Genemark auto-annotator

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Genemark auto-annotator

katebush-2
Hello,

Well, I've got MAKER up and running (Yeah, so far it is GREAT).  One
question.  Both snap and augustus have an "auto"-annotator output but
this doesn't seem to happen for genemark (is this normal)...I'm not
getting any error messages but just wanted to check and make sure I
wasn't skipping something or does the below output look good?

Thanks,

Kathryn

CTL_OPTIONS genome_gff
CTL_OPTIONS other_gff
CTL_OPTIONS est
CTL_OPTIONS est_reads
CTL_OPTIONS altest /raid4/spatafora/bushleyk/Sequences/ESTs/
Cmilitaris_ESTs.fasta
CTL_OPTIONS est_gff
CTL_OPTIONS altest_gff
CTL_OPTIONS protein /raid4/spatafora/yoderr/hal_contigs_run/genomes/
Fusarium_graminearum.fasta
CTL_OPTIONS protein_gff
CTL_OPTIONS model_org all
CTL_OPTIONS repeat_protein /raid4/spatafora/bushleyk/Sequences/Repeats/
Ti_TeProteins.txt
CTL_OPTIONS rmlib /raid4/spatafora/bushleyk/Sequences/Repeats/
Ti_RepeatLib.txt
CTL_OPTIONS rm_gff
CTL_OPTIONS organism_type eukaryotic
CTL_OPTIONS predictor est2genome,snap,augustus,genemark
CTL_OPTIONS run augustus,genemark,snap
CTL_OPTIONS snaphmm /local/cluster/spatafora/SNAP/snap/HMM/
fusarium_graminearum_1.length.hmm
CTL_OPTIONS gmhmm /local/cluster/spatafora/genemark_hmm_euk.linux/
Tinflatum_BH2_52310.mod
CTL_OPTIONS augustus_species fusarium_graminearum
CTL_OPTIONS fgenesh_par_file
CTL_OPTIONS model_gff
CTL_OPTIONS pred_gff
CTL_OPTIONS max_dna_len 100000
CTL_OPTIONS split_hit 10000
CTL_OPTIONS pred_flank 200
CTL_OPTIONS min_protein 0
CTL_OPTIONS single_exon 0
CTL_OPTIONS single_length 250
CTL_OPTIONS keep_preds 0
CTL_OPTIONS map_forward 0
CTL_OPTIONS alt_peptide C
CTL_OPTIONS evaluate 0
CTL_OPTIONS blast_type wublast
CTL_OPTIONS softmask 1
CTL_OPTIONS pcov_blastn 0.8
CTL_OPTIONS pid_blastn 0.85
CTL_OPTIONS eval_blastn 1e-10
CTL_OPTIONS bit_blastn 40
CTL_OPTIONS pcov_rm_blastx 0.5
CTL_OPTIONS pid_rm_blastx 0.4
CTL_OPTIONS eval_rm_blastx 1e-06
CTL_OPTIONS bit_rm_blastx 30
CTL_OPTIONS pcov_blastx 0.5
CTL_OPTIONS pid_blastx 0.4
CTL_OPTIONS eval_blastx 1e-06
CTL_OPTIONS bit_blastx 30
CTL_OPTIONS pcov_tblastx 0.8
CTL_OPTIONS pid_tblastx 0.85
CTL_OPTIONS eval_tblastx 1e-10
CTL_OPTIONS bit_tblastx 40
CTL_OPTIONS ep_score_limit 20
CTL_OPTIONS en_score_limit 20
CTL_OPTIONS enable_fathom 0
CTL_OPTIONS unmask 1
CTL_OPTIONS model_pass 1
CTL_OPTIONS est_pass 0
CTL_OPTIONS altest_pass 0
CTL_OPTIONS protein_pass 0
CTL_OPTIONS rm_pass 0
CTL_OPTIONS other_pass 0
CTL_OPTIONS pred_pass 0
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.out
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.out
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.specific.out
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.specific.out
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.genemark
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.genemark
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.genemark
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.genemark
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.snap
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.augustus
FINISHED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.augustus

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Re: Genemark auto-annotator

Carson Hinton Holt
Re: [maker-devel] Genemark auto-annotator The "auto"-annotator output are the hint based gene predictions where MAKER talks to the gene predictors and tells them where the most probable splice sites and protein coding regions are based on homology evidence.  GeneMark has not yet documented a hint based prediction procedure (although I think it does have one), so MAKER only produces ab initio predictions for GeneMark which means no "auto"-annotator output.

