-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_16183114-16382467 -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_16235-T1 Valid prediction for Augustus_model.g10891.t1 Valid prediction for GlimmerHMM_glimmerT_16253-T1 Valid prediction for snap_scaffold_6-snap.3444-T1 Valid prediction for snap_scaffold_6-snap.3458-T1 Valid prediction for snap_scaffold_6-snap.3462-T1 Valid prediction for GlimmerHMM_glimmerT_16245-T1 Valid prediction for GlimmerHMM_glimmerT_16242-T1 Valid prediction for GlimmerHMM_glimmerT_16250-T1 Valid prediction for snap_scaffold_6-snap.3440-T1 Valid prediction for GlimmerHMM_glimmerT_16234-T1 Valid prediction for snap_scaffold_6-snap.3429-T1 Valid prediction for snap_scaffold_6-snap.3449-T1 Couldn't classify 161195, 161373 Sorry, prediction pasa_asmbl_47693.p1 fails validation. (GCT) CA 161195-161373 GT AGG (CTG) AG 162726-162819 GT AGG (GAG) AG 163084-163216 GT CGG (CAC) AG 163676-163752 AT AGA -recovered pasa_asmbl_47693.p1, terminal, 163676, 163752 -recovered pasa_asmbl_47693.p1, internal, 162726, 162819 -recovered pasa_asmbl_47693.p1, internal, 163084, 163216 Valid prediction for snap_scaffold_6-snap.3461-T1 Valid prediction for GlimmerHMM_glimmerT_16228-T1 Valid prediction for GlimmerHMM_glimmerT_16248-T1 Valid prediction for snap_scaffold_6-snap.3427-T1 Valid prediction for snap_scaffold_6-snap.3452-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for Augustus_model.g10892.t1 Valid prediction for CodingQuarry_transcript_55372-T1 Valid prediction for Augustus_model.g10895.t1 Valid prediction for snap_scaffold_6-snap.3436-T1 Couldn't classify 105234, 105347 Sorry, prediction pasa_asmbl_47691.p2 fails validation. (GAT) GA 105234-105347 GT CGG (CCT) AG 105825-106026 GT AGG (GGG) AG 106110-106216 AC GAA -recovered pasa_asmbl_47691.p2, terminal, 106110, 106216 -recovered pasa_asmbl_47691.p2, internal, 105825, 106026 Valid prediction for snap_scaffold_6-snap.3445-T1 Valid prediction for Augustus_model.g10890.t1 Valid prediction for GlimmerHMM_glimmerT_16239-T1 Valid prediction for GlimmerHMM_glimmerT_16240-T1 Valid prediction for snap_scaffold_6-snap.3464-T1 Valid prediction for GlimmerHMM_glimmerT_16229-T1 Valid prediction for snap_scaffold_6-snap.3425-T1 Valid prediction for GlimmerHMM_glimmerT_16257-T1 Valid prediction for GlimmerHMM_glimmerT_16255-T1 Valid prediction for snap_scaffold_6-snap.3433-T1 Valid prediction for GlimmerHMM_glimmerT_16251-T1 Valid prediction for snap_scaffold_6-snap.3422-T1 Valid prediction for snap_scaffold_6-snap.3450-T1 Valid prediction for Augustus_model.g10898.t1 Valid prediction for snap_scaffold_6-snap.3456-T1 Valid prediction for snap_scaffold_6-snap.3424-T1 Valid prediction for snap_scaffold_6-snap.3451-T1 Valid prediction for snap_scaffold_6-snap.3460-T1 Valid prediction for snap_scaffold_6-snap.3437-T1 Couldn't classify 82487, 82555 Couldn't classify 86351, 86411 Sorry, prediction pasa_asmbl_47689.p1 fails validation. (TAT) CC 82487-82555 GT AGG (GTG) AG 82918-83100 GT CCG (GAG) AG 83652-83807 GT CTG (ATC) AG 83926-83980 GT AGG (GCT) AG 84094-84143 GT AGG (TAC) AG 84572-84724 GT AGG (GCT) AG 84960-85030 GT AGG (GTT) AG 85202-85250 GT GAG (GCG) AG 85404-85489 GT AAG (TGA) AG 85755-85877 GT AGG (AGT) AG 86351-86411 GT AGG -recovered pasa_asmbl_47689.p1, internal, 82918, 83100 -recovered pasa_asmbl_47689.p1, internal, 83652, 83807 -recovered pasa_asmbl_47689.p1, internal, 83926, 83980 -recovered pasa_asmbl_47689.p1, internal, 84094, 84143 -recovered pasa_asmbl_47689.p1, internal, 84572, 84724 -recovered pasa_asmbl_47689.p1, internal, 84960, 85030 -recovered pasa_asmbl_47689.p1, internal, 85202, 85250 -recovered pasa_asmbl_47689.p1, internal, 85404, 85489 -recovered