-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_18260228-18468104 -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_3-snap.3580-T1 Valid prediction for snap_scaffold_3-snap.3607-T1 Valid prediction for snap_scaffold_3-snap.3588-T1 Valid prediction for snap_scaffold_3-snap.3611-T1 Valid prediction for Augustus_model.g5498.t1 Valid prediction for CodingQuarry_transcript_46469-T1 Valid prediction for snap_scaffold_3-snap.3601-T1 Valid prediction for snap_scaffold_3-snap.3597-T1 Valid prediction for snap_scaffold_3-snap.3610-T1 Valid prediction for snap_scaffold_3-snap.3582-T1 Valid prediction for GlimmerHMM_glimmerT_8345-T1 Valid prediction for GlimmerHMM_glimmerT_8357-T1 Valid prediction for GlimmerHMM_glimmerT_8333-T1 Valid prediction for GlimmerHMM_glimmerT_8336-T1 Valid prediction for snap_scaffold_3-snap.3575-T1 Valid prediction for GlimmerHMM_glimmerT_8356-T1 Couldn't classify 107794, 107861 Couldn't classify 108615, 108681 Sorry, prediction pasa_asmbl_40737.p1 fails validation. (CAA) AT 107794-107861 GT AGG (AGT) AG 107955-108353 GT AGG (GTT) AG 108615-108681 AC ACA -recovered pasa_asmbl_40737.p1, internal, 107955, 108353 Valid prediction for GlimmerHMM_glimmerT_8353-T1 Valid prediction for snap_scaffold_3-snap.3595-T1 Valid prediction for snap_scaffold_3-snap.3583-T1 Valid prediction for GlimmerHMM_glimmerT_8355-T1 Valid prediction for GlimmerHMM_glimmerT_8354-T1 Valid prediction for snap_scaffold_3-snap.3587-T1 Valid prediction for snap_scaffold_3-snap.3613-T1 Valid prediction for Augustus_model.g5493.t1 Valid prediction for snap_scaffold_3-snap.3603-T1 Valid prediction for HiQ_model.g5488.t1 Valid prediction for snap_scaffold_3-snap.3590-T1 Valid prediction for snap_scaffold_3-snap.3609-T1 Valid prediction for snap_scaffold_3-snap.3585-T1 Valid prediction for snap_scaffold_3-snap.3614-T1 Valid prediction for snap_scaffold_3-snap.3578-T1 Valid prediction for GlimmerHMM_glimmerT_8332-T1 Valid prediction for GlimmerHMM_glimmerT_8339-T1 Valid prediction for GlimmerHMM_glimmerT_8352-T1 Valid prediction for snap_scaffold_3-snap.3586-T1 Valid prediction for GlimmerHMM_glimmerT_8335-T1 Valid prediction for Augustus_model.g5491.t1 Valid prediction for GlimmerHMM_glimmerT_8343-T1 Valid prediction for Augustus_model.g5499.t1 Valid prediction for snap_scaffold_3-snap.3591-T1 Valid prediction for snap_scaffold_3-snap.3605-T1 Couldn't classify 108873, 108949 Sorry, prediction pasa_asmbl_40738.p1 fails validation. (AGG) CC 108873-108949 GT AAG (GTG) AG 109154-109640 GT AGG (ATT) AG 109729-109843 GT CAG (GTT) AG 109922-110050 GT AAG (TCC) AG 110208-110447 GT CGG (GCT) AG 110673-110817 GT CGG (TGT) AG 110909-111023 GT AGG (ATC) AG 111112-111204 GA GAG -recovered pasa_asmbl_40738.p1, terminal, 111112, 111204 -recovered pasa_asmbl_40738.p1, internal, 109154, 109640 -recovered pasa_asmbl_40738.p1, internal, 109729, 109843 -recovered pasa_asmbl_40738.p1, internal, 109922, 110050 -recovered pasa_asmbl_40738.p1, internal, 110208, 110447 -recovered pasa_asmbl_40738.p1, internal, 110673, 110817 -recovered pasa_asmbl_40738.p1, internal, 110909, 111023 -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_8350-T1 Valid prediction for GlimmerHMM_glimmerT_8340-T1 Valid prediction for GlimmerHMM_glimmerT_8344-T1 Valid prediction for GlimmerHMM_glimmerT_8341-T1 Valid prediction for Augustus_model.g5497.t1 Valid prediction for snap_scaffold_3-snap.3617-T1 Valid prediction for Augustus_model.g5492.t1 Valid prediction for snap_scaffold_3-snap.3596-T1 Valid prediction for HiQ_model.g5489.t1 Couldn't classify 137173, 137253 Couldn't classify 141225, 141312 Sorry, prediction pasa_asmbl_39610.p1 fails validation. (CCC) AG 137173-137253 GT AGG (ATG) AG 137333-137437 GT AGG (GAG) AG 137927-138097 GT AGG (AAT) AG 138627-138659 GT AGG (AAC) AG 139675-140120 GT AGG (ACG) AG 141225-141312 GG TTG -recovered pasa_asmbl_39610.p1, initial, 137333, 137437 -recovered pasa_asmbl_39610.p1, internal, 137173, 137253 -recovered pasa_asmbl_39610.p1, internal, 137333, 137437 -recovered pasa_asmbl_39610.p1, internal, 137927, 138097 -recovered pasa_asmbl_39610.p1, internal, 138627, 138659 -recovered pasa_asmbl_39610.p1, internal, 139675, 140120 Valid prediction for snap_scaffold_3-snap.3579-T1 Couldn't classify 90556, 90654 Sorry, prediction pasa_asmbl_39622.p1 fails validation. (CTG) AA 90556-90654 GT AGG (ACT) AG 91245-91379 GT AGG (CCT) AG 91537-91620 GT CGG (GCT) AG 92728-92751 GT AGG (CAA) AG 92855-92956 AG GAA -recovered pasa_asmbl_39622.p1, terminal, 92855, 92956 -recovered pasa_asmbl_39622.p1, internal, 91245, 91379 -recovered pasa_asmbl_39622.p1, internal, 91537, 91620 -recovered pasa_asmbl_39622.p1, internal, 92728, 92751 Valid prediction for snap_scaffold_3-snap.3593-T1 Valid prediction for GlimmerHMM_glimmerT_8347-T1 Valid prediction for snap_scaffold_3-snap.3612-T1 Valid prediction for CodingQuarry_transcript_46471-T1 Valid prediction for pasa_asmbl_39614.p1 Valid prediction for snap_scaffold_3-snap.3592-T1 Valid prediction for GlimmerHMM_glimmerT_8342-T1 Valid prediction for snap_scaffold_3-snap.3576-T1 Couldn't classify 159966, 160012 Sorry, prediction pasa_asmbl_39604.p1 fails validation. (CTG) AC 159966-160012 GT CGG (TAG) AG 160423-160523 GT AGG (AAC) AG 162669-162793 GT AGG (AAT) AG 163891-163998 GT TGG (CTG) AG 164294-164419 GT CGG (GAG) AG 164754-164933 GT TGG (ACT) AG 166108-166317 GT TGG (CAC) AG 166598-166737 GT CGG (CCG) AG 167050-167167 AG GAA -recovered pasa_asmbl_39604.p1, terminal, 167050, 167167 -recovered pasa_asmbl_39604.p1, internal, 160423, 160523 -recovered pasa_asmbl_39604.p1, internal, 162669, 162793 -recovered pasa_asmbl_39604.p1, internal, 163891, 163998 -recovered pasa_asmbl_39604.p1, internal, 164294, 164419 -recovered pasa_asmbl_39604.p1, internal, 164754, 164933 -recovered pasa_asmbl_39604.p1, internal, 166108, 166317 -recovered pasa_asmbl_39604.p1, internal, 166598, 166737 Valid prediction for snap_scaffold_3-snap.3606-T1 Valid prediction for Augustus_model.g5496.t1 Valid prediction for GlimmerHMM_glimmerT_8334-T1 Valid prediction for pasa_asmbl_39619.p1 Valid prediction for snap_scaffold_3-snap.3594-T1 Valid prediction for snap_scaffold_3-snap.3618-T1 Valid prediction for Augustus_model.g5500.t1 Valid prediction for snap_scaffold_3-snap.3602-T1 