-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_18055416-18186839 -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_6-snap.3857-T1 Valid prediction for snap_scaffold_6-snap.3869-T1 Valid prediction for GlimmerHMM_glimmerT_16521-T1 Valid prediction for GlimmerHMM_glimmerT_16520-T1 Valid prediction for CodingQuarry_transcript_55428-T1 Valid prediction for GlimmerHMM_glimmerT_16532-T1 Valid prediction for snap_scaffold_6-snap.3858-T1 Valid prediction for GlimmerHMM_glimmerT_16523-T1 Valid prediction for snap_scaffold_6-snap.3855-T1 Valid prediction for HiQ_model.g11068.t1 Valid prediction for snap_scaffold_6-snap.3861-T1 Valid prediction for snap_scaffold_6-snap.3842-T1 Valid prediction for GlimmerHMM_glimmerT_16522-T1 Couldn't classify 5956, 6081 Couldn't classify 6284, 6349 Sorry, prediction CodingQuarry_transcript_55425-T1 fails validation. (ATG) AG 5956-6081 GA ATG (GAG) AT 6284-6349 AG GAA Valid prediction for snap_scaffold_6-snap.3839-T1 Valid prediction for Augustus_model.g11067.t1 Valid prediction for GlimmerHMM_glimmerT_16533-T1 Valid prediction for snap_scaffold_6-snap.3840-T1 Valid prediction for GlimmerHMM_glimmerT_16524-T1 Valid prediction for snap_scaffold_6-snap.3850-T1 Valid prediction for snap_scaffold_6-snap.3844-T1 Valid prediction for snap_scaffold_6-snap.3864-T1 Valid prediction for Augustus_model.g11069.t1 Valid prediction for GlimmerHMM_glimmerT_16534-T1 Valid prediction for snap_scaffold_6-snap.3868-T1 Valid prediction for snap_scaffold_6-snap.3851-T1 Valid prediction for snap_scaffold_6-snap.3841-T1 Valid prediction for snap_scaffold_6-snap.3862-T1 Valid prediction for snap_scaffold_6-snap.3848-T1 Valid prediction for snap_scaffold_6-snap.3859-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_6-snap.3866-T1 Couldn't classify 27879, 27934 Sorry, prediction pasa_asmbl_47819.p1 fails validation. (GGT) GA 27879-27934 GT AGG (AGA) AG 29097-29269 GT TGG (CCT) AG 29616-29748 GT AAG (GTA) AG 30096-30220 GT AGG (AGC) AG 32144-32249 GT TGG (GAT) AG 33615-33778 GT AGG (ATA) AG 33949-34114 GT AGG (GAC) AG 34620-34726 GT GGG (AAA) AG 34903-34932 GT AGG (ACC) AG 35122-35261 GT CTG (GTG) AG 35576-35735 GT TGG (ATG) AG 36229-36333 GT AGG (GCT) AG 36567-36814 GA AAG add_exon() Sorry, pasa_asmbl_47819.p1 36229-36333-initial-1 is invalid. -recovered pasa_asmbl_47819.p1, initial, 36229, 36333 -recovered pasa_asmbl_47819.p1, terminal, 36567, 36814 -recovered pasa_asmbl_47819.p1, internal, 29097, 29269 -recovered pasa_asmbl_47819.p1, internal, 29616, 29748 -recovered pasa_asmbl_47819.p1, internal, 30096, 30220 -recovered pasa_asmbl_47819.p1, internal, 32144, 32249 -recovered pasa_asmbl_47819.p1, internal, 33615, 33778 -recovered pasa_asmbl_47819.p1, internal, 33949, 34114 -recovered pasa_asmbl_47819.p1, internal, 34620, 34726 -recovered pasa_asmbl_47819.p1, internal, 34903, 34932 -recovered pasa_asmbl_47819.p1, internal, 35122, 35261 -recovered pasa_asmbl_47819.p1, internal, 35576, 35735 -recovered pasa_asmbl_47819.p1, internal, 36229, 36333 Valid prediction for snap_scaffold_6-snap.3846-T1 Valid prediction for GlimmerHMM_glimmerT_16528-T1 Couldn't classify 