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gatech-genemark / GeneMark-EP-plus

GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins
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not found output/gmhmm/dna.fa_1999.out #1

Open yexianingyue opened 4 years ago

yexianingyue commented 4 years ago

Hello: I run the command prothint.py seq.fna --workdir ./temp. I get the error 

warning on: gm_et_linux_64/gmhmme3  -m temp/GeneMark_ES/output/gmhmm.mod   -f lst -n   -o output/gmhmm/dna.fa_1999.out  temp/GeneMark_ES/output/data/dna.fa_1999
2290 contigs in training
error, file not found  output/gmhmm/dna.fa_1999.out
check before run
error, file not found gm_et_linux_64/gmes_petap.pl: ./temp/prothint.gff

And I run the command gm_et_linux_64/gmhmme3 -m temp/GeneMark_ES/output/gmhmm.mod -f lst -n ./dna.fa_1999,

The error:

GeneMark.hmm eukaryotic 3
18 days remaining in the license period.

GeneMark.hmm eukaryotic 3
18 days remaining in the license period.

段错误

dna.fa_1999 file

>dna.fa_1999    1999_dna    1   1814
CCCATCCGCCGGCCACCGGGCTTGGCGGTCGGCGGGCCCTGGCTGATGCCGAGGTCGCGCACGATGCCGTTCTCGAGCTGGTACACCCACCCGTGGACGG
TGACGCCAAACTGGCCGCGGCGCTTCCAGTCGTCCTGCACGATCTGGCTGGCGAGGAGGTTCTTGACCTGCTGCGCGACGTTCTCCTCGACGAGCAGGTC
GAGCGAGGGCGGGCCCTCCTCGGTCGCCATGACGCGCGCGAGCGCCGTGAGCGGCTTGAGGTAGCGCTGGATTGCCTGCGTCTCCGGCACGGGTGGGAGC
GTCGACGCGCGCAGGGCCGTCTGGCAGCCGACGCAGTTCGAGTGGCCCTGGGGTCAGCGGGTAGTGGGAGAGGCCTCGATCTGGGCCGGCGAACGACGCG
TCCGTTCCGCTCGAGCGCATTCCTTCTCCCCGTTTCACGTTGCGCTCGGCCCCGCGGCACTCACCGCCACGATGATATGCTTGACCTTGAAGTTGATGAG
GGCGATCATGAGCACGGCGTTCAGGCTGTCGTCGCTTGGCGTGTAGAGGTTGGCGATGCCGCGGTGCACGAAGATGTCGCCGGGCTGCGAGCCCATGATC
AAGGTTTCGGGGACGCGCGCGTCCGAGCCTGCTGTCAGCCTGGCTCTGCTGCACAGTGGCGCGACTCACAGCCAATCCACAACACCTCGGGGCGCTGGCC
CGGGTAGTGGCGGGGGAAGAAGGAGGGGTCCTTGGAGCTCGTGTGCTTTGCCCAGCGCTCGTTGCGCATCAGCAGCTCTTTCTGCCGTCAGCGCTGGCGG
ACACCACACACACCAGCTCGGGGTACACGTCTGAGCTGTGCTTCTCGTTGGCGTCGACGCGCGAGACCTCGCGGCCTATCCTCATTGGGGCGGTCATGTC
GTGTCTGGTTAGTGGGTCGTGAAGTGAGCAAGACAAACTACGGCCCCAGTCTTGATAAACAGGCGCGAGCAAGCCGGCGCACACTGATGCGTCCAGCACA
ACGTCGAAGGCAAGCGAGATCTGCCGCATGCCCCCGTAGTGGCGGTGGCGCCAGGCCAGGGCCGCCTTCCCATTGTCCGATGTTCGCTCGCACCTTTTGC
TCGCCGCCAACGCGCCTCTTCGGGCAGGCGTCGGCGGCGAGGTGATGGACGCAGGAACGTGAAGGTCAGGCGGGCAGGAGGAGGGCACAGAACAACGTGA
TCTGGAGTGGCGCGCGCCACCGCACGGACCCCCGGGCCCTTCCGAACAATCAGGCGGGCCACGGCCTTTGGTGCGCTGCCTGCGTGCGCGTCGCGCCGCG
TCTGCGTCCCTGGCGTGGGCTGTCAGTGGGCTCGATTGGCTGGCTGCGAGGCTGGGCGCGAGAGATTGATTGCTTGTCACGTCGAGCCAGAGCCATGGGG
ATGTCGCGTGGTCGAGGAGGTGCGGAGAGAGGGTGGAGAGGAAATGAATATGCCATGACATCTATCTACTTGACGCGCTTGCCGTTCTGGACGCGGGGGC
CCCATCTGTGAGTTCGAGTCGAGCTCGAGAGGTGACAGGCGGTGGGAGGAGGTAATGGGAGGAGAGGAGAGAGGAGAGACGGCGTGTTCGGAATGGGAGG
GTTGGACCAAAGATGGCGTCAGCTCCACTCTCTCGGTACACAAGCTAGGCGACCCCGGCGCACTGCGCGCCAGCTCCTCTGCACATGCGCACGCCGCCGC
AGATACTGCTGCGCACACCGGACACGCCTGGCCACACGCTCACTCACCCGCGGATCTTCTTGGGAGGCTTTGGCGGGCGGATGAACGTCGATGGCGCATC
GCCGTGCGAGTAGC
tomasbruna commented 4 years ago