pasa_asmbl_47689.p1, internal, 85755, 85877 -recovered pasa_asmbl_47689.p1, internal, 86351, 86411 -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_6-snap.3465-T1 Valid prediction for GlimmerHMM_glimmerT_16243-T1 Valid prediction for snap_scaffold_6-snap.3443-T1 Valid prediction for snap_scaffold_6-snap.3431-T1 Valid prediction for Augustus_model.g10896.t1 Valid prediction for snap_scaffold_6-snap.3432-T1 Valid prediction for snap_scaffold_6-snap.3455-T1 Valid prediction for snap_scaffold_6-snap.3454-T1 Valid prediction for snap_scaffold_6-snap.3439-T1 Couldn't classify 63096, 63192 Couldn't classify 64148, 64183 Sorry, prediction pasa_asmbl_49332.p2 fails validation. (GCA) CT 63096-63192 GT CGG (TGA) AG 63390-63534 GT AGG (CCA) AG 63757-63895 GT AGG (GAC) AG 64148-64183 GA AGG -recovered pasa_asmbl_49332.p2, internal, 63390, 63534 -recovered pasa_asmbl_49332.p2, internal, 63757, 63895 Valid prediction for GlimmerHMM_glimmerT_16256-T1 Valid prediction for GlimmerHMM_glimmerT_16247-T1 Valid prediction for GlimmerHMM_glimmerT_16249-T1 Valid prediction for snap_scaffold_6-snap.3442-T1 Valid prediction for Augustus_model.g10893.t1 Valid prediction for GlimmerHMM_glimmerT_16241-T1 Valid prediction for Augustus_model.g10897.t1 Valid prediction for GlimmerHMM_glimmerT_16231-T1 Couldn't classify 68675, 68725 Couldn't classify 70839, 70858 Sorry, prediction pasa_asmbl_49120.p1 fails validation. (GAA) AG 68675-68725 GT AGG (GCC) AG 68806-68944 GT AGG (GGA) AG 69086-69195 GT AGG (GTG) AG 69290-69508 GT AGG (GTG) AG 69800-69993 GT CGG (TTA) AG 70346-70518 GT GGG (GCC) AG 70839-70858 GC CAG -recovered pasa_asmbl_49120.p1, internal, 68675, 68725 -recovered pasa_asmbl_49120.p1, internal, 68806, 68944 -recovered pasa_asmbl_49120.p1, internal, 69086, 69195 -recovered pasa_asmbl_49120.p1, internal, 69290, 69508 -recovered pasa_asmbl_49120.p1, internal, 69800, 69993 -recovered pasa_asmbl_49120.p1, internal, 70346, 70518 -recovered pasa_asmbl_49120.p1, internal, 70839, 70858 Valid prediction for GlimmerHMM_glimmerT_16233-T1 Valid prediction for GlimmerHMM_glimmerT_16258-T1 Valid prediction for snap_scaffold_6-snap.3463-T1 Couldn't classify 81050, 81143 Sorry, prediction pasa_asmbl_49117.p1 fails validation. (AAC) AC 81050-81143 GT GGG (CTG) AG 81514-81693 GT AGG (CTG) AG 81808-81914 GT AGG (GTG) AG 82098-82175 AC GAA -recovered pasa_asmbl_49117.p1, terminal, 82098, 82175 -recovered pasa_asmbl_49117.p1, internal, 81514, 81693 -recovered pasa_asmbl_49117.p1, internal, 81808, 81914 Valid prediction for GlimmerHMM_glimmerT_16237-T1 Valid prediction for snap_scaffold_6-snap.3430-T1 Valid prediction for snap_scaffold_6-snap.3446-T1 Valid prediction for GlimmerHMM_glimmerT_16232-T1 Valid prediction for snap_scaffold_6-snap.3434-T1 Valid prediction for Augustus_model.g10900.t1 Valid prediction for snap_scaffold_6-snap.3441-T1 Valid prediction for GlimmerHMM_glimmerT_16254-T1 Couldn't classify 80261, 80443 Couldn't classify 80577, 80804 Sorry, prediction pasa_asmbl_49118.p1 fails validation. (CAG) TC 80261-80443 GT TGG (AGC) AG 80577-80804 GT AGG -recovered pasa_asmbl_49118.p1, internal, 80577, 80804 Valid prediction for snap_scaffold_6-snap.3426-T1 Valid prediction for snap_scaffold_6-snap.3459-T1 Valid prediction for snap_scaffold_6-snap.3428-T1 Valid prediction for GlimmerHMM_glimmerT_16238-T1 Valid prediction for snap_scaffold_6-snap.3438-T1 Couldn't classify 76641, 76913 Couldn't classify 79659, 79730 Sorry, prediction pasa_asmbl_49119.p1 fails validation. (GGC) CA 76641-76913 GT AGG (GTG) AG 77253-77462 GT AGG (TGG) AG 77656-77787 GT AGG (GAG) AG 79659-79730 GC TGG -recovered pasa_asmbl_49119.p1, internal, 77253, 77462 -recovered pasa_asmbl_49119.p1, internal, 77656, 77787 -recovered