-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_1-215286 -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_18-snap.31-T1 Couldn't classify 139282, 139408 Sorry, prediction pasa_asmbl_20257.p1 fails validation. (AGA) AG 139282-139408 GT GGG (AAA) AG 139849-140023 GT AGG (AGA) AG 140512-140695 CC AAC -recovered pasa_asmbl_20257.p1, terminal, 140512, 140695 -recovered pasa_asmbl_20257.p1, internal, 139282, 139408 -recovered pasa_asmbl_20257.p1, internal, 139849, 140023 Valid prediction for snap_scaffold_18-snap.28-T1 Valid prediction for Augustus_model.g27669.t1 Valid prediction for snap_scaffold_18-snap.35-T1 Couldn't classify 166387, 166471 Sorry, prediction pasa_asmbl_20265.p1 fails validation. (ATG) AT 164123-164206 GT AGG (TCT) AG 164706-164787 GT AGG (CTG) AG 164963-165119 GT CGG (GGC) AG 165381-165539 GT GAG (GTA) AG 165708-165864 GT AGG (TAC) AG 166002-166091 GT CAG (GAG) AG 166188-166282 GT AGG (GTA) AG 166387-166471 GT AGG -recovered pasa_asmbl_20265.p1, initial, 164123, 164206 add_exon() Sorry, pasa_asmbl_20265.p1 165381-165539-terminal-1 is invalid. -recovered pasa_asmbl_20265.p1, terminal, 165381, 165539 -recovered pasa_asmbl_20265.p1, internal, 164706, 164787 -recovered pasa_asmbl_20265.p1, internal, 164963, 165119 -recovered pasa_asmbl_20265.p1, internal, 165381, 165539 -recovered pasa_asmbl_20265.p1, internal, 165708, 165864 -recovered pasa_asmbl_20265.p1, internal, 166002, 166091 -recovered pasa_asmbl_20265.p1, internal, 166188, 166282 -recovered pasa_asmbl_20265.p1, internal, 166387, 166471 Valid prediction for snap_scaffold_18-snap.40-T1 Valid prediction for snap_scaffold_18-snap.42-T1 Valid prediction for snap_scaffold_18-snap.41-T1 Valid prediction for snap_scaffold_18-snap.5-T1 Valid prediction for snap_scaffold_18-snap.22-T1 Couldn't classify 77796, 77947 Couldn't classify 80064, 80204 Sorry, prediction pasa_asmbl_20254.p1 fails validation. (GTG) AG 77796-77947 GT AGG (ACC) AG 79256-79334 GT AGG (GTA) AG 79493-79561 GT AGG (AGA) AG 80064-80204 GA GTG -recovered pasa_asmbl_20254.p1, internal, 77796, 77947 -recovered pasa_asmbl_20254.p1, internal, 79256, 79334 -recovered pasa_asmbl_20254.p1, internal, 79493, 79561 Valid prediction for GlimmerHMM_glimmerT_41597-T1 Valid prediction for Augustus_model.g27683.t1 Valid prediction for snap_scaffold_18-snap.14-T1 Valid prediction for GlimmerHMM_glimmerT_41599-T1 Valid prediction for snap_scaffold_18-snap.32-T1 Valid prediction for Augustus_model.g27687.t1 Valid prediction for snap_scaffold_18-snap.23-T1 Valid prediction for Augustus_model.g27684.t1 Valid prediction for snap_scaffold_18-snap.15-T1 Valid prediction for Augustus_model.g27665.t1 Valid prediction for GlimmerHMM_glimmerT_41623-T1 Couldn't classify 198932, 199021 Sorry, prediction pasa_asmbl_20273.p1 fails validation. (CCT) CC 198932-199021 GT ATG (TGC) AG 199742-199857 GT AGG (AAA) AG 199954-200088 GT AGG (CAA) AG 200252-200357 GT AAG (AAA) AG 200482-200542 GT GGG (TGA) AG 201705-201850 GT AGG (ATG) AG 202337-202414 GT GGG (ATC) AG 202872-203097 GT TGG (AGT) AG 204304-204473 GT AAG (TGT) AG 205654-205751 GT CCG (GTG) AG 206199-206329 GT