-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_9243386-9461687 -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.g39328.t1 Valid prediction for snap_scaffold_28-snap.2109-T1 Valid prediction for Augustus_model.g39329.t1 Couldn't classify 25008, 25108 Sorry, prediction pasa_asmbl_37778.p1 fails validation. (CCA) GC 25008-25108 GT ATG (AAT) AG 26307-26376 GT AGG (GCC) AG 26748-26873 GT AGG (ATT) AG 27130-27238 GT AGG (GTA) AG 27429-27508 CA AAC -recovered pasa_asmbl_37778.p1, terminal, 27429, 27508 -recovered pasa_asmbl_37778.p1, internal, 26307, 26376 -recovered pasa_asmbl_37778.p1, internal, 26748, 26873 -recovered pasa_asmbl_37778.p1, internal, 27130, 27238 Couldn't classify 210359, 210460 Couldn't classify 210859, 211039 Sorry, prediction CodingQuarry_transcript_43762-T1 fails validation. (ATG) GG 205470-205485 GT AGG (GTG) AG 207277-207444 GT CGG (ACC) AG 207785-207924 GT TGG (ATA) AG 210359-210460 AT TGA (GAT) AC 210859-211039 GT AGG (AGC) AG 211849-212137 GT AGG (GCT) AG 212365-212671 TG GAT -recovered CodingQuarry_transcript_43762-T1, initial, 205470, 205485 -recovered CodingQuarry_transcript_43762-T1, terminal, 212365, 212671 -recovered CodingQuarry_transcript_43762-T1, internal, 207277, 207444 -recovered CodingQuarry_transcript_43762-T1, internal, 207785, 207924 -recovered CodingQuarry_transcript_43762-T1, internal, 211849, 212137 Valid prediction for GlimmerHMM_glimmerT_59365-T1 Valid prediction for snap_scaffold_28-snap.2105-T1 Valid prediction for snap_scaffold_28-snap.2087-T1 Valid prediction for snap_scaffold_28-snap.2078-T1 Valid prediction for GlimmerHMM_glimmerT_59373-T1 Valid prediction for snap_scaffold_28-snap.2091-T1 Valid prediction for HiQ_model.g39337.t1 Valid prediction for GlimmerHMM_glimmerT_59353-T1 Couldn't classify 207785, 207836 Couldn't classify 209364, 209451 Couldn't classify 210359, 210460 Couldn't classify 210859, 211039 Sorry, prediction CodingQuarry_transcript_43763-T1 fails validation. (ATG) GG 205470-205485 GT AGG (GTG) AG 207277-207444 GT CGG (ACC) AG 207785-207836 CT ACC (CTG) AC 209364-209451 GT TGG (ATA) AG 210359-210460 AT TGA (GAT) AC 210859-211039 GT AGG (AGC) AG 211849-212137 GT AGG (GCT) AG 212365-212671 TG GAT -recovered CodingQuarry_transcript_43763-T1, initial, 205470, 205485 -recovered CodingQuarry_transcript_43763-T1, terminal, 212365, 212671 -recovered CodingQuarry_transcript_43763-T1, internal, 207277, 207444 -recovered CodingQuarry_transcript_43763-T1, internal, 211849, 212137 Valid prediction for snap_scaffold_28-snap.2097-T1 Valid prediction for GlimmerHMM_glimmerT_59364-T1 Valid prediction for CodingQuarry_transcript_43759-T1 Valid prediction for snap_scaffold_28-snap.2094-T1 Valid prediction for GlimmerHMM_glimmerT_59362-T1 Valid prediction for Augustus_model.g39331.t1 Valid prediction for snap_scaffold_28-snap.2083-T1 Valid prediction for snap_scaffold_28-snap.2076-T1 Valid prediction for snap_scaffold_28-snap.2079-T1 Valid prediction for HiQ_model.g39324.t1 Valid prediction for GlimmerHMM_glimmerT_59361-T1 Valid prediction for GlimmerHMM_glimmerT_59374-T1 Valid prediction for GlimmerHMM_glimmerT_59366-T1 Valid prediction for snap_scaffold_28-snap.2081-T1 Couldn't classify 210359, 210460 Couldn't classify 210859, 211039 Sorry, prediction pasa_asmbl_37785.p1 fails validation. (ATG) GG 205470-205485 GT AGG (GTG) AG 207277-207444 GT CGG (ACC) AG 207785-207924 GT TGG (ATA) AG 210359-210460 AT TGA (GAT) AC 210859-211039 GT AGG (AGC) AG 211849-212137 GT AGG (GCT) AG 212365-212671 TG GAT -recovered pasa_asmbl_37785.p1, initial, 