error when ran TransDecoder.Predict in TransDecoder-v5.0.2

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Junxia Zhang

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Nov 30, 2017, 6:30:08 PM11/30/17
to TransDecoder-users
Hello,

I am using TransDecoder-v5.0.2 for coding region prediction of ~5000 transcripts. But when I execute "perl TransDecoder.Predict -t ChalcidCOS.5591.transcripts.fas", it always returns me following error message. Can anyone help me out with this?

Thanks a lot!

Junxia

....
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/feature_scores_to_ROC.pl ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.feature.scores > ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.feature.scores.roc
-parsing scores
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/plot_ROC.Rscript ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.feature.scores.roc || :
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/compute_AUC.pl ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.feature.scores.roc
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/make_seqLogo.Rscript ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.+.pwm || :
Error in library(seqLogo) : there is no package called ‘seqLogo’
Execution halted
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/make_seqLogo.Rscript ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.-.pwm || :
Error in library(seqLogo) : there is no package called ‘seqLogo’
Execution halted
* Running CMD: /Applications/TransDecoder-v5.0.2/util/PWM/deplete_feature_noise.pl  --features_plus ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.+.features  --pwm_minus ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.-.pwm  --out_prefix ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.enhanced
num features: 3 num_incorporate: 0
Error, len(target_sequence)=33 and pwm length = 0 at /Applications/TransDecoder-v5.0.2/util/PWM/deplete_feature_noise.pl line 116.
Error, cmd: /Applications/TransDecoder-v5.0.2/util/PWM/deplete_feature_noise.pl  --features_plus ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.+.features  --pwm_minus ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.-.pwm  --out_prefix ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement.enhanced died with ret 65280 at /Applications/TransDecoder-v5.0.2/util/../PerlLib/Pipeliner.pm line 166.
Pipeliner::run(Pipeliner=HASH(0x7f94f002d9e0)) called at /Applications/TransDecoder-v5.0.2/util/train_start_PWM.pl line 141
Error, cmd: /Applications/TransDecoder-v5.0.2/util/train_start_PWM.pl --transcripts ChalcidCOS.5591.transcripts.fas --selected_orfs ChalcidCOS.5591.transcripts.fas.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix ChalcidCOS.5591.transcripts.fas.transdecoder_dir/start_refinement died with ret 512 at /Applications/TransDecoder-v5.0.2/PerlLib/Pipeliner.pm line 166.
Pipeliner::run(Pipeliner=HASH(0x7ff7321d31a8)) called at TransDecoder.Predict line 321

Brian Haas

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Nov 30, 2017, 9:19:00 PM11/30/17
to Junxia Zhang, TransDecoder-users
Hi Junxia,

It looks like there are too few sequences for it to model the start site.   Try running it with --no_refine_starts

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Junxia Zhang

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Dec 1, 2017, 2:12:42 PM12/1/17
to Brian Haas, TransDecoder-users
Hello Brian,

Yes, it works! Thank you very much!

Best regards,
Junxia

Tyler Gibson

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Apr 8, 2019, 3:53:17 PM4/8/19
to TransDecoder-users
Dear Brian,

I have a slightly different warning message (or error message) to the one above.  I'm looking at about 7500 sequences, and filtering with Pfam and with BlastP.  Transdecoder.Predict finishes, but it does twice give me this set of messages (highlighted in red; see below).  I can't tell if the program is running properly or not.

Is this also due to insufficient training data for the start sites (as in the thread below)?

Best regards,
Tyler



* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scores_to_ROC.pl /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.feature.scores > /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.feature.scores.roc
-parsing scores
* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/plot_ROC.Rscript /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.feature.scores.roc || :
/usr/bin/env: Rscript: No such file or directory
* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/compute_AUC.pl /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.feature.scores.roc
Can't exec "Rscript": No such file or directory at /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/compute_AUC.pl line 82.
* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.+.pwm || :
/usr/bin/env: Rscript: No such file or directory
* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.-.pwm || :
/usr/bin/env: Rscript: No such file or directory
* Running CMD: /panfs/ds07/meyerowitz-lab/wtgibson/TransDecoder-TransDecoder-v5.5.0/util/PWM/deplete_feature_noise.pl  --features_plus /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.+.features  --pwm_minus /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.-.pwm  --out_prefix /panfs/ds07/meyerowitz-lab/wtgibson/BROADStrategy/BROAD_STRATEGY_APRIL2019/TransDecoder_ForCufflinksShortSettings/start_refinement.enhanced


Brian Haas

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Apr 8, 2019, 7:00:23 PM4/8/19
to Tyler Gibson, TransDecoder-users
Hi Tyler

You can safely ignore those errors.  It tries to print some diagnostic plots that only I use.  I need to turn that off in the next release.

-via googleFi

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Tyler Gibson

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Apr 8, 2019, 7:15:19 PM4/8/19
to TransDecoder-users
Thank you!

Best,
Tyler
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