Valid prediction for snap_scaffold_3-snap.3584-T1 Valid prediction for Augustus_model.g5482.t1 Valid prediction for CodingQuarry_transcript_46473-T1 Valid prediction for snap_scaffold_3-snap.3599-T1 Valid prediction for snap_scaffold_3-snap.3574-T1 Valid prediction for GlimmerHMM_glimmerT_8346-T1 Valid prediction for Augustus_model.g5483.t1 Valid prediction for HiQ_model.g5495.t1 Valid prediction for pasa_asmbl_39615.p1 Valid prediction for Augustus_model.g5484.t1 Valid prediction for CodingQuarry_transcript_46470-T1 Valid prediction for snap_scaffold_3-snap.3581-T1 Valid prediction for CodingQuarry_transcript_46472-T1 Valid prediction for GlimmerHMM_glimmerT_8351-T1 Valid prediction for GlimmerHMM_glimmerT_8330-T1 Valid prediction for snap_scaffold_3-snap.3589-T1 Valid prediction for HiQ_model.g5494.t1 Valid prediction for GlimmerHMM_glimmerT_8358-T1 Valid prediction for Augustus_model.g5490.t1 Valid prediction for Augustus_model.g5485.t1 Valid prediction for snap_scaffold_3-snap.3577-T1 Valid prediction for GlimmerHMM_glimmerT_8348-T1 Valid prediction for snap_scaffold_3-snap.3615-T1 Valid prediction for snap_scaffold_3-snap.3600-T1 Valid prediction for snap_scaffold_3-snap.3598-T1 Valid prediction for HiQ_model.g5501.t1 Valid prediction for HiQ_model.g5487.t1 Couldn't classify 150097, 150181 Sorry, prediction pasa_asmbl_39608.p1 fails validation. (ATG) CT 144459-144585 GT AGG (TGT) AG 145517-145650 GT ATG (AGT) AG 146526-146636 GT GGG (AAT) AG 146737-146937 GT CAG (ACG) AG 147426-147562 GT AGG (GAC) AG 150097-150181 AG TCA -recovered pasa_asmbl_39608.p1, initial, 144459, 144585 -recovered pasa_asmbl_39608.p1, internal, 145517, 145650 -recovered pasa_asmbl_39608.p1, internal, 146526, 146636 -recovered pasa_asmbl_39608.p1, internal, 146737, 146937 -recovered pasa_asmbl_39608.p1, internal, 147426, 147562 Valid prediction for GlimmerHMM_glimmerT_8331-T1 Valid prediction for GlimmerHMM_glimmerT_8349-T1 Valid prediction for HiQ_model.g5486.t1 Couldn't classify 134744, 134796 Sorry, prediction pasa_asmbl_39613.p1 fails validation. (ATG) GC 125792-126225 GT GGG (ATT) AG 126837-126976 GT AGG (ATA) AG 127178-127330 GT GGG (GTC) AG 127996-128169 GT AGG (GGG) AG 128283-128323 GT AGG (GAG) AG 128466-128532 GT AGG (ATC) AG 128731-128861 GT AGG (ATC) AG 129132-129360 GT AGG (ATG) AG 129561-129740 GT AGG (GTA) AG 130640-130773 GT AAG (GAG) AG 130909-130995 GT AGG (CCG) AG 131150-131219 GT AAG (TGA) AG 131363-131448 GT AGG (GCG) AG 131754-131882 GT AGG (GTT) AG 132109-132161 GT AGG (GTT) AG 132613-132746 GT TGG (GCA) AG 133239-133324 GT TTG (ATT) AG 133581-133722 GT AGG (CGG) AG 134744-134796 TA TCT -recovered pasa_asmbl_39613.p1, initial, 125792, 126225 add_exon() Sorry, pasa_asmbl_39613.p1 129561-129740-initial-1 is invalid. -recovered pasa_asmbl_39613.p1, initial, 129561, 129740 add_exon() Sorry, pasa_asmbl_39613.p1 127996-128169-terminal-1 is invalid. -recovered pasa_asmbl_39613.p1, terminal, 127996, 128169 -recovered pasa_asmbl_39613.p1, internal, 126837, 126976 -recovered pasa_asmbl_39613.p1, internal, 127178, 127330 -recovered pasa_asmbl_39613.p1, internal, 127996, 