151-T1 fails validation. (ATG) AA 78318-78441 GT TGG (AGC) AG 79598-79697 GT AAG (GAA) AG 81269-81383 GT AGG (GGG) AG 81505-81617 GT GCG (CCT) AG 81973-82034 GT AGG (CGA) AG 82216-82274 GT TGG (GTT) AG 82520-82570 GT TGG (GGC) AG 82676-82784 GT ACG (GGT) AG 82905-83002 AG TGA (ATT) GC 84075-84204 GT GGG (ACC) AG 84309-84401 GT AGG (GTT) AG 84499-84644 GT AGG (TAC) AG 85017-85164 GT GGG (TCC) AG 85449-85531 GT CGG (GAC) AG 85725-85793 GT CGG (CAA) AG 85912-86070 GT ATG (GAG) AG 86274-86435 GT AGG (GAG) AG 86594-86794 GT AGG (GTG) AG 87675-87779 GT AGG (CTG) AG 87953-88090 AC AGA -recovered CodingQuarry_transcript_18151-T1, initial, 78318, 78441 -recovered CodingQuarry_transcript_18151-T1, terminal, 87953, 88090 -recovered CodingQuarry_transcript_18151-T1, internal, 79598, 79697 -recovered CodingQuarry_transcript_18151-T1, internal, 81269, 81383 -recovered CodingQuarry_transcript_18151-T1, internal, 81505, 81617 -recovered CodingQuarry_transcript_18151-T1, internal, 81973, 82034 -recovered CodingQuarry_transcript_18151-T1, internal, 82216, 82274 -recovered CodingQuarry_transcript_18151-T1, internal, 82520, 82570 -recovered CodingQuarry_transcript_18151-T1, internal, 82676, 82784 -recovered CodingQuarry_transcript_18151-T1, internal, 84309, 84401 -recovered CodingQuarry_transcript_18151-T1, internal, 84499, 84644 -recovered CodingQuarry_transcript_18151-T1, internal, 85017, 85164 -recovered CodingQuarry_transcript_18151-T1, internal, 85449, 85531 -recovered CodingQuarry_transcript_18151-T1, internal, 85725, 85793 -recovered CodingQuarry_transcript_18151-T1, internal, 85912, 86070 -recovered CodingQuarry_transcript_18151-T1, internal, 86274, 86435 -recovered CodingQuarry_transcript_18151-T1, internal, 86594, 86794 -recovered CodingQuarry_transcript_18151-T1, internal, 87675, 87779 Valid prediction for snap_scaffold_15-snap.2390-T1 Valid prediction for snap_scaffold_15-snap.2401-T1 Valid prediction for Augustus_model.g24660.t1 Valid prediction for HiQ_model.g24657.t1 Valid prediction for Augustus_model.g24658.t1 Valid prediction for GlimmerHMM_glimmerT_37022-T1 Valid prediction for Augustus_model.g24659.t1 Valid prediction for snap_scaffold_15-snap.2394-T1 Valid prediction for Augustus_model.g24665.t1 Valid prediction for GlimmerHMM_glimmerT_37034-T1 Couldn't classify 108963, 109289 Sorry, prediction pasa_asmbl_15506.p3 fails validation. (AAC) TC 108963-109289 CC CTC Valid prediction for snap_scaffold_15-snap.2418-T1 Valid prediction for GlimmerHMM_glimmerT_37035-T1 Valid prediction for snap_scaffold_15-snap.2406-T1 Valid prediction for snap_scaffold_15-snap.2398-T1 Valid prediction for GlimmerHMM_glimmerT_37040-T1 Valid prediction for snap_scaffold_15-snap.2420-T1 Valid prediction for snap_scaffold_15-snap.2413-T1 Valid prediction for GlimmerHMM_glimmerT_37023-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 CodingQuarry_transcript_18150-T1 Valid prediction for GlimmerHMM_glimmerT_37038-T1 Couldn't classify 25405, 25464 Couldn't classify 27488, 27605 Sorry, prediction pasa_asmbl_14533.p1 fails validation. (GGC) GT 25405-25464 GT AGG (GGG) AG 