pasa_asmbl_49119.p1, internal, 79659, 79730 Valid prediction for snap_scaffold_6-snap.3448-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_6-snap.3435-T1 Valid prediction for GlimmerHMM_glimmerT_16244-T1 Valid prediction for GlimmerHMM_glimmerT_16236-T1 Couldn't classify 3545, 3904 Sorry, prediction pasa_asmbl_49124.p3 fails validation. (CCG) CC 3545-3904 CT GAC Valid prediction for snap_scaffold_6-snap.3457-T1 Valid prediction for snap_scaffold_6-snap.3453-T1 Valid prediction for Augustus_model.g10899.t1 Valid prediction for Augustus_model.g10894.t1 Valid prediction for GlimmerHMM_glimmerT_16252-T1 Couldn't classify 722, 1102 Sorry, prediction pasa_asmbl_49127.p1 fails validation. (ATG) GC 722-1102 CA CAC Couldn't classify 99896, 100053 Couldn't classify 102961, 103105 Sorry, prediction pasa_asmbl_49108.p1 fails validation. (GAG) AG 99896-100053 GT AGG (GGT) AG 100226-100409 GT AGG (GTG) AG 100658-100822 GT TGG (GTG) AG 100933-101056 GT GGG (AAA) AG 101286-101400 GT AGG (GAT) AG 102961-103105 GT CGG -recovered pasa_asmbl_49108.p1, internal, 99896, 100053 -recovered pasa_asmbl_49108.p1, internal, 100226, 100409 -recovered pasa_asmbl_49108.p1, internal, 100658, 100822 -recovered pasa_asmbl_49108.p1, internal, 100933, 101056 -recovered pasa_asmbl_49108.p1, internal, 101286, 101400 -recovered pasa_asmbl_49108.p1, internal, 102961, 103105 Valid prediction for HiQ_model.g10901.t1 Valid prediction for snap_scaffold_6-snap.3447-T1 Valid prediction for GlimmerHMM_glimmerT_16246-T1 Couldn't classify 65982, 66118 Couldn't classify 67115, 67337 Sorry, prediction pasa_asmbl_49376.p1 fails validation. (GAG) GG 65982-66118 GT AAG (GGA) AG 67115-67337 GT AGG -recovered pasa_asmbl_49376.p1, internal, 67115, 67337 Valid prediction for pasa_asmbl_49110.p1 Valid prediction for CodingQuarry_transcript_55373-T1 Valid prediction for snap_scaffold_6-snap.3423-T1 Sorry, intron length (3) is less than minimum required (10) Couldn't classify 2759, 3517 Sorry, prediction pasa_asmbl_49125.p1 fails validation. (AAG) TG 2759-3517 TG CCT Valid prediction for GlimmerHMM_glimmerT_16230-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7161, rend_intergenic: 6948 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27543, rend_intergenic: 25222 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36348, rend_intergenic: 33797 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 60994, rend_intergenic: 54136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64382, rend_intergenic: 61833 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87773, rend_intergenic: 76678 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99472, rend_intergenic: 89856 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 112156, rend_intergenic: 107921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 151501, rend_intergenic: 120799 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 164409, rend_intergenic: 159535 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 167005, rend_intergenic: 164816 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 181311, rend_intergenic: 173202 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192107, rend_intergenic: 182881 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 194468, rend_intergenic: 192826 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197176, rend_intergenic: 195451 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 109872, rend_intergenic: 109869 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 199354 -exon list size: 490 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.3 3.5 3.7 3.9 4.1 4.3 4.5 4.7 4.9 5.1 5.3 5.5 5.7 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.5 7.7 7.9 8.1 8.3 8.5 8.7 