Warning: Block unknown_A is not significant enough, removed from profile. Warning: Block unknown_M is not significant enough, removed from profile. Warning: Block unknown_O is not significant enough, removed from profile. examining piece 1..9095 (9095 bp) viterbi algorithm progress: [%]: .examining piece 37678..47833 (10156 bp) viterbi algorithm progress: [%]: ..examining piece 1602..9376 (7775 bp) viterbi algorithm progress: [%]: .examining piece 1551..9376 (7826 bp) .viterbi algorithm progress: [%]: ..examining piece 1..4199 (4199 bp) .viterbi algorithm progress: [%]: examining piece 653..20231 (19579 bp) ...viterbi algorithm progress: [%]: ..examining piece 9531..19672 (10142 bp) Warning: Block unknown_N is not significant enough, removed from profile. ..Warning: Block unknown_D is not significant enough, removed from profile. Warning: Block unknown_N is not significant enough, removed from profile. .viterbi algorithm progress: [%]: ....10Warning: Block unknown_D is not significant enough, removed from profile. ...Warning: Block unknown_N is not significant enough, removed from profile. Warning: Block unknown_Q is not significant enough, removed from profile. Warning: Block unknown_V is not significant enough, removed from profile. Warning: Block unknown_Z is not significant enough, removed from profile. ......Warning: Block unknown_F is not significant enough, removed from profile. .Warning: Block unknown_L is not significant enough, removed from profile. Warning: Block unknown_H is not significant enough, removed from profile. Warning: Block unknown_A is not significant enough, removed from profile. Warning: Block unknown_A is not significant enough, removed from profile. ..Warning: Block unknown_H is not significant enough, removed from profile. .examining piece 8600..18039 (9440 bp) 10.Warning: Block unknown_N is not significant enough, removed from profile. ...viterbi algorithm progress: [%]: .examining piece 1..5681 (5681 bp) ...Warning: Block unknown_G is not significant enough, removed from profile. viterbi algorithm progress: [%]: Warning: Block unknown_J is not significant enough, removed from profile. Warning: Block unknown_L is not significant enough, removed from profile. ..10..examining piece 20114..27746 (7633 bp) ..examining piece 10416..20133 (9718 bp) .viterbi algorithm progress: [%]: examining piece 1..4229 (4229 bp) ..viterbi algorithm progress: [%]: ...viterbi algorithm progress: [%]: Warning: Block unknown_Q is not significant enough, removed from profile. .....examining piece 13405..29618 (16214 bp) .........Warning: Block unknown_I is not significant enough, removed from profile. viterbi algorithm progress: [%]: .examining piece 1..6641 (6641 bp) .examining piece 1569..9376 (7808 bp) ..viterbi algorithm progress: [%]: Warning: Block unknown_S is not significant enough, removed from profile. examining piece 19511..29846 (10336 bp) viterbi algorithm progress: [%]: .Warning: Block unknown_X is not significant enough, removed from profile. ..examining piece 1..7243 (7243 bp) viterbi algorithm progress: [%]: .....20viterbi algorithm progress: [%]: .20examining piece 1..7189 (7189 bp) ..examining piece 3499..25070 (21572 bp) examining piece 1..2994 (2994 bp) .10...viterbi algorithm progress: [%]: viterbi algorithm progress: [%]: examining piece 1..7240 (7240 bp) ...examining piece 12255..22761 (10507 bp) .examining piece 1..6059 (6059 bp) ..viterbi algorithm progress: [%]: examining piece 6923..17250 (10328 bp) ...viterbi algorithm progress: [%]: .viterbi algorithm progress: [%]: .viterbi algorithm progress: [%]: viterbi algorithm progress: [%]: .....10..........examining piece 1..6082 (6082 bp) ....examining piece 1242..10108 (8867 bp) ..viterbi algorithm progress: [%]: .........viterbi algorithm progress: [%]: 20....................30........................examining piece 1..8628 (8628 bp) ..10.....viterbi algorithm progress: [%]: ........10................1010..........1010.........10....................10.30.........40.............20.10.......20...................20.....30...........20.10...............20.10......30........20...........10..............50.10...........................20.20..........40..10............20....10......30........10.....40..........30.....30................50..........60....1040................................20.....30................60..........10....20........20.......30.........50...4020.30.30..........70...........70............20.40....10......30.........20...40......20..........................80.20................20..................................80...............9040......60..........20.......30.....40.......1050...50............30....40..50..100.30....30..90.50......40....... ........sampling algorithm progress: [%]: ............................30................10........30............................1002030...10...............70..................30. ...........50....50..30.3040sampling