Hi,

thanks for using GeneMark-EP+!

Could you please share the full log file produced by ProtHint to help me solve this issue? If you could also add the contents of temp/GeneMark_ES/gmes.log, that would help too.

Tomas

yexianingyue commented 4 years ago

Hi, I'm glad to get your reply!

Here I list some logs

run.sh

prothint.py seq.fna --workdir ./temp
gmes_petap.pl --EP ./temp/prothint.gff --evidence ./temp/evidence.gff --seq P10-008.fna --soft_mask 1000  --verbose

run.sh.error

ProtHint Version 2.2.0
Copyright 2019, Georgia Institute of Technology, USA

Called from:  .P10-008
Cmd: prothint.py P10-008.fna --workdir ./temp --cleanup --threads 14

[Tue Feb  4 07:49:35 2020] Running GeneMark-ES.
GeneMark.hmm eukaryotic 3
GeneMark.hmm eukaryotic 3
18 days remaining in the license period.
GeneMark.hmm eukaryotic 3
18 days remaining in the license period.
...
...
...
GeneMark.hmm eukaryotic 3
18 days remaining in the license period.

[Tue Feb  4 08:03:40 2020] error: ProtHint exited due to an error in command: gmes_petap.pl --verbose --cores 14 --max_intergenic 50000 --ES --seq P10-008.fna --soft 1000