I hope that helps,
Carson



On 5/25/10 5:52 PM, "katebush" <kbushley@...> wrote:

Hello,

Well, I've got MAKER up and running (Yeah, so far it is GREAT).  One
question.  Both snap and augustus have an "auto"-annotator output but
this doesn't seem to happen for genemark (is this normal)...I'm not
getting any error messages but just wanted to check and make sure I
wasn't skipping something or does the below output look good?

Thanks,

Kathryn

CTL_OPTIONS     genome_gff
CTL_OPTIONS     other_gff
CTL_OPTIONS     est
CTL_OPTIONS     est_reads
CTL_OPTIONS     altest  /raid4/spatafora/bushleyk/Sequences/ESTs/
Cmilitaris_ESTs.fasta
CTL_OPTIONS     est_gff
CTL_OPTIONS     altest_gff
CTL_OPTIONS     protein /raid4/spatafora/yoderr/hal_contigs_run/genomes/
Fusarium_graminearum.fasta
CTL_OPTIONS     protein_gff
CTL_OPTIONS     model_org       all
CTL_OPTIONS     repeat_protein  /raid4/spatafora/bushleyk/Sequences/Repeats/
Ti_TeProteins.txt
CTL_OPTIONS     rmlib   /raid4/spatafora/bushleyk/Sequences/Repeats/
Ti_RepeatLib.txt
CTL_OPTIONS     rm_gff
CTL_OPTIONS     organism_type   eukaryotic
CTL_OPTIONS     predictor       est2genome,snap,augustus,genemark
CTL_OPTIONS     run     augustus,genemark,snap
CTL_OPTIONS     snaphmm /local/cluster/spatafora/SNAP/snap/HMM/
fusarium_graminearum_1.length.hmm
CTL_OPTIONS     gmhmm   /local/cluster/spatafora/genemark_hmm_euk.linux/
Tinflatum_BH2_52310.mod
CTL_OPTIONS     augustus_species        fusarium_graminearum
CTL_OPTIONS     fgenesh_par_file
CTL_OPTIONS     model_gff
CTL_OPTIONS     pred_gff
CTL_OPTIONS     max_dna_len     100000
CTL_OPTIONS     split_hit       10000
CTL_OPTIONS     pred_flank      200
CTL_OPTIONS     min_protein     0
CTL_OPTIONS     single_exon     0
CTL_OPTIONS     single_length   250
CTL_OPTIONS     keep_preds      0
CTL_OPTIONS     map_forward     0
CTL_OPTIONS     alt_peptide     C
CTL_OPTIONS     evaluate        0
CTL_OPTIONS     blast_type      wublast
CTL_OPTIONS     softmask        1
CTL_OPTIONS     pcov_blastn     0.8
CTL_OPTIONS     pid_blastn      0.85
CTL_OPTIONS     eval_blastn     1e-10
CTL_OPTIONS     bit_blastn      40
CTL_OPTIONS     pcov_rm_blastx  0.5
CTL_OPTIONS     pid_rm_blastx   0.4
CTL_OPTIONS     eval_rm_blastx  1e-06
CTL_OPTIONS     bit_rm_blastx   30
CTL_OPTIONS     pcov_blastx     0.5
CTL_OPTIONS     pid_blastx      0.4
CTL_OPTIONS     eval_blastx     1e-06
CTL_OPTIONS     bit_blastx      30
CTL_OPTIONS     pcov_tblastx    0.8
CTL_OPTIONS     pid_tblastx     0.85
CTL_OPTIONS     eval_tblastx    1e-10
CTL_OPTIONS     bit_tblastx     40
CTL_OPTIONS     ep_score_limit  20
CTL_OPTIONS     en_score_limit  20
CTL_OPTIONS     enable_fathom   0
CTL_OPTIONS     unmask  1
CTL_OPTIONS     model_pass      1
CTL_OPTIONS     est_pass        0
CTL_OPTIONS     altest_pass     0
CTL_OPTIONS     protein_pass    0
CTL_OPTIONS     rm_pass 0
CTL_OPTIONS     other_pass      0
CTL_OPTIONS     pred_pass       0
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.out
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.out
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.specific.out
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.specific.out
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.genemark
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.masked.all.genemark
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.genemark
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.all.genemark
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/
NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.snap
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.snap
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.augustus
STARTED BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.augustus
FINISHED        BH2Test.maker.output/BH2Test_datastore/
NODE_2_length_31385_cov_30.175402/
theVoid.NODE_2_length_31385_cov_30.175402/6.30252.auto_annotator.augustus

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Re: Genemark auto-annotator

katebush-2
Hello Carson,

Thanks.  I was trying to install the MPI version this week but then I
saw the release of the new version with paralellism (THANKS!) as now I
no longer have to meddle with the MPICH2 "daemons".