41276, 41435 Sorry, prediction CodingQuarry_transcript_55427-T1 fails validation. (ATG) AA 29239-29269 GT TGG (CCT) AG 29616-29748 GT AAG (GTA) AG 30096-30220 GT AGG (AGC) AG 32144-32249 GT TGG (GAT) AG 33615-33778 GT AGG (ATA) AG 33949-34114 GT AGG (GAC) AG 34620-34726 GT GGG (AAA) AG 34903-34932 GT AGG (ACC) AG 35122-35261 GT CTG (GTG) AG 35576-35735 GT TGG (ATG) AG 36229-36333 GT AGG (GCT) AG 36567-36755 GT CGG (CTC) AG 37331-37465 GT AGG (AGG) AG 37563-37730 GT GGG (AGC) AG 38619-38707 GT AGG (GGC) AG 39275-39470 GT CGG (ACA) AG 40367-40506 GT AGG (GAG) CA 41276-41435 GT AGG (GCC) AG 41785-41921 GT AGG (CCC) AG 43300-43486 GT AGG (CCT) AG 43824-43855 GC GAG -recovered CodingQuarry_transcript_55427-T1, initial, 29239, 29269 add_exon() Sorry, CodingQuarry_transcript_55427-T1 36229-36333-initial-1 is invalid. -recovered CodingQuarry_transcript_55427-T1, initial, 36229, 36333 -recovered CodingQuarry_transcript_55427-T1, terminal, 43824, 43855 -recovered CodingQuarry_transcript_55427-T1, internal, 29616, 29748 -recovered CodingQuarry_transcript_55427-T1, internal, 30096, 30220 -recovered CodingQuarry_transcript_55427-T1, internal, 32144, 32249 -recovered CodingQuarry_transcript_55427-T1, internal, 33615, 33778 -recovered CodingQuarry_transcript_55427-T1, internal, 33949, 34114 -recovered CodingQuarry_transcript_55427-T1, internal, 34620, 34726 -recovered CodingQuarry_transcript_55427-T1, internal, 34903, 34932 -recovered CodingQuarry_transcript_55427-T1, internal, 35122, 35261 -recovered CodingQuarry_transcript_55427-T1, internal, 35576, 35735 -recovered CodingQuarry_transcript_55427-T1, internal, 36229, 36333 -recovered CodingQuarry_transcript_55427-T1, internal, 36567, 36755 -recovered CodingQuarry_transcript_55427-T1, internal, 37331, 37465 -recovered CodingQuarry_transcript_55427-T1, internal, 37563, 37730 -recovered CodingQuarry_transcript_55427-T1, internal, 38619, 38707 -recovered CodingQuarry_transcript_55427-T1, internal, 39275, 39470 -recovered CodingQuarry_transcript_55427-T1, internal, 40367, 40506 -recovered CodingQuarry_transcript_55427-T1, internal, 41785, 41921 -recovered CodingQuarry_transcript_55427-T1, internal, 43300, 43486 -recovered CodingQuarry_transcript_55427-T1, internal, 43824, 43855 Valid prediction for snap_scaffold_6-snap.3860-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_6-snap.3863-T1 Couldn't classify 117297, 118094 Sorry, prediction pasa_asmbl_47807.p1 fails validation. (CAC) CA 117297-118094 AT GAA Valid prediction for Augustus_model.g11066.t1 Valid prediction for snap_scaffold_6-snap.3856-T1 Valid prediction for snap_scaffold_6-snap.3865-T1 Valid prediction for GlimmerHMM_glimmerT_16526-T1 Valid prediction for snap_scaffold_6-snap.3852-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_6-snap.3867-T1 Valid prediction for GlimmerHMM_glimmerT_16531-T1 Couldn't classify 1575, 1730 Sorry, prediction pasa_asmbl_49228.p1 fails validation. (ATC) CG 1575-1730 GT TGG (TCT) AG 3081-3229 GT GAG (GTA) AG 3319-3364 GT ATG (TAC) AG 3682-3806 GT CAG (GTT) AG 3931-4029 GT ATG (AGG) AG 5625-5745 GT ATG (AGA) AG 6004-6163 GT CTG (TAT) AG 