GGG (TAA) AG 206527-206732 GT ACG (GCA) AG 206831-207036 GT AGG (GTA) AG 207248-207353 GT AGG (CAC) AG 207632-207835 CT GAC -recovered pasa_asmbl_20273.p1, initial, 202337, 202414 add_exon() Sorry, pasa_asmbl_20273.p1 199742-199857-terminal-2 is invalid. -recovered pasa_asmbl_20273.p1, terminal, 199742, 199857 -recovered pasa_asmbl_20273.p1, terminal, 207632, 207835 -recovered pasa_asmbl_20273.p1, internal, 199742, 199857 -recovered pasa_asmbl_20273.p1, internal, 199954, 200088 -recovered pasa_asmbl_20273.p1, internal, 200252, 200357 -recovered pasa_asmbl_20273.p1, internal, 200482, 200542 -recovered pasa_asmbl_20273.p1, internal, 201705, 201850 -recovered pasa_asmbl_20273.p1, internal, 202337, 202414 -recovered pasa_asmbl_20273.p1, internal, 202872, 203097 -recovered pasa_asmbl_20273.p1, internal, 204304, 204473 -recovered pasa_asmbl_20273.p1, internal, 205654, 205751 -recovered pasa_asmbl_20273.p1, internal, 206199, 206329 -recovered pasa_asmbl_20273.p1, internal, 206527, 206732 -recovered pasa_asmbl_20273.p1, internal, 206831, 207036 -recovered pasa_asmbl_20273.p1, internal, 207248, 207353 Valid prediction for snap_scaffold_18-snap.18-T1 Couldn't classify 70295, 70491 Couldn't classify 70705, 70816 Sorry, prediction pasa_asmbl_21130.p1 fails validation. (AGG) AC 70295-70491 GT AGG (GGG) AG 70705-70816 GT AGG -recovered pasa_asmbl_21130.p1, internal, 70705, 70816 Valid prediction for GlimmerHMM_glimmerT_41610-T1 Couldn't classify 133782, 133854 Couldn't classify 135822, 135910 Sorry, prediction pasa_asmbl_20256.p1 fails validation. (CAG) AG 133782-133854 GT CAG (TGA) AG 134008-134153 GT ACG (TGT) AG 135249-135367 GT AAG (GTT) AG 135541-135728 GT CAG (AGC) AG 135822-135910 GT GTG -recovered pasa_asmbl_20256.p1, internal, 133782, 133854 -recovered pasa_asmbl_20256.p1, internal, 134008, 134153 -recovered pasa_asmbl_20256.p1, internal, 135249, 135367 -recovered pasa_asmbl_20256.p1, internal, 135541, 135728 -recovered pasa_asmbl_20256.p1, internal, 135822, 135910 Valid prediction for GlimmerHMM_glimmerT_41600-T1 Valid prediction for snap_scaffold_18-snap.7-T1 Couldn't classify 63302, 63409 Couldn't classify 66435, 66528 Sorry, prediction pasa_asmbl_20252.p1 fails validation. (TCT) CA 63302-63409 GT GGG (TCA) AG 63761-63920 GT AGG (ATG) AG 65928-66061 GT AGG (ACT) AG 66259-66335 GT AAG (GGT) AG 66435-66528 TT GGT add_exon() Sorry, pasa_asmbl_20252.p1 65928-66061-initial-1 is invalid. -recovered pasa_asmbl_20252.p1, initial, 65928, 66061 add_exon() Sorry, pasa_asmbl_20252.p1 66259-66335-terminal-2 is invalid. -recovered pasa_asmbl_20252.p1, terminal, 66259, 66335 -recovered pasa_asmbl_20252.p1, internal, 63761, 63920 -recovered pasa_asmbl_20252.p1, internal, 65928, 66061 -recovered pasa_asmbl_20252.p1, internal, 66259, 66335 Valid prediction for snap_scaffold_18-snap.25-T1 Valid prediction for snap_scaffold_18-snap.16-T1 Valid prediction for snap_scaffold_18-snap.27-T1 Valid prediction for Augustus_model.g27675.t1 Valid prediction for GlimmerHMM_glimmerT_41602-T1 Valid prediction for Augustus_model.g27663.t1 Valid prediction for GlimmerHMM_glimmerT_41620-T1 Valid prediction