One more question about output.  For some of my contigs, in the main
folder (not TheVoid) folder, I'm not getting a maker.proteins or
maker.transcrips files but from the log inside the void folder, it's
clear it ran Augustus and Snap also.  I'm assuming this means there
wasn't any agreement between all the methods for valid proteins?

Also, has anyone written a script to concatenate all the maker
annotations/results from all the contigs into a single file...or is
this in the output somewhere...about to do that.

Thanks,

Kathryn Bushley



On May 26, 8:39 am, Carson Holt <[hidden email]> wrote:

> The "auto"-annotator output are the hint based gene predictions where MAKER talks to the gene predictors and tells them where the most probable splice sites and protein coding regions are based on homology evidence.  GeneMark has not yet documented a hint based prediction procedure (although I think it does have one), so MAKER only produces ab initio predictions for GeneMark which means no "auto"-annotator output.
>
> I hope that helps,
> Carson
>
> On 5/25/10 5:52 PM, "katebush" <[hidden email]> wrote:
>
> Hello,
>
> Well, I've got MAKER up and running (Yeah, so far it is GREAT).  One
> question.  Both snap and augustus have an "auto"-annotator output but
> this doesn't seem to happen for genemark (is this normal)...I'm not
> getting any error messages but just wanted to check and make sure I
> wasn't skipping something or does the below output look good?
>
> Thanks,
>
> Kathryn
>
> CTL_OPTIONS     genome_gff
> CTL_OPTIONS     other_gff
> CTL_OPTIONS     est
> CTL_OPTIONS     est_reads
> CTL_OPTIONS     altest  /raid4/spatafora/bushleyk/Sequences/ESTs/
> Cmilitaris_ESTs.fasta
> CTL_OPTIONS     est_gff
> CTL_OPTIONS     altest_gff
> CTL_OPTIONS     protein /raid4/spatafora/yoderr/hal_contigs_run/genomes/
> Fusarium_graminearum.fasta
> CTL_OPTIONS     protein_gff
> CTL_OPTIONS     model_org       all
> CTL_OPTIONS     repeat_protein  /raid4/spatafora/bushleyk/Sequences/Repeats/
> Ti_TeProteins.txt
> CTL_OPTIONS     rmlib   /raid4/spatafora/bushleyk/Sequences/Repeats/
> Ti_RepeatLib.txt
> CTL_OPTIONS     rm_gff
> CTL_OPTIONS     organism_type   eukaryotic
> CTL_OPTIONS     predictor       est2genome,snap,augustus,genemark
> CTL_OPTIONS     run     augustus,genemark,snap
> CTL_OPTIONS     snaphmm /local/cluster/spatafora/SNAP/snap/HMM/
> fusarium_graminearum_1.length.hmm
> CTL_OPTIONS     gmhmm   /local/cluster/spatafora/genemark_hmm_euk.linux/
> Tinflatum_BH2_52310.mod
> CTL_OPTIONS     augustus_species        fusarium_graminearum
> CTL_OPTIONS     fgenesh_par_file
> CTL_OPTIONS     model_gff
> CTL_OPTIONS     pred_gff
> CTL_OPTIONS     max_dna_len     100000
> CTL_OPTIONS     split_hit       10000
> CTL_OPTIONS     pred_flank      200
> CTL_OPTIONS     min_protein     0
> CTL_OPTIONS     single_exon     0
> CTL_OPTIONS     single_length   250
> CTL_OPTIONS     keep_preds      0
> CTL_OPTIONS     map_forward     0
> CTL_OPTIONS     alt_peptide     C
> CTL_OPTIONS     evaluate        0
> CTL_OPTIONS     blast_type      wublast
> CTL_OPTIONS     softmask        1
> CTL_OPTIONS     pcov_blastn     0.8
> CTL_OPTIONS     pid_blastn      0.85
> CTL_OPTIONS     eval_blastn     1e-10
> CTL_OPTIONS     bit_blastn      40
> CTL_OPTIONS     pcov_rm_blastx  0.5
> CTL_OPTIONS     pid_rm_blastx   0.4
> CTL_OPTIONS     eval_rm_blastx  1e-06
> CTL_OPTIONS     bit_rm_blastx   30
> CTL_OPTIONS     pcov_blastx     0.5
> CTL_OPTIONS     pid_blastx      0.4
> CTL_OPTIONS     eval_blastx     1e-06
> CTL_OPTIONS     bit_blastx      30
> CTL_OPTIONS     pcov_tblastx    0.8
> CTL_OPTIONS     pid_tblastx     0.85
> CTL_OPTIONS     eval_tblastx    1e-10
> CTL_OPTIONS     bit_tblastx     40
> CTL_OPTIONS     ep_score_limit  20
> CTL_OPTIONS     en_score_limit  20
> CTL_OPTIONS     enable_fathom   0
> CTL_OPTIONS     unmask  1
> CTL_OPTIONS     model_pass      1
> CTL_OPTIONS     est_pass        0
> CTL_OPTIONS     altest_pass     0
> CTL_OPTIONS     protein_pass    0
> CTL_OPTIONS     rm_pass 0
> CTL_OPTIONS     other_pass      0
> CTL_OPTIONS     pred_pass       0
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.out
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.out
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.specific.out
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.specific.out
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.augustus
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.augustus
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.genemark
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.genemark
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.augustus
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.augustus
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.genemark
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.genemark
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/ ...
>
> read more »
>
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Re: Genemark auto-annotator