6271-6392 GT AGG (GCT) AG 6760-6835 GT CTG (TCC) AG 7089-7360 GT TGG (CCT) AG 7595-7687 GT AGG (AAG) AG 8728-8813 GT CTG (GAA) AG 9125-9182 GT TGG (ACG) AG 9374-9481 GT TTG (GCA) AG 11090-11263 GT CGG (CTG) AG 11902-12009 GT AGG (ATG) AG 14306-14476 GT CAG (CAG) AG 15735-15855 GT AGG (GCC) AG 17606-17709 CC GAC -recovered pasa_asmbl_49228.p1, initial, 14306, 14476 add_exon() Sorry, pasa_asmbl_49228.p1 3081-3229-terminal-2 is invalid. -recovered pasa_asmbl_49228.p1, terminal, 3081, 3229 -recovered pasa_asmbl_49228.p1, terminal, 17606, 17709 -recovered pasa_asmbl_49228.p1, internal, 3081, 3229 -recovered pasa_asmbl_49228.p1, internal, 3319, 3364 -recovered pasa_asmbl_49228.p1, internal, 3682, 3806 -recovered pasa_asmbl_49228.p1, internal, 3931, 4029 -recovered pasa_asmbl_49228.p1, internal, 5625, 5745 -recovered pasa_asmbl_49228.p1, internal, 6004, 6163 -recovered pasa_asmbl_49228.p1, internal, 6271, 6392 -recovered pasa_asmbl_49228.p1, internal, 6760, 6835 -recovered pasa_asmbl_49228.p1, internal, 7089, 7360 -recovered pasa_asmbl_49228.p1, internal, 7595, 7687 -recovered pasa_asmbl_49228.p1, internal, 8728, 8813 -recovered pasa_asmbl_49228.p1, internal, 9125, 9182 -recovered pasa_asmbl_49228.p1, internal, 9374, 9481 -recovered pasa_asmbl_49228.p1, internal, 11090, 11263 -recovered pasa_asmbl_49228.p1, internal, 11902, 12009 -recovered pasa_asmbl_49228.p1, internal, 14306, 14476 -recovered pasa_asmbl_49228.p1, internal, 15735, 15855 Valid prediction for snap_scaffold_6-snap.3847-T1 Valid prediction for GlimmerHMM_glimmerT_16525-T1 Valid prediction for snap_scaffold_6-snap.3837-T1 Valid prediction for snap_scaffold_6-snap.3838-T1 Valid prediction for HiQ_model.g11073.t1 Valid prediction for GlimmerHMM_glimmerT_16530-T1 Valid prediction for Augustus_model.g11071.t1 Valid prediction for snap_scaffold_6-snap.3843-T1 Valid prediction for Augustus_model.g11072.t1 Valid prediction for snap_scaffold_6-snap.3845-T1 Valid prediction for snap_scaffold_6-snap.3849-T1 Valid prediction for GlimmerHMM_glimmerT_16529-T1 Valid prediction for GlimmerHMM_glimmerT_16527-T1 Valid prediction for snap_scaffold_6-snap.3854-T1 Valid prediction for snap_scaffold_6-snap.3853-T1 Valid prediction for Augustus_model.g11070.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21664, rend_intergenic: 3961 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24920, rend_intergenic: 23595 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35943, rend_intergenic: 27290 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36814, rend_intergenic: 36158 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 39397, rend_intergenic: 37357 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 43926, rend_intergenic: 40326 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51562, rend_intergenic: 44236 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72162, rend_intergenic: 52260 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76730, rend_intergenic: 75283 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103584, rend_intergenic: 80778 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111695, rend_intergenic: 