205470, 205485 -recovered pasa_asmbl_37785.p1, terminal, 212365, 212671 -recovered pasa_asmbl_37785.p1, internal, 207277, 207444 -recovered pasa_asmbl_37785.p1, internal, 207785, 207924 -recovered pasa_asmbl_37785.p1, internal, 211849, 212137 Valid prediction for GlimmerHMM_glimmerT_59370-T1 Valid prediction for GlimmerHMM_glimmerT_59358-T1 Valid prediction for snap_scaffold_28-snap.2077-T1 Valid prediction for GlimmerHMM_glimmerT_59354-T1 Valid prediction for GlimmerHMM_glimmerT_59360-T1 Couldn't classify 170451, 170618 Sorry, prediction pasa_asmbl_37782.p1 fails validation. (ATG) GC 165806-166262 GT CGG (GAG) AG 166519-166606 GT AGG (GGA) AG 166692-166742 GT AGG (GTT) AG 166849-166939 GT CTG (GGT) AG 167089-167223 GT AGG (ACC) AG 167652-167757 GT CAG (TAA) AG 168110-168183 GT CTG (CTG) AG 168939-169099 GT GGG (GTT) AG 169259-169392 GT AAG (CCG) AG 169547-169727 GT GGG (GGT) AG 169975-170114 GT GAG (ATA) AG 170252-170289 GT AGG (CAT) AG 170451-170618 GG GGG -recovered pasa_asmbl_37782.p1, initial, 165806, 166262 -recovered pasa_asmbl_37782.p1, internal, 166519, 166606 -recovered pasa_asmbl_37782.p1, internal, 166692, 166742 -recovered pasa_asmbl_37782.p1, internal, 166849, 166939 -recovered pasa_asmbl_37782.p1, internal, 167089, 167223 -recovered pasa_asmbl_37782.p1, internal, 167652, 167757 -recovered pasa_asmbl_37782.p1, internal, 168110, 168183 -recovered pasa_asmbl_37782.p1, internal, 168939, 169099 -recovered pasa_asmbl_37782.p1, internal, 169259, 169392 -recovered pasa_asmbl_37782.p1, internal, 169547, 169727 -recovered pasa_asmbl_37782.p1, internal, 169975, 170114 -recovered pasa_asmbl_37782.p1, internal, 170252, 170289 Valid prediction for snap_scaffold_28-snap.2111-T1 Valid prediction for snap_scaffold_28-snap.2108-T1 Valid prediction for snap_scaffold_28-snap.2089-T1 Valid prediction for GlimmerHMM_glimmerT_59356-T1 Valid prediction for HiQ_model.g39332.t1 Valid prediction for HiQ_model.g39338.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 GlimmerHMM_glimmerT_59368-T1 Valid prediction for snap_scaffold_28-snap.2085-T1 Valid prediction for snap_scaffold_28-snap.2107-T1 Valid prediction for snap_scaffold_28-snap.2104-T1 Valid prediction for snap_scaffold_28-snap.2075-T1 Valid prediction for GlimmerHMM_glimmerT_59351-T1 Valid prediction for CodingQuarry_transcript_43760-T1 Valid prediction for snap_scaffold_28-snap.2110-T1 Couldn't classify 44339, 44554 Sorry, prediction pasa_asmbl_38511.p1 fails validation. (ATG) TC 38137-38139 GT TGG (GTG) AG 39079-39293 GT ACG (AGC) AG 40314-40495 GT AGG (GCG) AG 41192-41403 GT TGG (ATC) AG 41662-41846 GT AAG (ATA) AG 42088-42193 GT AGG (GTT) AG 42390-42503 GT AGG (GCA) AG 42849-42987 GT GGG (GCG) AG 43186-43381 GT AGG (GAC) AG 43635-43893 GT AGG (TGC) AG 44109-44216 GT AGG (AAA) AG 44339-44554 GA ATG -recovered pasa_asmbl_38511.p1, initial, 38137, 38139 -recovered pasa_asmbl_38511.p1, internal, 39079, 39293 -recovered pasa_asmbl_38511.p1, internal, 40314, 40495 -recovered pasa_asmbl_38511.p1, internal, 41192, 41403 -recovered pasa_asmbl_38511.p1, internal, 41662, 41846 -recovered pasa_asmbl_38511.p1, internal, 42088, 42193 -recovered pasa_asmbl_38511.p1, internal, 42390, 42503 -recovered pasa_asmbl_38511.p1, internal, 42849, 42987 -recovered pasa_asmbl_38511.p1, internal, 43186, 43381 -recovered pasa_asmbl_38511.p1, internal, 43635, 43893 -recovered pasa_asmbl_38511.p1, internal, 44109, 44216 Valid prediction for pasa_asmbl_38508.p1 Valid prediction for snap_scaffold_28-snap.2098-T1 Valid prediction for CodingQuarry_transcript_43761-T1 