Carson Hinton Holt
Re: [maker-devel] Genemark auto-annotator So if MAKER doesn’t believe there is enough evidence to support a gene model, then it won’t promote snap and augustus gene predictions to the status of gene annotation.  It is still in the evidence tier though, and MAKER will give you all the snap and augustus predictions for you to decide if you want to promote them yourself either via manual curation in Apollo or by adding them to GFF3 pass-through in the MAKER gff_model option.

To combine the GFF3 files use the gff3_merge script that comes with MAKER.  You can either give it a list of all GFF3 files to combine, or give it the master_datastore_index.log file that MAKER produced.  There is also a fasta_merge that works the same way.  I recommend giving both scripts the master_datastore_index.log rather than a list of files, because there are some exrta bells and whistles you get in the output especially for fasta_merge.

Thanks,
Carson


On 5/28/10 3:12 PM, "katebush" <kbushley@...> wrote:

Hello Carson,

Thanks.  I was trying to install the MPI version this week but then I
saw the release of the new version with paralellism (THANKS!) as now I
no longer have to meddle with the MPICH2 "daemons".

One more question about output.  For some of my contigs, in the main
folder (not TheVoid) folder, I'm not getting a maker.proteins or
maker.transcrips files but from the log inside the void folder, it's
clear it ran Augustus and Snap also.  I'm assuming this means there
wasn't any agreement between all the methods for valid proteins?

Also, has anyone written a script to concatenate all the maker
annotations/results from all the contigs into a single file...or is
this in the output somewhere...about to do that.