128169 -recovered pasa_asmbl_39613.p1, internal, 128283, 128323 -recovered pasa_asmbl_39613.p1, internal, 128466, 128532 -recovered pasa_asmbl_39613.p1, internal, 128731, 128861 -recovered pasa_asmbl_39613.p1, internal, 129132, 129360 -recovered pasa_asmbl_39613.p1, internal, 129561, 129740 -recovered pasa_asmbl_39613.p1, internal, 130640, 130773 -recovered pasa_asmbl_39613.p1, internal, 130909, 130995 -recovered pasa_asmbl_39613.p1, internal, 131150, 131219 -recovered pasa_asmbl_39613.p1, internal, 131363, 131448 -recovered pasa_asmbl_39613.p1, internal, 131754, 131882 -recovered pasa_asmbl_39613.p1, internal, 132109, 132161 -recovered pasa_asmbl_39613.p1, internal, 132613, 132746 -recovered pasa_asmbl_39613.p1, internal, 133239, 133324 -recovered pasa_asmbl_39613.p1, internal, 133581, 133722 Valid prediction for GlimmerHMM_glimmerT_8338-T1 Valid prediction for snap_scaffold_3-snap.3616-T1 Valid prediction for snap_scaffold_3-snap.3604-T1 Valid prediction for GlimmerHMM_glimmerT_8337-T1 Valid prediction for snap_scaffold_3-snap.3608-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12429, rend_intergenic: 7274 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34054, rend_intergenic: 26114 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47518, rend_intergenic: 44818 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56314, rend_intergenic: 48917 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 63419, rend_intergenic: 57379 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80974, rend_intergenic: 70343 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127036, rend_intergenic: 119908 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134661, rend_intergenic: 130731 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 154637, rend_intergenic: 148374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158718, rend_intergenic: 155987 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187916, rend_intergenic: 184569 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 190838, rend_intergenic: 188938 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197149, rend_intergenic: 196283 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 207877 -exon list size: 584 building trellis 0.2 0.3 0.5 0.7 0.9 1.0 1.2 1.4 1.5 1.7 1.9 2.0 2.2 2.4 2.6 2.7 2.9 3.1 3.2 3.4 3.6 3.8 3.9 4.1 4.3 4.4 4.6 4.8 4.9 5.1 5.3 5.5 5.6 5.8 6.0 6.1 6.3 6.5 6.7 6.8 7.0 7.2 7.3 7.5 7.7 7.8 8.0 8.2 8.4 8.5 8.7 8.9 9.0 9.2 9.4 9.6 9.7 9.9 10.1 10.2 10.4 10.6 10.8 10.9 11.1 11.3 11.4 11.6 11.8 11.9 12.1 12.3 12.5 12.6 12.8 13.0 13.1 13.3 13.5 13.7 13.8 14.0 14.2 14.3 14.5 14.7 14.8 15.0 15.2 15.4 15.5 15.7 15.9 16.0 16.2 16.4 16.6 16.7 16.9 17.1 17.2 17.4 17.6 17.7 17.9 18.1 18.3 18.4 18.6 18.8 18.9 19.1 19.3 19.5 19.6 19.8 20.0 20.1 20.3 20.5 20.6 20.8 21.0 21.2 21.3 21.5 21.7 21.8 22.0 22.2 22.4 22.5 22.7 22.9 23.0 23.2 23.4 23.5 23.7 23.9 24.1 24.2 24.4 24.6 24.7 24.9 25.1 25.3 25.4 25.6 25.8 25.9 26.1 26.3 26.5 26.6 26.8 27.0 27.1 27.3 27.5 27.6 27.8 28.0 28.2 28.3 28.5 28.7 28.8 29.0 29.2 29.4 29.5 29.7 29.9 30.0 30.2 30.4 30.5 30.7 30.9 31.1 31.2 31.4 31.6 31.7 31.9 32.1 