run.sh.output

check before run
create directories
commit input data
data report
commit training data
training data report
prepare initial model
get GC of sequence
GC 64
build initial ES model
running step ES_A
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_A_1
training level ES_A: .P10-008/temp/GeneMark_ES/run/ES_A_1
Initial 2919
Internal    4713
Terminal    3003
Single  714
Intron: 7787    3531526
Intergenic: 2648    2465312
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_A_2
training level ES_A: .P10-008/temp/GeneMark_ES/run/ES_A_2
Initial 3498
Internal    7735
Terminal    3574
Single  644
Intron: 11376   2774599
Intergenic: 3142    2657069
running step ES_B
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_B_1
training level ES_B: .P10-008/temp/GeneMark_ES/run/ES_B_1
Initial 3613
Internal    7980
Terminal    3682
Single  670
Intron: 11721   2389426
Intergenic: 3214    2710471
running step ES_C
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_C_1
training level ES_C: .P10-008/temp/GeneMark_ES/run/ES_C_1
Initial 3883
Internal    10520
Terminal    3941
Single  671
Intron: 14513   1548136
Intergenic: 3286    2686491
SvsM  0.146092730937982 vs 0.853907269062018
genes in IvsT: 3942
1, -1.55922333257737
2, -1.51095027606404
3, -1.69741834881984
4, -2.0372202222575
5, -2.4773251123356
6, -2.85449347023126
7, -3.34496955458197
8, -3.51726955291491
9, -4.25409179697752
10, -4.4952538537944
11, -4.94723897753746
12, -5.57139328661046
13, -5.14394927178352
14, -5.57139328661046
15, -5.79453683792467
IvsT  0.707260899781641 vs 0.292739100218359
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_C_2
training level ES_C: .P10-008/temp/GeneMark_ES/run/ES_C_2
Initial 3992
Internal    10969
Terminal    4048
Single  643
Intron: 15068   1497769
Intergenic: 3377    2749365
SvsM  0.137489822030941 vs 0.862510177969059
genes in IvsT: 4040
1, -1.56821995671287
2, -1.52521507327002
3, -1.68259431919106
4, -2.04633238307256
5, -2.44321374748933
6, -2.8615822604334
7, -3.35524008057703
8, -3.47568623365289
9, -4.16086524456366
10, -4.51981033703693
11, -5.04590343293371
12, -5.47078662689898
13, -5.41362821305903
14, -5.53141124871541
16, -5.66494264133994
IvsT  0.714832273882858 vs 0.285167726117142
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_C_3
training level ES_C: .P10-008/temp/GeneMark_ES/run/ES_C_3
Initial 4018
Internal    11009
Terminal    4074
Single  638
Intron: 15134   1486519
Intergenic: 3400    2794487
SvsM  0.135884057971014 vs 0.864115942028986
genes in IvsT: 4067
1, -1.55605680641926
2, -1.52846884990043
3, -1.68925525414309
4, -2.04916922158618
5, -2.44987468244136
6, -2.86392353424091
7, -3.32022831912849
8, -3.50663986117397
9, -4.18352652086213
10, -4.43945989499933
11, -5.09178508103902
12, -5.53807218366744
13, -5.42028914801106
14, -5.53807218366744
16, -5.60261070480501
IvsT  0.715138026760392 vs 0.284861973239608
running gm.hmm on local multi-core system
216 contigs in training
concatenate predictions: .P10-008/temp/GeneMark_ES/run/ES_C_4
training level ES_C: .P10-008/temp/GeneMark_ES/run/ES_C_4
Initial 4022
Internal    11006
Terminal    4078
Single  637
Intron: 15135   1473070
Intergenic: 3399    2790875
SvsM  0.135526468203406 vs 0.864473531796594
genes in IvsT: 4071
1, -1.55238867783929
2, -1.52718688586534
3, -1.69157074197262
4, -2.05015226418194
5, -2.44801277290488
6, -2.87792194494874
7, -3.32121136172424
8, -3.50762290376972
9, -4.15276086514331
10, -4.46149634679292
11, -5.09276812363478
12, -5.5390552262632
13, -5.42127219060681
14, -5.5390552262632
16, -5.60359374740077
IvsT  0.715058607464985 vs 0.284941392535015
predict final gene set
running gm.hmm on local multi-core system
2290 contigs in training
warning on: gm_et_linux_64/gmhmme3  -m .P10-008/temp/GeneMark_ES/output/gmhmm.mod   -f lst -n   -o output/gmhmm/dna.fa_1999.out  .P10-008/temp/GeneMark_ES/output/data/dna.fa_1999
2290 contigs in training
error, file not found gmes_petap.pl: output/gmhmm/dna.fa_1999.out
check before run
error, file not found gm_et_linux_64/gmes_petap.pl: ./temp/prothint.gff

