-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_2588545-2775931 -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 HiQ_model.g34864.t1 Couldn't classify 45222, 45452 Sorry, prediction pasa_asmbl_30714.p1 fails validation. (GCA) CG 45222-45452 GT AGG (AGG) AG 46251-46376 GT AGG (CTC) AG 46587-46647 GT ATG (TCA) AG 46826-46941 GC GAG -recovered pasa_asmbl_30714.p1, terminal, 46826, 46941 -recovered pasa_asmbl_30714.p1, internal, 46251, 46376 -recovered pasa_asmbl_30714.p1, internal, 46587, 46647 -recovered pasa_asmbl_30714.p1, internal, 46826, 46941 Valid prediction for snap_scaffold_23-snap.504-T1 Valid prediction for GlimmerHMM_glimmerT_51881-T1 Valid prediction for GeneMark_model.90147_t Valid prediction for GlimmerHMM_glimmerT_51899-T1 Valid prediction for snap_scaffold_23-snap.507-T1 Valid prediction for GeneMark_model.90151_t Valid prediction for snap_scaffold_23-snap.493-T1 Valid prediction for GlimmerHMM_glimmerT_51879-T1 Valid prediction for snap_scaffold_23-snap.513-T1 Valid prediction for Augustus_model.g34882.t1 Valid prediction for GeneMark_model.90138_t Valid prediction for GeneMark_model.90152_t Valid prediction for GeneMark_model.90163_t Valid prediction for GeneMark_model.90154_t Valid prediction for Augustus_model.g34865.t1 Valid prediction for snap_scaffold_23-snap.499-T1 Valid prediction for snap_scaffold_23-snap.496-T1 Valid prediction for GlimmerHMM_glimmerT_51883-T1 Valid prediction for GlimmerHMM_glimmerT_51893-T1 Valid prediction for GeneMark_model.90161_t Valid prediction for snap_scaffold_23-snap.511-T1 Couldn't classify 35126, 35188 Sorry, prediction pasa_asmbl_30711.p1 fails validation. (ATG) GA 33710-33829 GT GGG (ATG) AG 34018-34156 GT GGG (GTC) AG 34301-34349 GT AGG (GAG) AG 34467-34565 GT AGG (AGC) AG 34684-34744 GT TGG (CTC) AG 34956-35015 GT TGG (CTG) AG 35126-35188 TA AGT -recovered pasa_asmbl_30711.p1, initial, 33710, 33829 -recovered pasa_asmbl_30711.p1, initial, 34018, 34156 -recovered pasa_asmbl_30711.p1, internal, 34018, 34156 -recovered pasa_asmbl_30711.p1, internal, 34301, 34349 -recovered pasa_asmbl_30711.p1, internal, 34467, 34565 -recovered pasa_asmbl_30711.p1, internal, 34684, 34744 -recovered pasa_asmbl_30711.p1, internal, 34956, 35015 Valid prediction for HiQ_model.g34876.t1 Valid prediction for GeneMark_model.90157_t Valid prediction for snap_scaffold_23-snap.489-T1 Valid prediction for HiQ_model.g34862.t1 Valid prediction for GeneMark_model.90144_t Valid prediction for CodingQuarry_transcript_35529-T1 Valid prediction for Augustus_model.g34877.t1 Valid prediction for snap_scaffold_23-snap.508-T1 Valid prediction for GeneMark_model.90160_t Valid prediction for snap_scaffold_23-snap.506-T1 Valid prediction for snap_scaffold_23-snap.500-T1 Valid prediction for CodingQuarry_transcript_35530-T1 Couldn't classify 55071, 55377 Sorry, prediction pasa_asmbl_30718.p1 fails validation. (CCT) CA 55071-55377 GT AGG (CCG) AG 55912-56022 GT CGG (GGT) AG 56199-56351 GT AAG (AAT) AG 56489-56620 GT TGG (TTT) AG 56776-56913 GT AGG (CTT) AG 57014-57139 GT GGG (ACG) AG 57231-57376 GT ATG (CCG) AG 57462-57606 GT AGG (TGC) AG 57774-57932 GT AGG (TTA) AG 58375-58509 GT CGG (ATC) AG 58743-59030 GT TGG (AGT) AG 59169-59266 GT AGG (GTG) AG 59379-59637 GT TCG (GAC) AG 59906-60066 GT TAG (AGA) AG 60147-60357 GT AGG (AGT) AG 60569-60679 GT AGG (GCT) AG 60825-61015 GT AGG (TTC) AG 61119-61232 GT TGG (GGC) AG 61394-61464 GT GTG (GTG) AG 61590-61630 GT AGG (GAG) AG 61744-61840 GT GTG (GTA) AG 62356-62455 GC AGG (ATG) AG 62548-62622 TC GAT -recovered pasa_asmbl_30718.p1, terminal, 61590, 61630 -recovered pasa_asmbl_30718.p1, terminal, 62548, 62622 -recovered pasa_asmbl_30718.p1, internal, 55912, 56022 -recovered pasa_asmbl_30718.p1, internal, 56199, 56351 -recovered pasa_asmbl_30718.p1, internal, 56489, 56620 -recovered pasa_asmbl_30718.p1, internal, 56776, 56913 -recovered pasa_asmbl_30718.p1, internal, 57014, 57139 -recovered pasa_asmbl_30718.p1, internal, 57231, 57376 -recovered pasa_asmbl_30718.p1, internal, 57462, 57606 -recovered pasa_asmbl_30718.p1, internal, 57774, 57932 -recovered pasa_asmbl_30718.p1, internal, 58375, 58509 -recovered pasa_asmbl_30718.p1, internal, 58743, 59030 -recovered pasa_asmbl_30718.p1, internal, 59169, 59266 -recovered pasa_asmbl_30718.p1, internal, 59379, 59637 -recovered pasa_asmbl_30718.p1, internal, 59906, 60066 -recovered pasa_asmbl_30718.p1, internal, 60147, 60357 -recovered pasa_asmbl_30718.p1, internal, 60569, 60679 -recovered pasa_asmbl_30718.p1, internal, 60825, 61015 -recovered pasa_asmbl_30718.p1, internal, 61119, 61232 -recovered pasa_asmbl_30718.p1, internal, 61394, 61464 -recovered pasa_asmbl_30718.p1, internal, 61590, 61630 -recovered pasa_asmbl_30718.p1, internal, 61744, 61840 -recovered pasa_asmbl_30718.p1, internal, 62356, 62455 Valid prediction for snap_scaffold_23-snap.488-T1 Valid prediction for Augustus_model.g34868.t1 Valid prediction for GlimmerHMM_glimmerT_51889-T1 Valid prediction for GlimmerHMM_glimmerT_51901-T1 Valid prediction for GeneMark_model.90133_t Valid prediction for snap_scaffold_23-snap.487-T1 Valid prediction for GeneMark_model.90155_t Valid prediction for snap_scaffold_23-snap.512-T1 Valid prediction for GlimmerHMM_glimmerT_51898-T1 Valid prediction for GlimmerHMM_glimmerT_51895-T1 Valid prediction for snap_scaffold_23-snap.501-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for GeneMark_model.90131_t Valid prediction for pasa_asmbl_30712.p1 Valid prediction for GeneMark_model.90135_t Valid prediction for GlimmerHMM_glimmerT_51892-T1 Valid prediction for GeneMark_model.90149_t Valid prediction for GeneMark_model.90140_t Valid prediction for Augustus_model.g34873.t1 Valid prediction for GeneMark_model.90134_t Valid prediction for GlimmerHMM_glimmerT_51890-T1 Valid prediction for snap_scaffold_23-snap.494-T1 Valid prediction for pasa_asmbl_30724.p1 Valid prediction for snap_scaffold_23-snap.491-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 HiQ_model.g34875.t1 Valid prediction for GeneMark_model.90158_t Valid prediction for GeneMark_model.90139_t Valid prediction for snap_scaffold_23-snap.482-T1 Valid prediction for GlimmerHMM_glimmerT_51894-T1 Valid prediction for Augustus_model.g34874.t1 Valid prediction for GlimmerHMM_glimmerT_51885-T1 Valid prediction