32.3 32.4 32.6 32.8 32.9 33.1 33.3 33.4 33.6 33.8 34.0 34.1 34.3 34.5 34.6 34.8 35.0 35.2 35.3 35.5 35.7 35.8 36.0 36.2 36.3 36.5 36.7 36.9 37.0 37.2 37.4 37.5 37.7 37.9 38.1 38.2 38.4 38.6 38.7 38.9 39.1 39.2 39.4 39.6 39.8 39.9 40.1 40.3 40.4 40.6 40.8 41.0 41.1 41.3 41.5 41.6 41.8 42.0 42.2 42.3 42.5 42.7 42.8 43.0 43.2 43.3 43.5 43.7 43.9 44.0 44.2 44.4 44.5 44.7 44.9 45.1 45.2 45.4 45.6 45.7 45.9 46.1 46.2 46.4 46.6 46.8 46.9 47.1 47.3 47.4 47.6 47.8 48.0 48.1 48.3 48.5 48.6 48.8 49.0 49.1 49.3 49.5 49.7 49.8 50.0 50.2 50.3 50.5 50.7 50.9 51.0 51.2 51.4 51.5 51.7 51.9 52.0 52.2 52.4 52.6 52.7 52.9 53.1 53.2 53.4 53.6 53.8 53.9 54.1 54.3 54.4 54.6 54.8 54.9 55.1 55.3 55.5 55.6 55.8 56.0 56.1 56.3 56.5 56.7 56.8 57.0 57.2 57.3 57.5 57.7 57.8 58.0 58.2 58.4 58.5 58.7 58.9 59.0 59.2 59.4 59.6 59.7 59.9 60.1 60.2 60.4 60.6 60.8 60.9 61.1 61.3 61.4 61.6 61.8 61.9 62.1 62.3 62.5 62.6 62.8 63.0 63.1 63.3 63.5 63.7 63.8 64.0 64.2 64.3 64.5 64.7 64.8 65.0 65.2 65.4 65.5 65.7 65.9 66.0 66.2 66.4 66.6 66.7 66.9 67.1 67.2 67.4 67.6 67.7 67.9 68.1 68.3 68.4 68.6 68.8 68.9 69.1 69.3 69.5 69.6 69.8 70.0 70.1 70.3 70.5 70.6 70.8 71.0 71.2 71.3 71.5 71.7 71.8 72.0 72.2 72.4 72.5 72.7 72.9 73.0 73.2 73.4 73.5 73.7 73.9 74.1 74.2 74.4 74.6 74.7 74.9 75.1 75.3 75.4 75.6 75.8 75.9 76.1 76.3 76.5 76.6 76.8 77.0 77.1 77.3 77.5 77.6 77.8 78.0 78.2 78.3 78.5 78.7 78.8 79.0 79.2 79.4 79.5 79.7 79.9 80.0 80.2 80.4 80.5 80.7 80.9 81.1 81.2 81.4 81.6 81.7 81.9 82.1 82.3 82.4 82.6 82.8 82.9 83.1 83.3 83.4 83.6 83.8 84.0 84.1 84.3 84.5 84.6 84.8 85.0 85.2 85.3 85.5 85.7 85.8 86.0 86.2 86.3 86.5 86.7 86.9 87.0 87.2 87.4 87.5 87.7 87.9 88.1 88.2 88.4 88.6 88.7 88.9 89.1 89.2 89.4 89.6 89.8 89.9 90.1 90.3 90.4 90.6 90.8 91.0 91.1 91.3 91.5 91.6 91.8 92.0 92.2 92.3 92.5 92.7 92.8 93.0 93.2 93.3 93.5 93.7 93.9 94.0 94.2 94.4 94.5 94.7 94.9 95.1 95.2 95.4 95.6 95.7 95.9 96.1 96.2 96.4 96.6 96.8 96.9 97.1 97.3 97.4 97.6 97.8 98.0 98.1 98.3 98.5 98.6 98.8 99.0 99.1 99.3 99.5 99.7 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 12429, rend_intergenic: 7274 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34054, rend_intergenic: 26114 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47518, rend_intergenic: 44818 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56314, rend_intergenic: 48917 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 63419, rend_intergenic: 57379 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80974, rend_intergenic: 70343 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127036, rend_intergenic: 119908 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134661, rend_intergenic: 130731 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 154637, rend_intergenic: 148374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158718, rend_intergenic: 155987 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187916, rend_intergenic: 184569 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 190838, rend_intergenic: 188938 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197149, rend_intergenic: 196283 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