gmes.log

gmes_petap.pl : [Tue Feb  4 22:57:21 2020] gm_et_linux_64/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /share/data7/zhangy2/projects/fungi586/repeat/masked/P10-008.fna  --mask_soft 1000 
gmes_petap.pl : [Tue Feb  4 22:57:24 2020] gm_et_linux_64/probuild  --seq data/dna.fna  --allow_x  --stat info/dna.general  --details
gmes_petap.pl : [Tue Feb  4 22:57:27 2020] gm_et_linux_64/probuild  --seq data/dna.fna  --allow_x  --stat_fasta info/dna.multi_fasta
gmes_petap.pl : [Tue Feb  4 22:57:29 2020] gm_et_linux_64/probuild  --seq data/dna.fna  --allow_x  --substring_n_distr info/dna.gap_distr
gmes_petap.pl : [Tue Feb  4 22:57:32 2020] gm_et_linux_64/gc_distr.pl --in data/dna.fna  --out info/dna.gc.csv  --w 1000,8000
gmes_petap.pl : [Tue Feb  4 22:57:34 2020] gm_et_linux_64/probuild  --seq .P10-008/temp/GeneMark_ES/data/dna.fna  --split dna.fa  --max_contig 5000000 --min_contig 50000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n  --trace ../../info/training.trace 
gmes_petap.pl : [Tue Feb  4 22:57:37 2020] gm_et_linux_64/probuild --seq data/training.fna --stat info/training.general --allow_x  --GC_PRECISION 0  --details
gmes_petap.pl : [Tue Feb  4 22:57:37 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section ES_ini --def gm_et_linux_64/heu_dir/heu_05_gcode_1_gc_64.mod 
gmes_petap.pl : [Tue Feb  4 22:57:37 2020] ln -sf  .P10-008/temp/GeneMark_ES/run/ES_ini/es_ini.mod  run/ini.mod
gmes_petap.pl : [Tue Feb  4 22:57:37 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 22:58:00 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_ini/es_ini.mod  .P10-008/temp/GeneMark_ES/run/ES_A_1/prev.mod
gmes_petap.pl : [Tue Feb  4 22:58:02 2020] gm_et_linux_64/parse_set.pl --section ES_A --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v 
gmes_petap.pl : [Tue Feb  4 22:58:02 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 22:58:02 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 22:58:03 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 22:58:03 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 22:58:03 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR 
gmes_petap.pl : [Tue Feb  4 22:58:04 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR 
gmes_petap.pl : [Tue Feb  4 22:58:05 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 22:58:05 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_A --def prev.mod  --out ES_A_1.mod 
gmes_petap.pl : [Tue Feb  4 22:58:05 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 22:58:29 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_A_1/ES_A_1.mod  .P10-008/temp/GeneMark_ES/run/ES_A_2/prev.mod
gmes_petap.pl : [Tue Feb  4 22:58:31 2020] gm_et_linux_64/parse_set.pl --section ES_A --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v 
gmes_petap.pl : [Tue Feb  4 22:58:32 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 22:58:32 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 22:58:32 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 22:58:33 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 22:58:33 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR 
gmes_petap.pl : [Tue Feb  4 22:58:34 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR 
gmes_petap.pl : [Tue Feb  4 22:58:35 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 22:58:35 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_A --def prev.mod  --out ES_A_2.mod 
gmes_petap.pl : [Tue Feb  4 22:58:35 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 22:58:59 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_A_2/ES_A_2.mod  .P10-008/temp/GeneMark_ES/run/ES_B_1/prev.mod
gmes_petap.pl : [Tue Feb  4 22:59:01 2020] gm_et_linux_64/parse_set.pl --section ES_B --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v
gmes_petap.pl : [Tue Feb  4 22:59:01 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 22:59:01 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 22:59:02 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 22:59:02 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 22:59:02 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_0    --phase 0 
gmes_petap.pl : [Tue Feb  4 22:59:03 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
gmes_petap.pl : [Tue Feb  4 22:59:03 2020]  cat  GT.mat > donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:03 2020]  cat  AG.mat > acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:03 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_1    --phase 1 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_2    --phase 2 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  mv donor.mat     GT.mat 
gmes_petap.pl : [Tue Feb  4 22:59:04 2020]  mv acceptor.mat  AG.mat 
gmes_petap.pl : [Tue Feb  4 22:59:06 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 22:59:13 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section intron_DUR
gmes_petap.pl : [Tue Feb  4 22:59:14 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section initial_DUR
gmes_petap.pl : [Tue Feb  4 22:59:16 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section internal_DUR
gmes_petap.pl : [Tue Feb  4 22:59:17 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section terminal_DUR
gmes_petap.pl : [Tue Feb  4 22:59:18 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section single_DUR