for snap_scaffold_18-snap.36-T1 Valid prediction for GlimmerHMM_glimmerT_41590-T1 Valid prediction for Augustus_model.g27690.t1 Valid prediction for GlimmerHMM_glimmerT_41619-T1 Valid prediction for GlimmerHMM_glimmerT_41617-T1 Valid prediction for GlimmerHMM_glimmerT_41624-T1 Valid prediction for Augustus_model.g27670.t1 Valid prediction for Augustus_model.g27673.t1 Valid prediction for GlimmerHMM_glimmerT_41594-T1 Valid prediction for Augustus_model.g27691.t1 Couldn't classify 59721, 59879 Sorry, prediction pasa_asmbl_20251.p1 fails validation. (ATG) AG 59241-59402 GT AGG (GTG) AG 59721-59879 AG CCA -recovered pasa_asmbl_20251.p1, initial, 59241, 59402 -recovered pasa_asmbl_20251.p1, internal, 59241, 59402 Valid prediction for snap_scaffold_18-snap.19-T1 Valid prediction for snap_scaffold_18-snap.37-T1 Valid prediction for GlimmerHMM_glimmerT_41615-T1 Valid prediction for snap_scaffold_18-snap.38-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for snap_scaffold_18-snap.11-T1 Couldn't classify 154610, 154630 Couldn't classify 155449, 155511 Sorry, prediction pasa_asmbl_20261.p1 fails validation. (GTC) AG 154610-154630 GT ACG (TGT) AG 154739-154843 GT ATG (GAA) AG 154958-155056 GT CGG (ACA) AG 155142-155273 GT CTG (ATA) AG 155449-155511 GT GTG -recovered pasa_asmbl_20261.p1, internal, 154610, 154630 -recovered pasa_asmbl_20261.p1, internal, 154739, 154843 -recovered pasa_asmbl_20261.p1, internal, 154958, 155056 -recovered pasa_asmbl_20261.p1, internal, 155142, 155273 -recovered pasa_asmbl_20261.p1, internal, 155449, 155511 Valid prediction for snap_scaffold_18-snap.34-T1 Valid prediction for snap_scaffold_18-snap.33-T1 Valid prediction for snap_scaffold_18-snap.10-T1 Couldn't classify 170623, 170649 Sorry, prediction pasa_asmbl_20267.p1 fails validation. (TGG) CC 170623-170649 GT AGG (ACC) AG 170733-170832 GT CAG (ACT) AG 171014-171090 GT AGG (GTT) AG 171493-171609 GT AGG (AAG) AG 171728-171817 GT GGG (TCA) AG 172375-172540 GT AGG (CTA) AG 172712-172872 GT TGG (GCT) AG 173519-173644 GT AGG (ATT) AG 173745-173811 GT AGG (AGT) AG 174123-174248 GT AGG (ACA) AG 176781-176878 GT AGG (GTG) AG 178204-178299 GT AGG (GTC) AG 179038-179262 GG GAG add_exon() Sorry, pasa_asmbl_20267.p1 173745-173811-terminal-3 is invalid. -recovered pasa_asmbl_20267.p1, terminal, 173745, 173811 -recovered pasa_asmbl_20267.p1, terminal, 179038, 179262 -recovered pasa_asmbl_20267.p1, internal, 170733, 170832 -recovered pasa_asmbl_20267.p1, internal, 171014, 171090 -recovered pasa_asmbl_20267.p1, internal, 171493, 171609 -recovered pasa_asmbl_20267.p1, internal, 171728, 171817 -recovered pasa_asmbl_20267.p1, internal, 172375, 172540 -recovered pasa_asmbl_20267.p1, internal, 172712, 172872 -recovered pasa_asmbl_20267.p1, internal, 173519, 173644 -recovered pasa_asmbl_20267.p1, internal, 173745, 173811 -recovered pasa_asmbl_20267.p1, internal, 174123, 174248 -recovered pasa_asmbl_20267.p1, internal, 176781, 176878 -recovered pasa_asmbl_20267.p1, internal, 178204, 178299 Valid prediction for GlimmerHMM_glimmerT_41608-T1 Valid prediction for Augustus_model.g27682.t1 Valid prediction for GlimmerHMM_glimmerT_41605-T1 