algorithm progress: [%]: ...........40......40................20........60.......10...50...50.60..40...50...60......................40.......6020............................6020...............30.70...........30..................40............80.....80.....60...50......40........................4040.1090............40....60..4050....20...................100.... ..........60....70.70.6050................70.........60..70........................................408090................70..................9060...............................100... .......70....30.50..70...80.50..............30.50......50.......80.....70....10050..70.....50......80...80............... ...............................sampling algorithm progress: [%]: .......70.......50......90.......50...........80..............60.10..........................40......80........60.....90......902080.90.......................80...............60........30...60...60...........60.....100.......70...80.........90....40.............40..40..................60.90. .....50...................100.60.....50..............30......100...60sampling algorithm progress: [%]: ........ .......90.70.90....80100..90....100...........70...70..........sampling algorithm progress: [%]: ....70....10....70.......... ... .......... ..10080.......................10...........sampling algorithm progress: [%]: 20.... ....20................sampling algorithm progress: [%]: ..90..............................sampling algorithm progress: [%]: 20.100...6010........70...10......30...sampling algorithm progress: [%]: ...100..... 90.........100....... ..........100....20...20.....30..50...... ..................40.........10.80.......sampling algorithm progress: [%]: 30.....10 ..........30...sampling algorithm progress: [%]: .....40...............70....70....80.....20.5040................20..80.................40............50...10.50..20...........................................60........50..60...1060...sampling algorithm progress: [%]: ..30.................60......80.........20..............70..........30..........60........100........70.......40.......80....80.70....................70.30......20......70..50...................10. ...80...90...80..50.................80.....90..................40.80100.......40. .........................90............sampling algorithm progress: [%]: .60.......90.......30..........90.............60.50...909020........................50..100.......... .....100.10.70... .100....... ..............................60..........60.40..8020...........80........30..............................40...100......3070..70..........90....50..90.... ..........100.......80..........40...40.80.80.....100...... ................... .......6090.....90........90....30sampling algorithm progress: [%]: 50..90..50.....60..........................sampling algorithm progress: [%]: ...100...100......30.. .10.70100....... ....................70.....6060.....20...... .........70...10..80....................30.....70........100...........70..90...........40.90...........80......20...........sampling algorithm progress: [%]: .......50 ........................100..10080..90 .........60.......90..............30 ........100..70 .100..............10......sampling algorithm progress: [%]: ...90..80..... ................10040........90.........sampling algorithm progress: [%]: ......70...80.......100. ..10.100 ... ...20......50...............sampling algorithm progress: [%]: ...10..........sampling algorithm progress: [%]: 20........50..........40...60.80.30............10..20.........................1030........................20.70.......30....40................20.....40........100..30......................40..80.50.....80........30..40..........50......................50..............50...40...60.........90...........90.....60......60....60........50....................... ........70...100.....70 70...70.....60.....90...........90.............80..........80.8080.70....50............sampling algorithm progress: [%]: ..........90..........................80....90..90......90..100.. ..........10...................90...100..... .100.. .....100... .20......100.. 