25552-25631 GT CAG (GCC) AG 25743-25799 GT GGG (AAT) AG 26471-26539 GT AAG (GCT) AG 26789-26917 GT GGG (TCA) AG 27488-27605 CG CAC -recovered pasa_asmbl_14533.p1, terminal, 26471, 26539 -recovered pasa_asmbl_14533.p1, internal, 25552, 25631 -recovered pasa_asmbl_14533.p1, internal, 25743, 25799 -recovered pasa_asmbl_14533.p1, internal, 26471, 26539 -recovered pasa_asmbl_14533.p1, internal, 26789, 26917 Valid prediction for Augustus_model.g24651.t1 Valid prediction for snap_scaffold_15-snap.2424-T1 Valid prediction for HiQ_model.g24669.t1 Valid prediction for snap_scaffold_15-snap.2417-T1 Valid prediction for Augustus_model.g24654.t1 Valid prediction for snap_scaffold_15-snap.2396-T1 Valid prediction for snap_scaffold_15-snap.2389-T1 Valid prediction for GlimmerHMM_glimmerT_37043-T1 Valid prediction for GlimmerHMM_glimmerT_37048-T1 Valid prediction for GlimmerHMM_glimmerT_37046-T1 Valid prediction for CodingQuarry_transcript_18156-T1 Valid prediction for snap_scaffold_15-snap.2391-T1 Valid prediction for CodingQuarry_transcript_18155-T1 Valid prediction for snap_scaffold_15-snap.2402-T1 Valid prediction for GlimmerHMM_glimmerT_37018-T1 Valid prediction for snap_scaffold_15-snap.2409-T1 Valid prediction for GlimmerHMM_glimmerT_37030-T1 Valid prediction for GlimmerHMM_glimmerT_37024-T1 Valid prediction for HiQ_model.g24670.t1 Valid prediction for CodingQuarry_transcript_18153-T1 Valid prediction for GlimmerHMM_glimmerT_37045-T1 Valid prediction for Augustus_model.g24650.t1 Valid prediction for snap_scaffold_15-snap.2426-T1 Valid prediction for Augustus_model.g24666.t1 Valid prediction for Augustus_model.g24655.t1 Valid prediction for snap_scaffold_15-snap.2392-T1 Valid prediction for snap_scaffold_15-snap.2400-T1 Valid prediction for GlimmerHMM_glimmerT_37041-T1 Valid prediction for GlimmerHMM_glimmerT_37026-T1 Valid prediction for pasa_asmbl_14536.p1 Valid prediction for Augustus_model.g24653.t1 Valid prediction for CodingQuarry_transcript_18154-T1 Valid prediction for Augustus_model.g24668.t1 Valid prediction for Augustus_model.g24648.t1 Valid prediction for snap_scaffold_15-snap.2407-T1 Valid prediction for snap_scaffold_15-snap.2425-T1 Valid prediction for pasa_asmbl_14532.p2 Valid prediction for snap_scaffold_15-snap.2410-T1 Valid prediction for snap_scaffold_15-snap.2414-T1 Valid prediction for GlimmerHMM_glimmerT_37047-T1 Valid prediction for GlimmerHMM_glimmerT_37033-T1 Valid prediction for snap_scaffold_15-snap.2393-T1 Valid prediction for snap_scaffold_15-snap.2423-T1 Valid prediction for snap_scaffold_15-snap.2399-T1 Couldn't classify 25156, 25238 Sorry, prediction pasa_asmbl_14534.p1 fails validation. (ATG) AG 15442-15516 GT GGG (TCA) AG 15879-16006 GT AAG (GCC) AG 16093-16204 GT TGG (GCC) AG 16325-16436 GT AGG (GAG) AG 16595-16653 GT CAG (GGA) AG 16762-16851 GT CGG (GTT) AG 16977-17049 GT AGG (CTC) AG 17219-17269 GT CGG (CTG) AG 19214-19371 GT AGG (CAT) AG 19501-19575 GT AGG (TAC) AG 19757-19890 GT AGG (AGA) AG 19980-20037 GT GAG (GGC) AG 20170-20277 GT ATG (GAG) AG 20577-20621 GT AAG (GCC) AG 20818-20958 GT AGG (GAT) AG 21102-21146 