Valid prediction for GlimmerHMM_glimmerT_41613-T1 Valid prediction for snap_scaffold_18-snap.26-T1 Valid prediction for Augustus_model.g27680.t1 Valid prediction for snap_scaffold_18-snap.13-T1 Valid prediction for GlimmerHMM_glimmerT_41596-T1 Valid prediction for Augustus_model.g27661.t1 Valid prediction for Augustus_model.g27666.t1 Valid prediction for CodingQuarry_transcript_23633-T1 Valid prediction for snap_scaffold_18-snap.9-T1 Couldn't classify 151261, 151295 Couldn't classify 152254, 152313 Sorry, prediction pasa_asmbl_21103.p1 fails validation. (AAT) AA 151261-151295 GT GGG (GAA) AG 151736-151982 GT AGG (ATT) AG 152114-152176 GT TTG (GAA) AG 152254-152313 AA ATA -recovered pasa_asmbl_21103.p1, internal, 151736, 151982 -recovered pasa_asmbl_21103.p1, internal, 152114, 152176 Valid prediction for snap_scaffold_18-snap.29-T1 Valid prediction for snap_scaffold_18-snap.6-T1 Valid prediction for Augustus_model.g27686.t1 Couldn't classify 148111, 148259 Couldn't classify 148455, 148650 Sorry, prediction pasa_asmbl_21107.p1 fails validation. (TCC) AC 148111-148259 GT AGG (ACG) AG 148455-148650 AA GGA Valid prediction for snap_scaffold_18-snap.3-T1 Couldn't classify 155907, 156176 Sorry, prediction pasa_asmbl_20264.p1 fails validation. (TCT) CT 155907-156176 GT GGG (GAC) AG 156314-156380 GT CGG (GCT) AG 156622-157181 GC GAG -recovered pasa_asmbl_20264.p1, terminal, 156622, 157181 -recovered pasa_asmbl_20264.p1, internal, 156314, 156380 -recovered pasa_asmbl_20264.p1, internal, 156622, 157181 Valid prediction for GlimmerHMM_glimmerT_41595-T1 Valid prediction for Augustus_model.g27688.t1 Valid prediction for GlimmerHMM_glimmerT_41618-T1 Valid prediction for snap_scaffold_18-snap.8-T1 Valid prediction for GlimmerHMM_glimmerT_41593-T1 Valid prediction for Augustus_model.g27664.t1 Valid prediction for Augustus_model.g27671.t1 Valid prediction for Augustus_model.g27667.t1 Valid prediction for Augustus_model.g27668.t1 Valid prediction for snap_scaffold_18-snap.4-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 snap_scaffold_18-snap.12-T1 Valid prediction for snap_scaffold_18-snap.20-T1 Valid prediction for snap_scaffold_18-snap.21-T1 Valid prediction for GlimmerHMM_glimmerT_41622-T1 Valid prediction for GlimmerHMM_glimmerT_41604-T1 Valid prediction for snap_scaffold_18-snap.30-T1 Valid prediction for GlimmerHMM_glimmerT_41601-T1 Valid prediction for snap_scaffold_18-snap.39-T1 Valid prediction for GlimmerHMM_glimmerT_41603-T1 Valid prediction for Augustus_model.g27681.t1 Valid prediction for Augustus_model.g27677.t1 Valid prediction for GlimmerHMM_glimmerT_41589-T1 Valid prediction for GlimmerHMM_glimmerT_41621-T1 Valid prediction for Augustus_model.g27685.t1 Valid prediction for snap_scaffold_18-snap.17-T1 Valid prediction for GlimmerHMM_glimmerT_41592-T1 Valid prediction for Augustus_model.g27678.t1 Valid prediction for GlimmerHMM_glimmerT_41591-T1 Valid prediction for Augustus_model.g27660.t1 Valid prediction for snap_scaffold_18-snap.24-T1 Valid prediction for GlimmerHMM_glimmerT_41611-T1 Valid prediction for Augustus_model.g27662.t1 Valid prediction for