40......30.....100.....40....100...60...50.... .........60...........70..... .60....10080...........90...........100 ...sampling algorithm progress: [%]: .....sampling algorithm progress: [%]: .......10.................1020..................sampling algorithm progress: [%]: 20.30.....................30.40.............50..70.40..10.70..50.............50...............60.......60....20.................7070.....................30.80.....80..............90......80........90.....100..40 ..........100. .......50..............60..90............70...............80...100.... ...8090....60....100. ....sampling algorithm progress: [%]: ............10............20.......70...30...........40.........9050..........60............70.........80.80............90............100 ....100.90 .......sampling algorithm progress: [%]: .........10....100....20... .....30........40........50........sampling algorithm progress: [%]: 60................70..10............80.....20............90...30..............100 40........50........60........70........80........90........100 Will create parameters for a EUKARYOTIC species! creating directory /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/ ... creating /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/BUSCO_cbai_genome_v1.0.fasta_1620787020_parameters.cfg ... creating /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/BUSCO_cbai_genome_v1.0.fasta_1620787020_weightmatrix.txt ... creating /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/BUSCO_cbai_genome_v1.0.fasta_1620787020_metapars.cfg ... The necessary files for training BUSCO_cbai_genome_v1.0.fasta_1620787020 have been created. Now, either run etraining or optimize_parameters.pl with --species=BUSCO_cbai_genome_v1.0.fasta_1620787020. etraining quickly estimates the parameters from a file with training genes. optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters. # Read in 3 genbank sequences. Quantiles of the GC contents in the training set: 0% 0.418 5% 0.418 10% 0.418 15% 0.418 20% 0.418 25% 0.418 30% 0.418 35% 0.418 40% 0.418 45% 0.418 50% 0.494 55% 0.494 60% 0.494 65% 0.494 70% 0.494 75% 0.494 80% 0.494 85% 0.494 90% 0.494 95% 0.494 100% 0.524 HMM-training the parameters... i= 0 bc= (0.237, 0.263, 0.263, 0.237) ** building model for exons *EXON* start codon frequencies: ATG(3) # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) number of bases in the reading frames: 1008 1011 1011 --- frame = 0 --- minPatSum = 233 --- frame = 1 --- minPatSum = 233 --- frame = 2 --- minPatSum = 233 --- initial frame = 0 --- minPatSum = 233 --- initial frame = 1 --- minPatSum = 233 --- initial frame = 2 --- minPatSum = 233 --- internal exon terminal frame = 0 --- minPatSum = 233 --- internal exon terminal frame = 1 --- minPatSum = 233 --- internal exon terminal frame = 2 --- minPatSum = 233 single, initial, internal, terminal mean exon lengths : 918 146 92 394 single exon : 1 initial exon 0 : 1 initial exon 1 : 1 initial exon 2 : 0 internal exon 0 : 3 internal exon 1 : 6 internal exon 2 : 4 terminal exon : 2 Frequency of stop codons: tag: 0 (0) taa: 1 (0.333) tga: 2 (0.667) end *EXON* Storing parameters to file... Writing exon model parameters [1] to file /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/BUSCO_cbai_genome_v1.0.fasta_1620787020_exon_probs.pbl. Splitting training file into 8 buckets... Number of training sequences is too small # Read in 3 genbank sequences. Quantiles of the GC contents in the training set: 0% 0.418 5% 0.418 10% 0.418 15% 0.418 20% 0.418 25% 0.418 30% 0.418 35% 0.418 40% 0.418 45% 0.418 50% 0.494 55% 0.494 60% 0.494 65% 0.494 70% 0.494 75% 0.494 80% 0.494 85% 0.494 90% 0.494 95% 0.494 100% 0.524 HMM-training the parameters... i= 0 bc= (0.237, 0.263, 0.263, 0.237) ** building model for exons *EXON* start codon frequencies: ATG(3) # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) number of bases in the reading frames: 1008 1011 1011 --- frame = 0 --- minPatSum = 233 --- frame = 1 --- minPatSum = 233 --- frame = 2 --- minPatSum = 233 --- initial frame = 0 --- minPatSum = 233 --- initial frame = 1 --- minPatSum = 233 --- initial frame = 2 --- minPatSum = 233 --- internal exon terminal frame = 0 --- minPatSum = 233 --- internal exon terminal frame = 1 --- minPatSum = 233 --- internal exon terminal frame = 2 --- minPatSum = 233 single, initial, internal, terminal mean exon lengths : 918 146 92 394 single exon : 1 initial exon 0 : 1 initial exon 1 : 1 initial exon 2 : 0 internal exon 0 : 3 internal exon 1 : 6 internal exon 2 : 4 terminal exon : 2 Frequency of stop codons: tag: 0 (0) taa: 1 (0.333) tga: 2 (0.667) end *EXON* Storing parameters to file... Writing exon model parameters [1] to file /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/cbai_genome_v1.0.fasta_augustus/config/species/BUSCO_cbai_genome_v1.0.fasta_1620787020/BUSCO_cbai_genome_v1.0.fasta_1620787020_exon_probs.pbl. Warning: Block unknown_D is not significant enough, removed from profile. Warning: Block unknown_N is not significant enough, removed from profile. Warning: Block unknown_Q is not significant enough, removed from profile. Warning: Block unknown_V is not significant enough, removed from profile. Warning: Block unknown_Z is not significant enough, removed from profile. Warning: Block unknown_Q is not significant enough, removed from profile. Warning: Block unknown_H is not significant enough, removed from profile. Warning: Block unknown_I is not significant enough, removed from profile. Warning: Block unknown_S is not significant enough, removed from profile. Warning: Block unknown_X is not