for Augustus_model.g34880.t1 Valid prediction for Augustus_model.g34860.t1 Valid prediction for snap_scaffold_23-snap.514-T1 Valid prediction for CodingQuarry_transcript_35526-T1 Valid prediction for Augustus_model.g34878.t1 Valid prediction for snap_scaffold_23-snap.483-T1 Valid prediction for CodingQuarry_transcript_35527-T1 Valid prediction for snap_scaffold_23-snap.495-T1 Valid prediction for HiQ_model.g34861.t1 Valid prediction for snap_scaffold_23-snap.486-T1 Couldn't classify 182456, 182601 Sorry, prediction pasa_asmbl_31970.p1 fails validation. (CCA) TC 182456-182601 GT TCG (GTA) AG 182778-183060 TG GAT -recovered pasa_asmbl_31970.p1, terminal, 182778, 183060 Valid prediction for GeneMark_model.90153_t Valid prediction for GeneMark_model.90130_t Valid prediction for GlimmerHMM_glimmerT_51886-T1 Valid prediction for GeneMark_model.90136_t Valid prediction for GeneMark_model.90127_t Valid prediction for GlimmerHMM_glimmerT_51878-T1 Valid prediction for GeneMark_model.90137_t Valid prediction for GeneMark_model.90146_t Valid prediction for GeneMark_model.90129_t Valid prediction for Augustus_model.g34879.t1 Valid prediction for GeneMark_model.90159_t Valid prediction for GlimmerHMM_glimmerT_51888-T1 Valid prediction for GeneMark_model.90132_t Valid prediction for GeneMark_model.90143_t Valid prediction for snap_scaffold_23-snap.490-T1 Valid prediction for GlimmerHMM_glimmerT_51903-T1 Valid prediction for Augustus_model.g34867.t1 Valid prediction for HiQ_model.g34870.t1 Valid prediction for GlimmerHMM_glimmerT_51891-T1 Valid prediction for GeneMark_model.90148_t Valid prediction for pasa_asmbl_31481.p1 Valid prediction for GlimmerHMM_glimmerT_51875-T1 Couldn't classify 92463, 93212 Sorry, prediction pasa_asmbl_31482.p1 fails validation. (GAG) TT 92463-93212 GC GAG Valid prediction for snap_scaffold_23-snap.503-T1 Valid prediction for GeneMark_model.90150_t Valid prediction for pasa_asmbl_31483.p1 Valid prediction for GlimmerHMM_glimmerT_51900-T1 Valid prediction for GlimmerHMM_glimmerT_51884-T1 Valid prediction for GlimmerHMM_glimmerT_51880-T1 Valid prediction for GlimmerHMM_glimmerT_51882-T1 Valid prediction for snap_scaffold_23-snap.502-T1 Couldn't classify 169657, 169806 Sorry, prediction pasa_asmbl_31467.p1 fails validation. (TTC) TG 169657-169806 GT ACG (CCT) AG 169909-170186 GT AGG (GCC) AG 170287-170419 GT AGG (ATG) AG 170538-170667 GT AGG (GCT) AG 171006-171139 GT AGG (GTT) AG 171332-171456 GT AAG (GTA) AG 171616-171829 GC GAG -recovered pasa_asmbl_31467.p1, initial, 170538, 170667 add_exon() Sorry, pasa_asmbl_31467.p1 170538-170667-terminal-3 is invalid. -recovered pasa_asmbl_31467.p1, terminal, 170538, 170667 -recovered pasa_asmbl_31467.p1, terminal, 171616, 171829 -recovered pasa_asmbl_31467.p1, internal, 169909, 170186 -recovered pasa_asmbl_31467.p1, internal, 170287, 170419 -recovered pasa_asmbl_31467.p1, internal, 170538, 170667 -recovered pasa_asmbl_31467.p1, internal, 171006, 171139 -recovered pasa_asmbl_31467.p1, internal, 171332, 171456 -recovered pasa_asmbl_31467.p1, internal, 171616, 171829 Valid prediction for GeneMark_model.90145_t Valid prediction for