gmes_petap.pl : [Tue Feb  4 22:59:18 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_B --def prev.mod  --out ES_B_1.mod 
gmes_petap.pl : [Tue Feb  4 22:59:18 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 22:59:42 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_B_1/ES_B_1.mod  .P10-008/temp/GeneMark_ES/run/ES_C_1/prev.mod
gmes_petap.pl : [Tue Feb  4 22:59:45 2020] gm_et_linux_64/parse_set.pl --section ES_C --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v
gmes_petap.pl : [Tue Feb  4 22:59:45 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 22:59:45 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 22:59:46 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 22:59:46 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 22:59:46 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_0    --phase 0  --quiet
gmes_petap.pl : [Tue Feb  4 22:59:47 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
gmes_petap.pl : [Tue Feb  4 22:59:47 2020]  cat  GT.mat > donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:47 2020]  cat  AG.mat > acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:47 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_1    --phase 1  --quiet
gmes_petap.pl : [Tue Feb  4 22:59:48 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
gmes_petap.pl : [Tue Feb  4 22:59:48 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:48 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:48 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_2    --phase 2  --quiet
gmes_petap.pl : [Tue Feb  4 22:59:49 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  mv donor.mat     GT.mat 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  mv acceptor.mat  AG.mat 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_0  --phase 0  --force
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  cat  GC.mat > donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 22:59:49 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_1  --phase 1  --force
gmes_petap.pl : [Tue Feb  4 22:59:49 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 22:59:50 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_2  --phase 2  --force
gmes_petap.pl : [Tue Feb  4 22:59:50 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 22:59:50 2020]  mv donor_GC.mat GC.mat 
gmes_petap.pl : [Tue Feb  4 22:59:51 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 22:59:59 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section intron_DUR
gmes_petap.pl : [Tue Feb  4 23:00:01 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section initial_DUR
gmes_petap.pl : [Tue Feb  4 23:00:03 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section internal_DUR
gmes_petap.pl : [Tue Feb  4 23:00:04 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section terminal_DUR
gmes_petap.pl : [Tue Feb  4 23:00:05 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section single_DUR
gmes_petap.pl : [Tue Feb  4 23:00:06 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_C --def prev.mod  --out ES_C_1.mod 
gmes_petap.pl : [Tue Feb  4 23:00:06 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 23:00:51 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_C_1/ES_C_1.mod  .P10-008/temp/GeneMark_ES/run/ES_C_2/prev.mod
gmes_petap.pl : [Tue Feb  4 23:00:54 2020] gm_et_linux_64/parse_set.pl --section ES_C --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v
gmes_petap.pl : [Tue Feb  4 23:00:54 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 23:00:55 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 23:00:55 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 23:00:55 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 23:00:56 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_0    --phase 0  --quiet
gmes_petap.pl : [Tue Feb  4 23:00:56 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
gmes_petap.pl : [Tue Feb  4 23:00:56 2020]  cat  GT.mat > donor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:56 2020]  cat  AG.mat > acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:56 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_1    --phase 1  --quiet
gmes_petap.pl : [Tue Feb  4 23:00:57 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
gmes_petap.pl : [Tue Feb  4 23:00:57 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:57 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:57 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_2    --phase 2  --quiet
gmes_petap.pl : [Tue Feb  4 23:00:58 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
gmes_petap.pl : [Tue Feb  4 23:00:58 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:58 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:00:58 2020]  mv donor.mat     GT.mat 
gmes_petap.pl : [Tue Feb  4 23:00:58 2020]  mv acceptor.mat  AG.mat 
gmes_petap.pl : [Tue Feb  4 23:00:58 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_0  --phase 0  --force
gmes_petap.pl : [Tue Feb  4 23:00:58 2020]  cat  GC.mat > donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:00:59 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_1  --phase 1  --force
gmes_petap.pl : [Tue Feb  4 23:00:59 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:00:59 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_2  --phase 2  --force