Valid prediction for snap_scaffold_28-snap.2093-T1 Valid prediction for snap_scaffold_28-snap.2092-T1 Valid prediction for GlimmerHMM_glimmerT_59371-T1 Valid prediction for GlimmerHMM_glimmerT_59355-T1 Valid prediction for snap_scaffold_28-snap.2082-T1 Valid prediction for snap_scaffold_28-snap.2080-T1 Valid prediction for GlimmerHMM_glimmerT_59363-T1 Couldn't classify 201356, 201572 Couldn't classify 204751, 204930 Sorry, prediction pasa_asmbl_38506.p1 fails validation. (ACT) AG 201356-201572 GT GGG (GAG) AG 202409-202590 GT AGG (GTA) AG 202694-202813 GT AGG (AAA) AG 203757-203902 GT AGG (GCG) AG 204309-204474 GT TGG (CCA) AG 204751-204930 AA ACA -recovered pasa_asmbl_38506.p1, internal, 201356, 201572 -recovered pasa_asmbl_38506.p1, internal, 202409, 202590 -recovered pasa_asmbl_38506.p1, internal, 202694, 202813 -recovered pasa_asmbl_38506.p1, internal, 203757, 203902 -recovered pasa_asmbl_38506.p1, internal, 204309, 204474 Valid prediction for Augustus_model.g39333.t1 Valid prediction for snap_scaffold_28-snap.2096-T1 Valid prediction for snap_scaffold_28-snap.2088-T1 Valid prediction for snap_scaffold_28-snap.2090-T1 Valid prediction for GlimmerHMM_glimmerT_59372-T1 Valid prediction for snap_scaffold_28-snap.2102-T1 Valid prediction for Augustus_model.g39334.t1 Valid prediction for snap_scaffold_28-snap.2100-T1 Valid prediction for snap_scaffold_28-snap.2101-T1 Valid prediction for snap_scaffold_28-snap.2099-T1 Valid prediction for snap_scaffold_28-snap.2106-T1 Valid prediction for snap_scaffold_28-snap.2086-T1 Valid prediction for Augustus_model.g39326.t1 Valid prediction for GlimmerHMM_glimmerT_59359-T1 Valid prediction for snap_scaffold_28-snap.2084-T1 Valid prediction for GlimmerHMM_glimmerT_59357-T1 Valid prediction for HiQ_model.g39335.t1 Couldn't classify 198371, 198460 Couldn't classify 201257, 201286 Sorry, prediction pasa_asmbl_38507.p1 fails validation. (CCG) AG 198371-198460 GT AGG (GAC) AG 199212-199398 GT AGG (CTC) AG 199709-199921 GT CGG (GTA) AG 200060-200322 GT AGG (ACC) AG 200443-200652 GT AGG (GTG) AG 201257-201286 CC AGC -recovered pasa_asmbl_38507.p1, internal, 198371, 198460 -recovered pasa_asmbl_38507.p1, internal, 199212, 199398 -recovered pasa_asmbl_38507.p1, internal, 199709, 199921 -recovered pasa_asmbl_38507.p1, internal, 200060, 200322 -recovered pasa_asmbl_38507.p1, internal, 200443, 200652 Valid prediction for Augustus_model.g39330.t1 Valid prediction for CodingQuarry_transcript_43758-T1 Couldn't classify 205151, 205303 Sorry, prediction pasa_asmbl_38505.p1 fails validation. (AGG) GC 205151-205303 GT CGG (CTG) AG 205716-205857 GT AGG (ATG) AG 208456-208553 GT AGG (GCG) AG 209510-209605 GT GGG (GCT) AG 210222-210333 GT TGG (GTG) AG 210446-210543 GT AGG (TTT) AG 211796-211978 GC AGG add_exon() Sorry, pasa_asmbl_38505.p1 208456-208553-initial-1 is invalid. -recovered pasa_asmbl_38505.p1, initial, 208456, 208553 -recovered pasa_asmbl_38505.p1, terminal, 211796, 211978 -recovered pasa_asmbl_38505.p1, internal, 205716, 205857 -recovered pasa_asmbl_38505.p1, internal, 208456, 208553 -recovered pasa_asmbl_38505.p1, internal, 209510, 209605 -recovered pasa_asmbl_38505.p1, internal, 210222, 210333 -recovered pasa_asmbl_38505.p1, internal, 210446, 210543 -recovered pasa_asmbl_38505.p1, internal, 211796, 211978 Valid prediction for Augustus_model.g39325.t1 Valid prediction for snap_scaffold_28-snap.2074-T1 Valid prediction for Augustus_model.g39336.t1 Valid prediction for GlimmerHMM_glimmerT_59367-T1 Valid prediction for snap_scaffold_28-snap.2103-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_59369-T1 Valid prediction for Augustus_model.g39327.t1 Valid prediction for GlimmerHMM_glimmerT_59352-T1 Valid prediction for Augustus_model.g39323.t1 Valid prediction for snap_scaffold_28-snap.2095-T1 Valid prediction for pasa_asmbl_38515.