Thanks,

Kathryn Bushley



On May 26, 8:39 am, Carson Holt <carson.h...@...> wrote:
> The "auto"-annotator output are the hint based gene predictions where MAKER talks to the gene predictors and tells them where the most probable splice sites and protein coding regions are based on homology evidence.  GeneMark has not yet documented a hint based prediction procedure (although I think it does have one), so MAKER only produces ab initio predictions for GeneMark which means no "auto"-annotator output.
>
> I hope that helps,
> Carson
>
> On 5/25/10 5:52 PM, "katebush" <kbush...@...> wrote:
>
> Hello,
>
> Well, I've got MAKER up and running (Yeah, so far it is GREAT).  One
> question.  Both snap and augustus have an "auto"-annotator output but
> this doesn't seem to happen for genemark (is this normal)...I'm not
> getting any error messages but just wanted to check and make sure I
> wasn't skipping something or does the below output look good?
>
> Thanks,
>
> Kathryn
>
> CTL_OPTIONS     genome_gff
> CTL_OPTIONS     other_gff
> CTL_OPTIONS     est
> CTL_OPTIONS     est_reads
> CTL_OPTIONS     altest  /raid4/spatafora/bushleyk/Sequences/ESTs/
> Cmilitaris_ESTs.fasta
> CTL_OPTIONS     est_gff
> CTL_OPTIONS     altest_gff
> CTL_OPTIONS     protein /raid4/spatafora/yoderr/hal_contigs_run/genomes/
> Fusarium_graminearum.fasta
> CTL_OPTIONS     protein_gff
> CTL_OPTIONS     model_org       all
> CTL_OPTIONS     repeat_protein  /raid4/spatafora/bushleyk/Sequences/Repeats/
> Ti_TeProteins.txt
> CTL_OPTIONS     rmlib   /raid4/spatafora/bushleyk/Sequences/Repeats/
> Ti_RepeatLib.txt
> CTL_OPTIONS     rm_gff
> CTL_OPTIONS     organism_type   eukaryotic
> CTL_OPTIONS     predictor       est2genome,snap,augustus,genemark
> CTL_OPTIONS     run     augustus,genemark,snap
> CTL_OPTIONS     snaphmm /local/cluster/spatafora/SNAP/snap/HMM/
> fusarium_graminearum_1.length.hmm
> CTL_OPTIONS     gmhmm   /local/cluster/spatafora/genemark_hmm_euk.linux/
> Tinflatum_BH2_52310.mod
> CTL_OPTIONS     augustus_species        fusarium_graminearum
> CTL_OPTIONS     fgenesh_par_file
> CTL_OPTIONS     model_gff
> CTL_OPTIONS     pred_gff
> CTL_OPTIONS     max_dna_len     100000
> CTL_OPTIONS     split_hit       10000
> CTL_OPTIONS     pred_flank      200
> CTL_OPTIONS     min_protein     0
> CTL_OPTIONS     single_exon     0
> CTL_OPTIONS     single_length   250
> CTL_OPTIONS     keep_preds      0
> CTL_OPTIONS     map_forward     0
> CTL_OPTIONS     alt_peptide     C
> CTL_OPTIONS     evaluate        0
> CTL_OPTIONS     blast_type      wublast
> CTL_OPTIONS     softmask        1
> CTL_OPTIONS     pcov_blastn     0.8
> CTL_OPTIONS     pid_blastn      0.85
> CTL_OPTIONS     eval_blastn     1e-10
> CTL_OPTIONS     bit_blastn      40
> CTL_OPTIONS     pcov_rm_blastx  0.5
> CTL_OPTIONS     pid_rm_blastx   0.4
> CTL_OPTIONS     eval_rm_blastx  1e-06
> CTL_OPTIONS     bit_rm_blastx   30
> CTL_OPTIONS     pcov_blastx     0.5
> CTL_OPTIONS     pid_blastx      0.4
> CTL_OPTIONS     eval_blastx     1e-06
> CTL_OPTIONS     bit_blastx      30
> CTL_OPTIONS     pcov_tblastx    0.8
> CTL_OPTIONS     pid_tblastx     0.85
> CTL_OPTIONS     eval_tblastx    1e-10
> CTL_OPTIONS     bit_tblastx     40
> CTL_OPTIONS     ep_score_limit  20
> CTL_OPTIONS     en_score_limit  20
> CTL_OPTIONS     enable_fathom   0
> CTL_OPTIONS     unmask  1
> CTL_OPTIONS     model_pass      1
> CTL_OPTIONS     est_pass        0
> CTL_OPTIONS     altest_pass     0
> CTL_OPTIONS     protein_pass    0
> CTL_OPTIONS     rm_pass 0
> CTL_OPTIONS     other_pass      0
> CTL_OPTIONS     pred_pass       0
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.out
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.out
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.specific.out
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.specific.out
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Ti_TeProteins.txt.blastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.augustus
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.augustus
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.genemark
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.masked.all.genemark
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.augustus
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.augustus
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.genemark
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.all.genemark
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Fusarium_graminearum.blastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.0.Cmilitaris_ESTs.tblastx
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.4691.6314.FGSG_05375.p_exonerate
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/
> NODE_2_length_31385_cov_30.175402.20045.21449.FGSG_04023.p_exonerate
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/0.4540.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/1.11892.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/2.1207.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/3.4510.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/4.17225.auto_annotator.snap
> STARTED BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/
> theVoid.NODE_2_length_31385_cov_30.175402/5.19362.auto_annotator.snap
> FINISHED        BH2Test.maker.output/BH2Test_datastore/
> NODE_2_length_31385_cov_30.175402/ ...
>
> read more »
>
> _______________________________________________
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