snap_scaffold_23-snap.498-T1 Valid prediction for snap_scaffold_23-snap.509-T1 Valid prediction for Augustus_model.g34871.t1 Valid prediction for GlimmerHMM_glimmerT_51896-T1 Valid prediction for snap_scaffold_23-snap.484-T1 Valid prediction for snap_scaffold_23-snap.497-T1 Valid prediction for snap_scaffold_23-snap.516-T1 Valid prediction for GlimmerHMM_glimmerT_51877-T1 Valid prediction for pasa_asmbl_31469.p1 Valid prediction for Augustus_model.g34866.t1 Valid prediction for CodingQuarry_transcript_35525-T1 Valid prediction for GlimmerHMM_glimmerT_51876-T1 Valid prediction for snap_scaffold_23-snap.505-T1 Valid prediction for GeneMark_model.90128_t Valid prediction for GlimmerHMM_glimmerT_51887-T1 Valid prediction for GlimmerHMM_glimmerT_51897-T1 Valid prediction for HiQ_model.g34863.t1 Valid prediction for snap_scaffold_23-snap.485-T1 Valid prediction for Augustus_model.g34872.t1 Valid prediction for GlimmerHMM_glimmerT_51902-T1 Valid prediction for snap_scaffold_23-snap.510-T1 Valid prediction for Augustus_model.g34881.t1 Couldn't classify 179555, 179744 Sorry, prediction pasa_asmbl_31966.p1 fails validation. (ATG) CA 178516-178650 GT CAG (GAA) AG 178749-178880 GT AGG (GTG) AG 178967-179054 GT GGG (GAC) AG 179159-179378 GT TCG (GTA) AG 179555-179744 AT TAA -recovered pasa_asmbl_31966.p1, initial, 178516, 178650 -recovered pasa_asmbl_31966.p1, internal, 178749, 178880 -recovered pasa_asmbl_31966.p1, internal, 178967, 179054 -recovered pasa_asmbl_31966.p1, internal, 179159, 179378 Couldn't classify 150498, 150684 Sorry, prediction pasa_asmbl_31479.p1 fails validation. (CCG) CT 150498-150684 GT AAG (GCA) AG 150862-151044 GT AGG (ACC) AG 151286-151659 TG GAT -recovered pasa_asmbl_31479.p1, terminal, 151286, 151659 -recovered pasa_asmbl_31479.p1, internal, 150862, 151044 Valid prediction for snap_scaffold_23-snap.515-T1 Valid prediction for GeneMark_model.90156_t Couldn't classify 174843, 174854 Couldn't classify 175769, 176021 Sorry, prediction pasa_asmbl_31466.p1 fails validation. (CCG) AG 174843-174854 GT CAG (GAA) AG 174955-175086 GT AGG (GTA) AG 175172-175259 GT AGG (GCC) AG 175373-175592 GT TCG (GTA) AG 175769-176021 AA GGA -recovered pasa_asmbl_31466.p1, terminal, 175172, 175259 -recovered pasa_asmbl_31466.p1, internal, 174843, 174854 -recovered pasa_asmbl_31466.p1, internal, 174955, 175086 -recovered pasa_asmbl_31466.p1, internal, 175172, 175259 -recovered pasa_asmbl_31466.p1, internal, 175373, 175592 Valid prediction for Augustus_model.g34869.t1 Valid prediction for snap_scaffold_23-snap.492-T1 Valid prediction for GeneMark_model.90162_t -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 181480, rend_intergenic: 181477 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30792, rend_intergenic: 25084 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76420, rend_intergenic: 72809 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145303, rend_intergenic: 142671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 187387 -exon list size: 536 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 3.3 3.5 3.7 3.9 4.1 4.3 4.5 4.6 4.8 5.0 5.2 5.4 5.6 5.8 