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22077, rend_intergenic: 12432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 66470, rend_intergenic: 66448 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73309, rend_intergenic: 69328 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105441, rend_intergenic: 97532 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128204, rend_intergenic: 126812 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 170681, rend_intergenic: 167634 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191562, rend_intergenic: 183418 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210523, rend_intergenic: 209153 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211630, rend_intergenic: 210892 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 218302 -exon list size: 305 building trellis 0.3 0.7 1.0 1.3 1.6 2.0 2.3 2.6 2.9 3.3 3.6 3.9 4.2 4.6 4.9 5.2 5.5 5.9 6.2 6.5 6.8 7.2 7.5 7.8 8.1 8.5 8.8 9.1 9.4 9.8 10.1 10.4 10.7 11.1 11.4 11.7 12.1 12.4 12.7 13.0 13.4 13.7 14.0 14.3 14.7 15.0 15.3 15.6 16.0 16.3 16.6 16.9 17.3 17.6 17.9 18.2 18.6 18.9 19.2 19.5 19.9 20.2 20.5 20.8 21.2 21.5 21.8 22.1 22.5 22.8 23.1 23.5 23.8 24.1 24.4 24.8 25.1 25.4 25.7 26.1 26.4 26.7 27.0 27.4 27.7 28.0 28.3 28.7 29.0 29.3 29.6 30.0 30.3 30.6 30.9 31.3 31.6 31.9 32.2 32.6 32.9 33.2 33.6 33.9 34.2 34.5 34.9 35.2 35.5 35.8 36.2 36.5 36.8 37.1 37.5 37.8 38.1 38.4 38.8 39.1 39.4 39.7 40.1 40.4 40.7 41.0 41.4 41.7 42.0 42.3 42.7 43.0 43.3 43.6 44.0 44.3 44.6 45.0 45.3 45.6 45.9 46.3 46.6 46.9 47.2 47.6 47.9 48.2 48.5 48.9 49.2 49.5 49.8 50.2 50.5 50.8 51.1 51.5 51.8 52.1 52.4 52.8 53.1 53.4 53.7 54.1 54.4 54.7 55.0 55.4 55.7 56.0 56.4 56.7 57.0 57.3 57.7 58.0 58.3 58.6 59.0 59.3 59.6 59.9 60.3 60.6 60.9 61.2 61.6 61.9 62.2 62.5 62.9 63.2 63.5 63.8 64.2 64.5 64.8 65.1 65.5 65.8 66.1 66.4 66.8 67.1 67.4 67.8 68.1 68.4 68.7 69.1 69.4 69.7 70.0 70.4 70.7 71.0 71.3 71.7 72.0 72.3 72.6 73.0 73.3 73.6 73.9 74.3 74.6 74.9 75.2 75.6 75.9 76.2 76.5 76.9 77.2 77.5 77.9 78.2 78.5 78.8 79.2 79.5 79.8 80.1 80.5 80.8 81.1 81.4 81.8 82.1 82.4 82.7 83.1 83.4 83.7 84.0 84.4 84.7 85.0 85.3 85.7 86.0 86.3 86.6 87.0 87.3 87.6 87.9 88.3 88.6 88.9 89.3 89.6 89.9 90.2 90.6 90.9 91.2 91.5 91.9 92.2 92.5 92.8 93.2 93.5 93.8 94.1 94.5 94.8 95.1 95.4 95.8 96.1 96.4 96.7 97.1 97.4 97.7 98.0 98.4 98.7 99.0 99.3 99.7 -found 28 predictions from path traversal Error with prediction: snap lend_intergenic: 22077, rend_intergenic: 12432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 66470, rend_intergenic: 66448 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73309, rend_intergenic: 69328 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105441, rend_intergenic: 97532 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128204, rend_intergenic: 126812 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 170681, rend_intergenic: 167634 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191562, rend_intergenic: 183418 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210523, rend_intergenic: 209153 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211630, rend_intergenic: 210892 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 21 predictions persist after filtering for low support