significant enough, removed from profile. Warning: Block unknown_M is not significant enough, removed from profile. Warning: Block unknown_O is not significant enough, removed from profile. Warning: Block unknown_O is not significant enough, removed from profile. Warning: Block unknown_P is not significant enough, removed from profile. Warning: Block unknown_R is not significant enough, removed from profile. Warning: Block unknown_U is not significant enough, removed from profile. Warning: Block unknown_X is not significant enough, removed from profile. Warning: Block unknown_Y is not significant enough, removed from profile. Warning: Block unknown_L is not significant enough, removed from profile. Warning: Block unknown_Z is not significant enough, removed from profile. Warning: Block unknown_AE is not significant enough, removed from profile. Warning: Block unknown_F is not significant enough, removed from profile. Warning: Block unknown_AF is not significant enough, removed from profile. Warning: Block unknown_O is not significant enough, removed from profile. Warning: Block unknown_P is not significant enough, removed from profile. Warning: Block unknown_R is not significant enough, removed from profile. examining piece 1..4229 (4229 bp) Warning: Block unknown_U is not significant enough, removed from profile. examining piece 8728..19675 (10948 bp) Warning: Block unknown_X is not significant enough, removed from profile. Warning: Block viterbi algorithm progress: [%]: unknown_Y is not significant enough, removed from profile. Warning: Block unknown_Z is not significant enough, removed from profile. .Warning: Block unknown_AE is not significant enough, removed from profile. Warning: Block unknown_AF is not significant enough, removed from profile. viterbi algorithm progress: [%]: examining piece 1..6082 (6082 bp) .examining piece 1..2994 (2994 bp) Warning: Block unknown_B is not significant enough, removed from profile. Warning: Block unknown_B is not significant enough, removed from profile. viterbi algorithm progress: [%]: .examining piece 1..7207 (7207 bp) viterbi algorithm progress: [%]: .Warning: Block unknown_H is not significant enough, removed from profile. examining piece 1509..9376 (7868 bp) Warning: Block unknown_H is not significant enough, removed from profile. Warning: Block unknown_D is not significant enough, removed from profile. viterbi algorithm progress: [%]: .examining piece 1..10102 (10102 bp) Warning: Block unknown_H is not significant enough, removed from profile. viterbi algorithm progress: [%]: ...viterbi algorithm progress: [%]: .examining piece 1..7243 (7243 bp) examining piece 1..8640 (8640 bp) .viterbi algorithm progress: [%]: .viterbi algorithm progress: [%]: ....examining piece 19511..29846 (10336 bp) ..examining piece 3499..25070 (21572 bp) examining piece 37672..47833 (10162 bp) examining piece 1239..10108 (8870 bp) examining piece 1..7282 (7282 bp) viterbi algorithm progress: [%]: ...viterbi algorithm progress: [%]: examining piece 1584..9376 (7793 bp) ...examining piece 8600..18039 (9440 bp) .viterbi algorithm progress: [%]: .viterbi algorithm progress: [%]: ..viterbi algorithm progress: [%]: viterbi algorithm progress: [%]: ..viterbi algorithm progress: [%]: ...examining piece 10617..20802 (10186 bp) examining piece 1..4199 (4199 bp) ...viterbi algorithm progress: [%]: .....examining piece 1..7378 (7378 bp) examining piece 1548..9376 (7829 bp) viterbi algorithm progress: [%]: ..examining piece 11837..19072 (7236 bp) ......viterbi algorithm progress: [%]: viterbi algorithm progress: [%]: ...viterbi algorithm progress: [%]: .......10....examining piece 1413..9376 (7964 bp) ......examining piece 13375..47980 (34606 bp) ..viterbi algorithm progress: [%]: 10.........10..........10.......10...10........20viterbi algorithm progress: [%]: ........examining piece 1..9753 (9753 bp) .........20......viterbi algorithm progress: [%]: ...........10.....10...30.....................20.examining piece 1..3744 (3744 bp) ......20.viterbi algorithm progress: [%]: ...........................1010.20..40........................30...........1020..........10...20......50............10...........20.................10...........10..3060...30.....................10..30.......10.................20.................30.....70........................40.......10..20....20...30.........10.....20.80...........1030.........................20..................40.........90.....40.........30.....2040....10.............40.......20.....100.....50.. .20...20...40.........30sampling algorithm progress: [%]: ........50...................30.40.............30........60..20........20.................10................30.........50.......40..................50.5050............30...70..60................20...............50................30...30...............................30...60....3040...30.............8010..40............20.............40....20......30.....60......70.40.60.....4040............60.......9050........................60...........70............................50..............40........10050.........50. ...40....................sampling