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.2 7.4 7.6 7.8 8.0 8.2 8.4 8.6 8.7 8.9 9.1 9.3 9.5 9.7 9.9 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.3 11.5 11.7 11.9 12.1 12.3 12.5 12.6 12.8 13.0 13.2 13.4 13.6 13.8 13.9 14.1 14.3 14.5 14.7 14.9 15.1 15.2 15.4 15.6 15.8 16.0 16.2 16.4 16.5 16.7 16.9 17.1 17.3 17.5 17.7 17.8 18.0 18.2 18.4 18.6 18.8 19.0 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.4 20.6 20.8 21.0 21.2 21.4 21.6 21.7 21.9 22.1 22.3 22.5 22.7 22.9 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.3 24.5 24.7 24.9 25.1 25.3 25.5 25.7 25.8 26.0 26.2 26.4 26.6 26.8 27.0 27.1 27.3 27.5 27.7 27.9 28.1 28.3 28.4 28.6 28.8 29.0 29.2 29.4 29.6 29.7 29.9 30.1 30.3 30.5 30.7 30.9 31.0 31.2 31.4 31.6 31.8 32.0 32.2 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.6 33.8 34.0 34.2 34.4 34.6 34.8 34.9 35.1 35.3 35.5 35.7 35.9 36.1 36.2 36.4 36.6 36.8 37.0 37.2 37.4 37.5 37.7 37.9 38.1 38.3 38.5 38.7 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.1 40.3 40.5 40.7 40.9 41.1 41.3 41.4 41.6 41.8 42.0 42.2 42.4 42.6 42.8 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.2 44.4 44.6 44.8 45.0 45.2 45.4 45.5 45.7 45.9 46.1 46.3 46.5 46.7 46.8 47.0 47.2 47.4 47.6 47.8 48.0 48.1 48.3 48.5 48.7 48.9 49.1 49.3 49.4 49.6 49.8 50.0 50.2 50.4 50.6 50.7 50.9 51.1 51.3 51.5 51.7 51.9 52.0 52.2 52.4 52.6 52.8 53.0 53.2 53.3 53.5 53.7 53.9 54.1 54.3 54.5 54.6 54.8 55.0 55.2 55.4 55.6 55.8 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.2 57.4 57.6 57.8 58.0 58.2 58.4 58.6 58.7 58.9 59.1 59.3 59.5 59.7 59.9 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.3 61.5 61.7 61.9 62.1 62.3 62.5 62.6 62.8 63.0 63.2 63.4 63.6 63.8 63.9 64.1 64.3 64.5 64.7 64.9 65.1 65.2 65.4 65.6 65.8 66.0 66.2 66.4 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.8 68.0 68.2 68.4 68.6 68.8 69.0 69.1 69.3 69.5 69.7 69.9 70.1 70.3 70.4 70.6 70.8 71.0 71.2 71.4 71.6 71.7 71.9 72.1 72.3 72.5 72.7 72.9 73.0 73.2 73.4 73.6 73.8 74.0 74.2 74.3 74.5 74.7 74.9 75.1 75.3 75.5 75.7 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.1 77.3 77.5 77.7 77.9 78.1 78.3 78.4 78.6 78.8 79.0 79.2 79.4 79.6 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.0 81.2 81.4 81.6 81.8 82.0 82.2 82.3 82.5 82.7 82.9 83.1 83.3 83.5 83.6 83.8 84.0 84.2 84.4 84.6 84.8 84.9 85.1 85.3 85.5 85.7 85.9 86.1 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.5 87.7 87.9 88.1 88.3 88.5 88.7 88.8 89.0 89.2 89.4 89.6 89.8 90.0 90.1 90.3 90.5 90.7 90.9 91.1 91.3 91.4 91.6 91.8 92.0 92.2 92.4 92.6 92.8 92.9 93.1 93.3 93.5 93.7 93.9 94.1 94.2 94.4 94.6 94.8 95.0 95.2 95.4 95.5 95.7 95.9 96.1 96.3 96.5 96.7 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 32 predictions from path traversal Error with prediction: GlimmerHMM lend_intergenic: 181480, rend_intergenic: 181477 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30792, rend_intergenic: 25084 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76420, rend_intergenic: 72809 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145303, rend_intergenic: 142671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 29 predictions persist after filtering for low support