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-------------------------------------------------
start time : Sun Jan 17 06:46:02 2021
working directory : /home/jmaky/NetBeansProjects/CREOLE/creole
command line : --format GFF --strand both --faa --fnn --prok --output tests/joe datas/sirvs_ERR2680377_brain_c1_cDNA.fq --verbose
output file with predictions : tests/joe
input sequence : datas/sirvs_ERR2680377_brain_c1_cDNA.fq
number of bins : 1
filter : 0
strand : both
markov chain order : cod = 2, non = 2
genetic code : 11
search for motif : 1
motif width : 6
prestart length : 40
fixed motif position : 0
off overlap : 0
identity threshold : 0.99
maximum iteration : 10
gene overlap off : 0
strand to predict on : both
GeneMarkS parameters : /home/jmaky/Documents/tools/gmst_linux_64/par_11.default
initial hmm model :
output format : GFF
output nucleotides : 1
output proteins : 1
gibbs_version : 3
run starts here:
prepare sequence
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --clean_join sequence --seq datas/sirvs_ERR2680377_brain_c1_cDNA.fq --log gms.log
Clean-Join IN OUT
Contigs - 1 1
All letters - 36853121 36853121
Unambiguous letters - 36494148 36494148
A - 9816693 9816693
C - 8108167 8108167
G - 8025999 8025999
T - 10543289 10543289
N - 358973 358973
Parameters:
Minimum of unambiguous letters per record: 1000
Trim down substrings "N...N" to maximum length: 50
Connect records using gap filler: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Minimum of unambiguous letters in output: 50000
system call done
do_iterations = 1
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --stat_fasta --seq datas/sirvs_ERR2680377_brain_c1_cDNA.fq > initial.meta.lst.feature
system call done
min_GC= max_GC= total_seq_length=0
()->()
()->()
()->()
bin number = 1
GC range = ,
prepare sequence
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --clean_join sequence --seq datas/sirvs_ERR2680377_brain_c1_cDNA.fq --log gms.log
Clean-Join IN OUT
Contigs - 1 1
All letters - 36853121 36853121
Unambiguous letters - 36494148 36494148
A - 9816693 9816693
C - 8108167 8108167
G - 8025999 8025999
T - 10543289 10543289
N - 358973 358973
Parameters:
Minimum of unambiguous letters per record: 1000
Trim down substrings "N...N" to maximum length: 50
Connect records using gap filler: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Minimum of unambiguous letters in output: 50000
system call done
do_iterations = 1
run initial prediction
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m /home/jmaky/Documents/tools/gmst_linux_64/MetaGeneMark_v1.mod -o itr_0.lst
system call done
entering iteration loop
build model: itr_1.mod for iteration: 1
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_1.mod --seq sequence --geneset itr_0.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.1 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.1 6 -o gibbs_out.1 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.1 --mod itr_1.mod --seq startseq.1 --log gms.log
-34 0.028
-33 0.037
-32 0.040
-31 0.034
-30 0.032
-29 0.033
-28 0.029
-27 0.027
-26 0.027
-25 0.027
-24 0.028
-23 0.030
-22 0.027
-21 0.027
-20 0.028
-19 0.030
-18 0.032
-17 0.028
-16 0.026
-15 0.025
-14 0.024
-13 0.023
-12 0.028
-11 0.032
-10 0.034
-9 0.035
-8 0.028
-7 0.026
-6 0.028
-5 0.024
-4 0.022
-3 0.022
-2 0.021
-1 0.023
0 0.024
Pos A C G T
1 0.434 0.015 0.296 0.254
2 0.371 0.111 0.231 0.287
3 0.256 0.445 0.001 0.298
4 0.009 0.001 0.985 0.006
5 0.091 0.199 0.354 0.356
6 0.136 0.239 0.061 0.564
system call done
prediction, iteration: 1
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_1.mod -o itr_1.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_1.lst --target itr_0.lst
compare itr_0.lst and itr_1.lst: 0.2708
build model: itr_2.mod for iteration: 2
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_2.mod --seq sequence --geneset itr_1.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.2 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.2 6 -o gibbs_out.2 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.2 --mod itr_2.mod --seq startseq.2 --log gms.log