8.9 9.1 9.3 9.6 9.8 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.6 11.8 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.7 15.9 16.1 16.3 16.5 16.7 16.9 17.1 17.3 17.5 17.7 17.9 18.1 18.3 18.5 18.7 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.1 21.3 21.5 21.7 22.0 22.2 22.4 22.6 22.8 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.0 25.2 25.4 25.6 25.8 26.0 26.2 26.4 26.6 26.8 27.0 27.2 27.4 27.6 27.8 28.0 28.3 28.5 28.7 28.9 29.1 29.3 29.5 29.7 29.9 30.1 30.3 30.5 30.7 30.9 31.1 31.3 31.5 31.7 31.9 32.1 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.6 34.8 35.0 35.2 35.4 35.6 35.8 36.0 36.2 36.4 36.6 36.8 37.0 37.2 37.4 37.6 37.8 38.0 38.2 38.4 38.6 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.2 40.4 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.1 42.3 42.5 42.7 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.5 45.7 45.9 46.1 46.3 46.5 46.7 47.0 47.2 47.4 47.6 47.8 48.0 48.2 48.4 48.6 48.8 49.0 49.2 49.4 49.6 49.8 50.0 50.2 50.4 50.6 50.8 51.0 51.2 51.4 51.6 51.8 52.0 52.2 52.4 52.6 52.8 53.0 53.3 53.5 53.7 53.9 54.1 54.3 54.5 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.3 57.5 57.7 57.9 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.6 59.8 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.4 61.6 61.8 62.0 62.2 62.4 62.6 62.8 63.0 63.2 63.4 63.6 63.8 64.0 64.2 64.4 64.6 64.8 65.0 65.2 65.4 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.9 68.1 68.3 68.5 68.7 68.9 69.1 69.3 69.5 69.7 69.9 70.1 70.3 70.5 70.7 70.9 71.1 71.3 71.5 71.7 72.0 72.2 72.4 72.6 72.8 73.0 73.2 73.4 73.6 73.8 74.0 74.2 74.4 74.6 74.8 75.0 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.2 77.4 77.6 77.8 78.0 78.3 78.5 78.7 78.9 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.3 81.5 81.7 81.9 82.1 82.3 82.5 82.7 82.9 83.1 83.3 83.5 83.7 83.9 84.1 84.3 84.6 84.8 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.6 87.8 88.0 88.2 88.4 88.6 88.8 89.0 89.2 89.4 89.6 89.8 90.0 90.2 90.4 90.7 90.9 91.1 91.3 91.5 91.7 91.9 92.1 92.3 92.5 92.7 92.9 93.1 93.3 93.5 93.7 93.9 94.1 94.3 94.5 94.7 94.9 95.1 95.3 95.5 95.7 95.9 96.1 96.3 96.5 96.7 97.0 97.2 97.4 97.6 97.8 98.0 98.2 98.4 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 30 predictions from path traversal Error with prediction: snap lend_intergenic: 7161, rend_intergenic: 6948 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27543, rend_intergenic: 25222 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36348, rend_intergenic: 33797 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 60994, rend_intergenic: 54136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64382, rend_intergenic: 61833 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87773, rend_intergenic: 76678 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99472, rend_intergenic: 89856 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 112156, rend_intergenic: 107921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 151501, rend_intergenic: 120799 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 164409, rend_intergenic: 159535 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 167005, rend_intergenic: 164816 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 181311, rend_intergenic: 173202 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192107, rend_intergenic: 182881 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 194468, rend_intergenic: 192826 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197176, rend_intergenic: 195451 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 109872, rend_intergenic: 109869 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 20 predictions persist after filtering for low support