gmes_petap.pl : [Tue Feb  4 23:00:59 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:00:59 2020]  mv donor_GC.mat GC.mat 
gmes_petap.pl : [Tue Feb  4 23:01:00 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 23:01:09 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section intron_DUR
gmes_petap.pl : [Tue Feb  4 23:01:11 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section initial_DUR
gmes_petap.pl : [Tue Feb  4 23:01:12 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section internal_DUR
gmes_petap.pl : [Tue Feb  4 23:01:14 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section terminal_DUR
gmes_petap.pl : [Tue Feb  4 23:01:15 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section single_DUR
gmes_petap.pl : [Tue Feb  4 23:01:15 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_C --def prev.mod  --out ES_C_2.mod 
gmes_petap.pl : [Tue Feb  4 23:01:15 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 23:02:02 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_C_2/ES_C_2.mod  .P10-008/temp/GeneMark_ES/run/ES_C_3/prev.mod
gmes_petap.pl : [Tue Feb  4 23:02:05 2020] gm_et_linux_64/parse_set.pl --section ES_C --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v
gmes_petap.pl : [Tue Feb  4 23:02:05 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 23:02:05 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 23:02:06 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 23:02:06 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 23:02:06 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_0    --phase 0  --quiet
gmes_petap.pl : [Tue Feb  4 23:02:07 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
gmes_petap.pl : [Tue Feb  4 23:02:07 2020]  cat  GT.mat > donor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:07 2020]  cat  AG.mat > acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:07 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_1    --phase 1  --quiet
gmes_petap.pl : [Tue Feb  4 23:02:08 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
gmes_petap.pl : [Tue Feb  4 23:02:08 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:08 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:08 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_2    --phase 2  --quiet
gmes_petap.pl : [Tue Feb  4 23:02:09 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
gmes_petap.pl : [Tue Feb  4 23:02:09 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:09 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:02:09 2020]  mv donor.mat     GT.mat 
gmes_petap.pl : [Tue Feb  4 23:02:09 2020]  mv acceptor.mat  AG.mat 
gmes_petap.pl : [Tue Feb  4 23:02:09 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_0  --phase 0  --force
gmes_petap.pl : [Tue Feb  4 23:02:09 2020]  cat  GC.mat > donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:02:10 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_1  --phase 1  --force
gmes_petap.pl : [Tue Feb  4 23:02:10 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:02:10 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_2  --phase 2  --force
gmes_petap.pl : [Tue Feb  4 23:02:10 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:02:10 2020]  mv donor_GC.mat GC.mat 
gmes_petap.pl : [Tue Feb  4 23:02:11 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 23:02:19 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section intron_DUR
gmes_petap.pl : [Tue Feb  4 23:02:21 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section initial_DUR
gmes_petap.pl : [Tue Feb  4 23:02:22 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section internal_DUR
gmes_petap.pl : [Tue Feb  4 23:02:24 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section terminal_DUR
gmes_petap.pl : [Tue Feb  4 23:02:25 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section single_DUR
gmes_petap.pl : [Tue Feb  4 23:02:25 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_C --def prev.mod  --out ES_C_3.mod 
gmes_petap.pl : [Tue Feb  4 23:02:25 2020] 216 contigs in training
gmes_petap.pl : [Tue Feb  4 23:03:11 2020] ln -sf .P10-008/temp/GeneMark_ES/run/ES_C_3/ES_C_3.mod  .P10-008/temp/GeneMark_ES/run/ES_C_4/prev.mod
gmes_petap.pl : [Tue Feb  4 23:03:14 2020] gm_et_linux_64/parse_set.pl --section ES_C --cfg  .P10-008/temp/GeneMark_ES/run.cfg  --v
gmes_petap.pl : [Tue Feb  4 23:03:14 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section start_ATG   --format INI
gmes_petap.pl : [Tue Feb  4 23:03:14 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAA    --format TERM_TAA
gmes_petap.pl : [Tue Feb  4 23:03:15 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TAG    --format TERM_TAG
gmes_petap.pl : [Tue Feb  4 23:03:15 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section stop_TGA    --format TERM_TGA
gmes_petap.pl : [Tue Feb  4 23:03:15 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_0    --phase 0  --quiet
gmes_petap.pl : [Tue Feb  4 23:03:16 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
gmes_petap.pl : [Tue Feb  4 23:03:16 2020]  cat  GT.mat > donor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:16 2020]  cat  AG.mat > acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:16 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_1    --phase 1  --quiet
gmes_petap.pl : [Tue Feb  4 23:03:16 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