GT AGG (AGC) AG 21739-21833 GT AGG (GTT) AG 22510-22645 GT AGG (GGG) AG 24061-24168 GT CGG (TTC) AG 24296-24385 GT CAG (GAC) AG 24483-24555 GT AGG (GTG) AG 25156-25238 GG AAG -recovered pasa_asmbl_14534.p1, initial, 15442, 15516 -recovered pasa_asmbl_14534.p1, internal, 15442, 15516 -recovered pasa_asmbl_14534.p1, internal, 15879, 16006 -recovered pasa_asmbl_14534.p1, internal, 16093, 16204 -recovered pasa_asmbl_14534.p1, internal, 16325, 16436 -recovered pasa_asmbl_14534.p1, internal, 16595, 16653 -recovered pasa_asmbl_14534.p1, internal, 16762, 16851 -recovered pasa_asmbl_14534.p1, internal, 16977, 17049 -recovered pasa_asmbl_14534.p1, internal, 17219, 17269 -recovered pasa_asmbl_14534.p1, internal, 19214, 19371 -recovered pasa_asmbl_14534.p1, internal, 19501, 19575 -recovered pasa_asmbl_14534.p1, internal, 19757, 19890 -recovered pasa_asmbl_14534.p1, internal, 19980, 20037 -recovered pasa_asmbl_14534.p1, internal, 20170, 20277 -recovered pasa_asmbl_14534.p1, internal, 20577, 20621 -recovered pasa_asmbl_14534.p1, internal, 20818, 20958 -recovered pasa_asmbl_14534.p1, internal, 21102, 21146 -recovered pasa_asmbl_14534.p1, internal, 21739, 21833 -recovered pasa_asmbl_14534.p1, internal, 22510, 22645 -recovered pasa_asmbl_14534.p1, internal, 24061, 24168 -recovered pasa_asmbl_14534.p1, internal, 24296, 24385 -recovered pasa_asmbl_14534.p1, internal, 24483, 24555 Valid prediction for snap_scaffold_15-snap.2416-T1 Valid prediction for GlimmerHMM_glimmerT_37039-T1 Valid prediction for GlimmerHMM_glimmerT_37028-T1 Valid prediction for snap_scaffold_15-snap.2419-T1 Valid prediction for GlimmerHMM_glimmerT_37021-T1 Valid prediction for Augustus_model.g24662.t1 Valid prediction for snap_scaffold_15-snap.2422-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11990, rend_intergenic: 7172 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20492, rend_intergenic: 12118 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33312, rend_intergenic: 30789 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47739, rend_intergenic: 34231 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 49879, rend_intergenic: 48097 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58392, rend_intergenic: 54943 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74434, rend_intergenic: 62462 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 88090, rend_intergenic: 79934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95533, rend_intergenic: 93101 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100546, rend_intergenic: 97352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211330, rend_intergenic: 204105 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 213971 -exon list size: 432 building trellis 0.2 0.5 0.7 0.9 1.2 1.4 1.6 1.8 2.1 2.3 2.5 2.8 3.0 3.2 3.5 3.7 3.9 4.1 4.4 4.6 4.8 5.1 5.3 5.5 5.8 6.0 6.2 6.5 6.7 6.9 7.1 7.4 7.6 7.8 8.1 8.3 8.5 8.8 9.0 9.2 9.4 9.7 9.9 10.1 10.4 10.6 10.8 11.1 11.3 11.5 11.8 12.0 12.2 12.4 12.7 12.9 13.1 13.4 13.6 13.8 14.1 14.3 14.5 14.7 15.0 15.2 15.4 15.7 15.9 16.1 16.4 16.6 16.8 17.1 17.3 17.5 17.7 18.0 18.2 