-34 0.026
-33 0.037
-32 0.041
-31 0.035
-30 0.029
-29 0.028
-28 0.022
-27 0.022
-26 0.026
-25 0.029
-24 0.030
-23 0.030
-22 0.029
-21 0.031
-20 0.031
-19 0.034
-18 0.032
-17 0.026
-16 0.023
-15 0.024
-14 0.025
-13 0.026
-12 0.028
-11 0.028
-10 0.032
-9 0.033
-8 0.027
-7 0.026
-6 0.032
-5 0.032
-4 0.024
-3 0.020
-2 0.022
-1 0.025
0 0.023
Pos A C G T
1 0.405 0.002 0.346 0.247
2 0.461 0.034 0.252 0.253
3 0.222 0.539 0.003 0.237
4 0.032 0.092 0.858 0.018
5 0.046 0.129 0.453 0.373
6 0.037 0.154 0.020 0.789
system call done
prediction, iteration: 2
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_2.mod -o itr_2.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_2.lst --target itr_1.lst
compare itr_1.lst and itr_2.lst: 0.5758
build model: itr_3.mod for iteration: 3
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_3.mod --seq sequence --geneset itr_2.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.3 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.3 6 -o gibbs_out.3 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.3 --mod itr_3.mod --seq startseq.3 --log gms.log
-34 0.025
-33 0.035
-32 0.038
-31 0.034
-30 0.030
-29 0.032
-28 0.025
-27 0.023
-26 0.025
-25 0.026
-24 0.029
-23 0.029
-22 0.031
-21 0.030
-20 0.029
-19 0.032
-18 0.030
-17 0.026
-16 0.026
-15 0.026
-14 0.025
-13 0.026
-12 0.024
-11 0.025
-10 0.032
-9 0.035
-8 0.026
-7 0.024
-6 0.031
-5 0.035
-4 0.025
-3 0.022
-2 0.024
-1 0.027
0 0.024
Pos A C G T
1 0.346 0.002 0.413 0.238
2 0.497 0.029 0.248 0.226
3 0.248 0.531 0.002 0.219
4 0.052 0.119 0.806 0.024
5 0.022 0.088 0.531 0.360
6 0.018 0.055 0.021 0.907
system call done
prediction, iteration: 3
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_3.mod -o itr_3.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_3.lst --target itr_2.lst
compare itr_2.lst and itr_3.lst: 0.8088
build model: itr_4.mod for iteration: 4
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_4.mod --seq sequence --geneset itr_3.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.4 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.4 6 -o gibbs_out.4 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.4 --mod itr_4.mod --seq startseq.4 --log gms.log
-34 0.026
-33 0.037
-32 0.040
-31 0.033
-30 0.030
-29 0.032
-28 0.026
-27 0.023
-26 0.026
-25 0.027
-24 0.027
-23 0.031
-22 0.033
-21 0.032
-20 0.032
-19 0.029
-18 0.027
-17 0.027
-16 0.025
-15 0.023
-14 0.025
-13 0.024
-12 0.023
-11 0.027
-10 0.034
-9 0.037
-8 0.028
-7 0.026
-6 0.032
-5 0.034
-4 0.024
-3 0.020
-2 0.021
-1 0.025
0 0.023
Pos A C G T
1 0.343 0.003 0.422 0.232
2 0.514 0.028 0.238 0.220
3 0.273 0.512 0.001 0.214
4 0.055 0.164 0.763 0.018
5 0.019 0.089 0.561 0.332
6 0.014 0.023 0.024 0.939
system call done
prediction, iteration: 4
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_4.mod -o itr_4.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_4.lst --target itr_3.lst
compare itr_3.lst and itr_4.lst: 0.9166
build model: itr_5.mod for iteration: 5
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_5.mod --seq sequence --geneset itr_4.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.5 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.5 6 -o gibbs_out.5 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.5 --mod itr_5.mod --seq startseq.5 --log gms.log
-34 0.026
-33 0.039
-32 0.044
-31 0.037
-30 0.034
-29 0.030
-28 0.025
-27 0.022
-26 0.025
-25 0.024
-24 0.026
-23 0.031
-22 0.032
-21 0.031
-20 0.029
-19 0.030
-18 0.028
-17 0.027
-16 0.026
-15 0.026
-14 0.028
-13 0.027
-12 0.024
-11 0.026
-10 0.031
-9 0.031
-8 0.025
-7 0.022
-6 0.031
-5 0.035
-4 0.024
-3 0.020
-2 0.022
-1 0.026
0 0.023
Pos A C G T
1 0.331 0.014 0.415 0.240
2 0.514 0.036 0.236 0.214
3 0.281 0.491 0.004 0.223
4 0.063 0.163 0.754 0.020
5 0.013 0.088 0.568 0.332
6 0.017 0.016 0.012 0.955
system call done
prediction, iteration: 5