gmes_petap.pl : [Tue Feb  4 23:03:16 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:16 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:17 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section donor_GT    --format DONOR_2    --phase 2  --quiet
gmes_petap.pl : [Tue Feb  4 23:03:17 2020] gm_et_linux_64/make_nt_freq_mat.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
gmes_petap.pl : [Tue Feb  4 23:03:17 2020]  cat  GT.mat >> donor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:17 2020]  cat  AG.mat >> acceptor.mat 
gmes_petap.pl : [Tue Feb  4 23:03:17 2020]  mv donor.mat     GT.mat 
gmes_petap.pl : [Tue Feb  4 23:03:17 2020]  mv acceptor.mat  AG.mat 
gmes_petap.pl : [Tue Feb  4 23:03:18 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_0  --phase 0  --force
gmes_petap.pl : [Tue Feb  4 23:03:18 2020]  cat  GC.mat > donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:03:18 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_1  --phase 1  --force
gmes_petap.pl : [Tue Feb  4 23:03:18 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:03:19 2020] gm_et_linux_64/make_nt_freq_mat.pl  --cfg .P10-008/temp/GeneMark_ES/run.cfg  --section donor_GC  --format DONOR_GC_2  --phase 2  --force
gmes_petap.pl : [Tue Feb  4 23:03:19 2020]  cat  GC.mat >> donor_GC.mat 
gmes_petap.pl : [Tue Feb  4 23:03:19 2020]  mv donor_GC.mat GC.mat 
gmes_petap.pl : [Tue Feb  4 23:03:21 2020] gm_et_linux_64/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
gmes_petap.pl : [Tue Feb  4 23:03:31 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section intron_DUR
gmes_petap.pl : [Tue Feb  4 23:03:32 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section initial_DUR
gmes_petap.pl : [Tue Feb  4 23:03:33 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section internal_DUR
gmes_petap.pl : [Tue Feb  4 23:03:35 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section terminal_DUR
gmes_petap.pl : [Tue Feb  4 23:03:35 2020] gm_et_linux_64/histogram.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section single_DUR
gmes_petap.pl : [Tue Feb  4 23:03:36 2020] gm_et_linux_64/build_mod.pl --cfg .P10-008/temp/GeneMark_ES/run.cfg --section ES_C --def prev.mod  --out ES_C_4.mod 
gmes_petap.pl : [Tue Feb  4 23:03:36 2020] cp .P10-008/temp/GeneMark_ES/run/ES_C_4/ES_C_4.mod .P10-008/temp/GeneMark_ES/gmhmm.mod
gmes_petap.pl : [Tue Feb  4 23:03:36 2020] cp .P10-008/temp/GeneMark_ES/run/ES_C_4/ES_C_4.mod output/gmhmm.mod
gmes_petap.pl : [Tue Feb  4 23:03:42 2020] gm_et_linux_64/probuild  --seq .P10-008/temp/GeneMark_ES/data/dna.fna  --split dna.fa  --max_contig 5000000 --min_contig 500 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n  --trace ../../info/prediction.trace 
gmes_petap.pl : [Tue Feb  4 23:03:43 2020] 2290 contigs in training
gmes_petap.pl : [Tue Feb  4 23:05:56 2020] warning on: gm_et_linux_64/gmhmme3  -m .P10-008/temp/GeneMark_ES/output/gmhmm.mod   -f lst -n   -o output/gmhmm/dna.fa_1999.out  .P10-008/temp/GeneMark_ES/output/data/dna.fa_1999
gmes_petap.pl : [Tue Feb  4 23:06:07 2020] 2290 contigs in training
gmes_petap.pl : [Tue Feb  4 23:06:07 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:06:07 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_2.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:06:08 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_3.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:06:08 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_4.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:06:08 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_5.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:06:08 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_6.out  --app  --out genemark.gtf  --min 300 
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gmes_petap.pl : [Tue Feb  4 23:08:55 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1993.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:08:55 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1994.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:08:55 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1995.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:08:55 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1996.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:08:55 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1997.out  --app  --out genemark.gtf  --min 300 
gmes_petap.pl : [Tue Feb  4 23:08:56 2020] gm_et_linux_64/hmm_to_gtf.pl  --in .P10-008/temp/GeneMark_ES/output/gmhmm/dna.fa_1998.out  --app  --out genemark.gtf  --min 300
tomasbruna commented 4 years ago

Hello,

can you try using the latest version of gmes_petap, from http://topaz.gatech.edu/GeneMark/license_download.cgi -- If you are not already using it. Just want to make sure the error has not been fixed in gmhmm3 already.

If the error persists, please share the model file .P10-008/temp/GeneMark_ES/output/gmhmm.mod, which will give me all necessary data to replicate the error and hopefully figure out what went wrong.

The problem is clearly in the GeneMark-ES section of ProtHint, but I want to make sure -- did you really use the command prothint.py seq.fna --workdir ./temp to run prothint? It should give a warning and exit without a fasta file with proteins as a second argument, I'm surprised it didn't.

Best regards, Tomas