algorithm progress: [%]: .................80.....3060.........80.........7040............40..4050..........60..10.............70...........70.50..........10...907070....50.................10.....50...............................60..80..........................60100.... ..20.......90....80................50........90..............70.3050.......sampling algorithm progress: [%]: ..40...............80......80...80.50..30100....60.. ...........50................70............60........10..............................40.........6090......2070.100.......60........80.....90........ ............20....60..............50................90...90.......80...70........60...70.........sampling algorithm progress: [%]: ....................30.......70....60............60..100.....100.80......20 .......60.. ...........40.....................70...100......90.40sampling algorithm progress: [%]: ..90.....70 ........80..............50...20sampling algorithm progress: [%]: ...............10080...70.....1090...80.......50.........30........ .sampling algorithm progress: [%]: .............70.................90.70..10...............90..............80.........80.............60........100...........sampling algorithm progress: [%]: 100..... .... .............9010.....100...........102020....100sampling algorithm progress: [%]: ........ ........ ...70..........80.100...9050............ ......................70............80..20...80...80..30100......sampling algorithm progress: [%]: 30..... ...............100...sampling algorithm progress: [%]: .....sampling algorithm progress: [%]: ..3040 .................10..10.....90.9020..........................30.........40.90.60...............90.................10.......100.....sampling algorithm progress: [%]: .. .............sampling algorithm progress: [%]: ..........10........50....40..40.60....10............90.......................30...20................10.20..100...20........100... .30....50..60.80 ...10....10...50.......50..............20.....................................100...............60...30. .70.30....40...........40..100......20..20... .60....sampling algorithm progress: [%]: ....sampling algorithm progress: [%]: .....20.............3030...70................70..........80........................40...............................40sampling algorithm progress: [%]: 7050....30...30.70...10......60.....80.........90..sampling algorithm progress: [%]: ......40................10..................50...30........................................40.......100.90... ........4050...20.4080..........90......50........60........80................60.........100.80.... .............20.........50...............40......5050....30...........90..50.....6060.....70..............70..70.......................................10..............30....1040....60..60100........ ........70....50........80....9070.........................80...................50.....60..........100..70......90...70...40.....80......90............. ............60.....80.........40..20...60..90...........80...................80100..9080..... ....50..............70...20.........70.......60........sampling algorithm progress: [%]: ........100..90....20...70... ....100.... .....90......90..............60...80...100............................... 80.....10.100........ 100..100.... ..80....90..100...............70......... .......2030.....100....90.. .....90...3090..............sampling algorithm progress: [%]: ....80.........30.................100...... .100..sampling algorithm progress: [%]: .... ..70....90.........40.50....40...................100100 40...50... .10.......................60.30......50....10...sampling algorithm progress: [%]: ............70..50.................80.20.......80........................60......90.......20........6010...........100..... ...30........60....70....90..................30....70......40.......20.40....80...............................80...40....100.....50... .90...............30................5090..50..100... ..60........70...sampling algorithm progress: [%]: ............40...100.... ..60....70.........................50........70...80...............10...6080......60...80.90.............................10070. 90.....................20....100.80 .....90..............90........30......10070. ...........100. .40...........50sampling algorithm progress: [%]: ...............10....80..60.......20..............30.............7040..............50.........90...60....80........70...............80.......90......90.............100. ..100 100 sampling algorithm progress: [%]: ........10........20........30........40........50........60........70........80........90........100