107900 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119691, rend_intergenic: 113716 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128320, rend_intergenic: 119919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 131424 -exon list size: 288 building trellis 0.3 0.7 1.0 1.4 1.7 2.1 2.4 2.8 3.1 3.4 3.8 4.1 4.5 4.8 5.2 5.5 5.9 6.2 6.6 6.9 7.2 7.6 7.9 8.3 8.6 9.0 9.3 9.7 10.0 10.3 10.7 11.0 11.4 11.7 12.1 12.4 12.8 13.1 13.4 13.8 14.1 14.5 14.8 15.2 15.5 15.9 16.2 16.6 16.9 17.2 17.6 17.9 18.3 18.6 19.0 19.3 19.7 20.0 20.3 20.7 21.0 21.4 21.7 22.1 22.4 22.8 23.1 23.4 23.8 24.1 24.5 24.8 25.2 25.5 25.9 26.2 26.6 26.9 27.2 27.6 27.9 28.3 28.6 29.0 29.3 29.7 30.0 30.3 30.7 31.0 31.4 31.7 32.1 32.4 32.8 33.1 33.4 33.8 34.1 34.5 34.8 35.2 35.5 35.9 36.2 36.6 36.9 37.2 37.6 37.9 38.3 38.6 39.0 39.3 39.7 40.0 40.3 40.7 41.0 41.4 41.7 42.1 42.4 42.8 43.1 43.4 43.8 44.1 44.5 44.8 45.2 45.5 45.9 46.2 46.6 46.9 47.2 47.6 47.9 48.3 48.6 49.0 49.3 49.7 50.0 50.3 50.7 51.0 51.4 51.7 52.1 52.4 52.8 53.1 53.4 53.8 54.1 54.5 54.8 55.2 55.5 55.9 56.2 56.6 56.9 57.2 57.6 57.9 58.3 58.6 59.0 59.3 59.7 60.0 60.3 60.7 61.0 61.4 61.7 62.1 62.4 62.8 63.1 63.4 63.8 64.1 64.5 64.8 65.2 65.5 65.9 66.2 66.6 66.9 67.2 67.6 67.9 68.3 68.6 69.0 69.3 69.7 70.0 70.3 70.7 71.0 71.4 71.7 72.1 72.4 72.8 73.1 73.4 73.8 74.1 74.5 74.8 75.2 75.5 75.9 76.2 76.6 76.9 77.2 77.6 77.9 78.3 78.6 79.0 79.3 79.7 80.0 80.3 80.7 81.0 81.4 81.7 82.1 82.4 82.8 83.1 83.4 83.8 84.1 84.5 84.8 85.2 85.5 85.9 86.2 86.6 86.9 87.2 87.6 87.9 88.3 88.6 89.0 89.3 89.7 90.0 90.3 90.7 91.0 91.4 91.7 92.1 92.4 92.8 93.1 93.4 93.8 94.1 94.5 94.8 95.2 95.5 95.9 96.2 96.6 96.9 97.2 97.6 97.9 98.3 98.6 99.0 99.3 99.7 -found 15 predictions from path traversal Error with prediction: snap lend_intergenic: 21664, rend_intergenic: 3961 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24920, rend_intergenic: 23595 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35943, rend_intergenic: 27290 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36814, rend_intergenic: 36158 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 39397, rend_intergenic: 37357 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 43926, rend_intergenic: 40326 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51562, rend_intergenic: 44236 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72162, rend_intergenic: 52260 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76730, rend_intergenic: 75283 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103584, rend_intergenic: 80778 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111695, rend_intergenic: 107900 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119691, rend_intergenic: 113716 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128320, rend_intergenic: 119919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 8 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 10626 -exon list size: 17 building trellis 5.3 10.5 15.8 21.1 26.3 31.6 36.8 42.1 47.4 52.6 57.9 63.2 68.4 73.7 78.9 84.2 89.5 94.7 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support