18.4 18.7 18.9 19.1 19.4 19.6 19.8 20.0 20.3 20.5 20.7 21.0 21.2 21.4 21.7 21.9 22.1 22.4 22.6 22.8 23.0 23.3 23.5 23.7 24.0 24.2 24.4 24.7 24.9 25.1 25.3 25.6 25.8 26.0 26.3 26.5 26.7 27.0 27.2 27.4 27.6 27.9 28.1 28.3 28.6 28.8 29.0 29.3 29.5 29.7 30.0 30.2 30.4 30.6 30.9 31.1 31.3 31.6 31.8 32.0 32.3 32.5 32.7 32.9 33.2 33.4 33.6 33.9 34.1 34.3 34.6 34.8 35.0 35.3 35.5 35.7 35.9 36.2 36.4 36.6 36.9 37.1 37.3 37.6 37.8 38.0 38.2 38.5 38.7 38.9 39.2 39.4 39.6 39.9 40.1 40.3 40.6 40.8 41.0 41.2 41.5 41.7 41.9 42.2 42.4 42.6 42.9 43.1 43.3 43.5 43.8 44.0 44.2 44.5 44.7 44.9 45.2 45.4 45.6 45.9 46.1 46.3 46.5 46.8 47.0 47.2 47.5 47.7 47.9 48.2 48.4 48.6 48.8 49.1 49.3 49.5 49.8 50.0 50.2 50.5 50.7 50.9 51.2 51.4 51.6 51.8 52.1 52.3 52.5 52.8 53.0 53.2 53.5 53.7 53.9 54.1 54.4 54.6 54.8 55.1 55.3 55.5 55.8 56.0 56.2 56.5 56.7 56.9 57.1 57.4 57.6 57.8 58.1 58.3 58.5 58.8 59.0 59.2 59.4 59.7 59.9 60.1 60.4 60.6 60.8 61.1 61.3 61.5 61.8 62.0 62.2 62.4 62.7 62.9 63.1 63.4 63.6 63.8 64.1 64.3 64.5 64.7 65.0 65.2 65.4 65.7 65.9 66.1 66.4 66.6 66.8 67.1 67.3 67.5 67.7 68.0 68.2 68.4 68.7 68.9 69.1 69.4 69.6 69.8 70.0 70.3 70.5 70.7 71.0 71.2 71.4 71.7 71.9 72.1 72.4 72.6 72.8 73.0 73.3 73.5 73.7 74.0 74.2 74.4 74.7 74.9 75.1 75.3 75.6 75.8 76.0 76.3 76.5 76.7 77.0 77.2 77.4 77.6 77.9 78.1 78.3 78.6 78.8 79.0 79.3 79.5 79.7 80.0 80.2 80.4 80.6 80.9 81.1 81.3 81.6 81.8 82.0 82.3 82.5 82.7 82.9 83.2 83.4 83.6 83.9 84.1 84.3 84.6 84.8 85.0 85.3 85.5 85.7 85.9 86.2 86.4 86.6 86.9 87.1 87.3 87.6 87.8 88.0 88.2 88.5 88.7 88.9 89.2 89.4 89.6 89.9 90.1 90.3 90.6 90.8 91.0 91.2 91.5 91.7 91.9 92.2 92.4 92.6 92.9 93.1 93.3 93.5 93.8 94.0 94.2 94.5 94.7 94.9 95.2 95.4 95.6 95.9 96.1 96.3 96.5 96.8 97.0 97.2 97.5 97.7 97.9 98.2 98.4 98.6 98.8 99.1 99.3 99.5 99.8 -found 32 predictions from path traversal Error with prediction: snap lend_intergenic: 11990, rend_intergenic: 7172 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20492, rend_intergenic: 12118 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33312, rend_intergenic: 30789 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47739, rend_intergenic: 34231 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 49879, rend_intergenic: 48097 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58392, rend_intergenic: 54943 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74434, rend_intergenic: 62462 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 88090, rend_intergenic: 79934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95533, rend_intergenic: 93101 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100546, rend_intergenic: 97352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211330, rend_intergenic: 204105 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 -building DP trellis -building trellis in range 1 - 10904 -exon list size: 7 building trellis 11.1 22.2 33.3 44.4 55.6 66.7 77.8 88.9 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 10753 -exon list size: 6 building trellis 12.5 25.0 37.5 50.0 62.5 75.0 87.5 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support