Augustus_model.g27672.t1 Valid prediction for snap_scaffold_18-snap.2-T1 Valid prediction for GlimmerHMM_glimmerT_41609-T1 Valid prediction for GlimmerHMM_glimmerT_41598-T1 Valid prediction for snap_scaffold_18-snap.1-T1 Valid prediction for GlimmerHMM_glimmerT_41612-T1 Valid prediction for Augustus_model.g27674.t1 Valid prediction for Augustus_model.g27689.t1 Valid prediction for GlimmerHMM_glimmerT_41607-T1 Valid prediction for GlimmerHMM_glimmerT_41616-T1 Valid prediction for Augustus_model.g27676.t1 Valid prediction for GlimmerHMM_glimmerT_41606-T1 Valid prediction for Augustus_model.g27679.t1 Valid prediction for GlimmerHMM_glimmerT_41614-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 84456, rend_intergenic: 82483 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 215286 -exon list size: 410 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 1.9 2.2 2.4 2.7 2.9 3.2 3.4 3.6 3.9 4.1 4.4 4.6 4.9 5.1 5.3 5.6 5.8 6.1 6.3 6.6 6.8 7.0 7.3 7.5 7.8 8.0 8.3 8.5 8.7 9.0 9.2 9.5 9.7 10.0 10.2 10.4 10.7 10.9 11.2 11.4 11.7 11.9 12.1 12.4 12.6 12.9 13.1 13.3 13.6 13.8 14.1 14.3 14.6 14.8 15.0 15.3 15.5 15.8 16.0 16.3 16.5 16.7 17.0 17.2 17.5 17.7 18.0 18.2 18.4 18.7 18.9 19.2 19.4 19.7 19.9 20.1 20.4 20.6 20.9 21.1 21.4 21.6 21.8 22.1 22.3 22.6 22.8 23.1 23.3 23.5 23.8 24.0 24.3 24.5 24.8 25.0 25.2 25.5 25.7 26.0 26.2 26.5 26.7 26.9 27.2 27.4 27.7 27.9 28.2 28.4 28.6 28.9 29.1 29.4 29.6 29.9 30.1 30.3 30.6 30.8 31.1 31.3 31.6 31.8 32.0 32.3 32.5 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.5 34.7 35.0 35.2 35.4 35.7 35.9 36.2 36.4 36.7 36.9 37.1 37.4 37.6 37.9 38.1 38.3 38.6 38.8 39.1 39.3 39.6 39.8 40.0 40.3 40.5 40.8 41.0 41.3 41.5 41.7 42.0 42.2 42.5 42.7 43.0 43.2 43.4 43.7 43.9 44.2 44.4 44.7 44.9 45.1 45.4 45.6 45.9 46.1 46.4 46.6 46.8 47.1 47.3 47.6 47.8 48.1 48.3 48.5 48.8 49.0 49.3 49.5 49.8 50.0 50.2 50.5 50.7 51.0 51.2 51.5 51.7 51.9 52.2 52.4 52.7 52.9 53.2 53.4 53.6 53.9 54.1 54.4 54.6 54.9 55.1 55.3 55.6 55.8 56.1 56.3 56.6 56.8 57.0 57.3 57.5 57.8 58.0 58.3 58.5 58.7 59.0 59.2 59.5 59.7 60.0 60.2 60.4 60.7 60.9 61.2 61.4 61.7 61.9 62.1 62.4 62.6 62.9 63.1 63.3 63.6 63.8 64.1 64.3 64.6 64.8 65.0 65.3 65.5 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.5 67.7 68.0 68.2 68.4 68.7 68.9 69.2 69.4 69.7 69.9 70.1 70.4 70.6 70.9 71.1 71.4 71.6 71.8 72.1 72.3 72.6 72.8 73.1 73.3 73.5 73.8 74.0 74.3 74.5 74.8 75.0 75.2 75.5 75.7 76.0 76.2 76.5 76.7 76.9 77.2 77.4 77.7 77.9 78.2 78.4 78.6 78.9 79.1 79.4 79.6 79.9 80.1 80.3 80.6 80.8 81.1 81.3 81.6 81.8 82.0 82.3 82.5 82.8 83.0 83.3 83.5 83.7 84.0 84.2 84.5 84.7 85.0 85.2 85.4 85.7 85.9 86.2 86.4 86.7 86.9 87.1 87.4 87.6 87.9 88.1 88.3 88.6 88.8 89.1 89.3 89.6 89.8 90.0 90.3 90.5 90.8 91.0 91.3 91.5 91.7 92.0 92.2 92.5 92.7 93.0 93.2 93.4 93.7 93.9 94.2 94.4 94.7 94.9 95.1 95.4 95.6 95.9 96.1 96.4 96.6 96.8 97.1 97.3 97.6 97.8 98.1 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 51 predictions from path traversal Error with prediction: snap lend_intergenic: 84456, rend_intergenic: 82483 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 47 predictions persist after filtering for low support