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_5.mod -o itr_5.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_5.lst --target itr_4.lst
compare itr_4.lst and itr_5.lst: 0.9459
build model: itr_6.mod for iteration: 6
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_6.mod --seq sequence --geneset itr_5.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.6 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.6 6 -o gibbs_out.6 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.6 --mod itr_6.mod --seq startseq.6 --log gms.log
-34 0.026
-33 0.041
-32 0.044
-31 0.038
-30 0.035
-29 0.031
-28 0.026
-27 0.024
-26 0.025
-25 0.024
-24 0.027
-23 0.032
-22 0.033
-21 0.031
-20 0.030
-19 0.029
-18 0.027
-17 0.026
-16 0.025
-15 0.025
-14 0.028
-13 0.026
-12 0.022
-11 0.025
-10 0.031
-9 0.030
-8 0.026
-7 0.024
-6 0.031
-5 0.032
-4 0.022
-3 0.020
-2 0.021
-1 0.027
0 0.025
Pos A C G T
1 0.332 0.017 0.422 0.229
2 0.512 0.039 0.252 0.197
3 0.296 0.485 0.004 0.214
4 0.061 0.187 0.728 0.024
5 0.010 0.071 0.594 0.325
6 0.019 0.010 0.011 0.960
system call done
prediction, iteration: 6
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_6.mod -o itr_6.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_6.lst --target itr_5.lst
compare itr_5.lst and itr_6.lst: 0.9587
build model: itr_7.mod for iteration: 7
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_7.mod --seq sequence --geneset itr_6.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.7 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.7 6 -o gibbs_out.7 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.7 --mod itr_7.mod --seq startseq.7 --log gms.log
-34 0.026
-33 0.037
-32 0.042
-31 0.034
-30 0.031
-29 0.033
-28 0.030
-27 0.026
-26 0.027
-25 0.025
-24 0.024
-23 0.027
-22 0.029
-21 0.030
-20 0.030
-19 0.030
-18 0.027
-17 0.026
-16 0.027
-15 0.026
-14 0.029
-13 0.027
-12 0.022
-11 0.025
-10 0.031
-9 0.030
-8 0.027
-7 0.026
-6 0.033
-5 0.035
-4 0.024
-3 0.020
-2 0.022
-1 0.025
0 0.024
Pos A C G T
1 0.334 0.031 0.421 0.214
2 0.534 0.050 0.244 0.172
3 0.308 0.480 0.004 0.208
4 0.075 0.200 0.686 0.040
5 0.006 0.071 0.586 0.337
6 0.016 0.002 0.006 0.975
system call done
prediction, iteration: 7
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_7.mod -o itr_7.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_7.lst --target itr_6.lst
compare itr_6.lst and itr_7.lst: 0.9482
build model: itr_8.mod for iteration: 8
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_8.mod --seq sequence --geneset itr_7.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.8 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.8 6 -o gibbs_out.8 -F -Z -n -r -y -x -m -s 1 -w 0.01
system call done
make prestart model
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --gibbs gibbs_out.8 --mod itr_8.mod --seq startseq.8 --log gms.log
-34 0.031
-33 0.041
-32 0.042
-31 0.034
-30 0.032
-29 0.034
-28 0.029
-27 0.026
-26 0.027
-25 0.024
-24 0.027
-23 0.029
-22 0.028
-21 0.030
-20 0.030
-19 0.028
-18 0.026
-17 0.029
-16 0.028
-15 0.028
-14 0.030
-13 0.027
-12 0.024
-11 0.026
-10 0.028
-9 0.029
-8 0.024
-7 0.024
-6 0.031
-5 0.032
-4 0.021
-3 0.016
-2 0.022
-1 0.025
0 0.025
Pos A C G T
1 0.320 0.042 0.420 0.218
2 0.557 0.056 0.240 0.147
3 0.319 0.466 0.008 0.208
4 0.088 0.225 0.641 0.045
5 0.005 0.058 0.604 0.334
6 0.018 0.004 0.002 0.976
system call done
prediction, iteration: 8
/home/jmaky/Documents/tools/gmst_linux_64/gmhmmp sequence -m itr_8.mod -o itr_8.lst -r
system call done
compare:
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --compare --source itr_8.lst --target itr_7.lst
compare itr_7.lst and itr_8.lst: 0.9522
build model: itr_9.mod for iteration: 9
/home/jmaky/Documents/tools/gmst_linux_64/probuild --par /home/jmaky/Documents/tools/gmst_linux_64/par_11.default --mkmod itr_9.mod --seq sequence --geneset itr_8.lst --ORDM 2 --order_non 2 --revcomp_non 1 --pre_start startseq.9 --PRE_START_WIDTH 40
system call done
run gibbs3 sampler
/home/jmaky/Documents/tools/gmst_linux_64/Gibbs3 startseq.9 6 -o gibbs_out.9 -F -Z -n -r -y -x -m -s 1 -w 0.01