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TransDecoder.Predict produces empty .pep file #145

Closed zjlahey closed 2 years ago

zjlahey commented 2 years ago

Hi,

I'm running TransDecoder (v 5.5.0) on a Trinity (v 2.13.2) transcriptome assembly. The TransDecoder.LongOrfs script works fine, but I'm running into problems with TransDecoder.Predict. The relevant portions of the log file are below. The problems start with the "Training start codon pattern recognition" step. I'm running both the LongOrfs and Predict scripts from the same directory.

Commands used: /project/usvl_vector/TransDecoder/TransDecoder.LongOrfs -t 8_exitianus_SRA_reads_adapters_removed_corrected_trinity.Trinity.fasta -O transdecoder

/project/usvl_vector/TransDecoder/TransDecoder.Predict -t transdecoder/longest_orfs.pep -O transdecoder

Log: Training start codon pattern recognition* Running CMD: /lustre/project/usvl_vect or/TransDecoder/util/PWM/buildatgPWM+-.pl --transcripts transdecoder/longest_ orfs.pep --selected_orfs transdecoder/longest_orfs.cds.top_500_longest --out_p refix transdecoder/start_refinement --pwm_left 20 --pwm_right 10 Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91. substr outside of string at /lustre/project/usvl_vector/TransDecoder/util/PWM/bu ildatgPWM+-.pl line 99. Use of uninitialized value $start_codon in string ne at /lustre/project/usvl_vec tor/TransDecoder/util/PWM/buildatgPWM+-.pl line 100. Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91. substr outside of string at /lustre/project/usvl_vector/TransDecoder/util/PWM/bu ildatgPWM+-.pl line 99. Use of uninitialized value $start_codon in string ne at /lustre/project/usvl_vec tor/TransDecoder/util/PWM/buildatgPWM+-.pl line 100. Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91.

brianjohnhaas commented 2 years ago

Hi,

The parameter "-t 8_exitianus_SRA_reads_adapters_removed_corrected_trinity.Trinity.fasta" should be the same for both transdecoder steps.

You might need to rerun it in a new directory so it avoids reusing any of the earlier outputs up to the stage where it crashed.

best,

~b

On Sun, Feb 20, 2022 at 8:45 AM Zachary Lahey @.***> wrote:

Hi,

I'm running TransDecoder (v 5.5.0) on a Trinity (v 2.13.2) transcriptome assembly. The TransDecoder.LongOrfs script works fine, but I'm running into problems with TransDecoder.Predict. The relevant portions of the log file are below. The problems start with the "Training start codon pattern recognition" step. I'm running both the LongOrfs and Predict scripts from the same directory.

Commands used: `/project/usvl_vector/TransDecoder/TransDecoder.LongOrfs -t 8_exitianus_SRA_reads_adapters_removed_corrected_trinity.Trinity.fasta -O transdecoder

/project/usvl_vector/TransDecoder/TransDecoder.Predict -t transdecoder/longest_orfs.pep -O transdecoder`

Log: `Training start codon pattern recognition* Running CMD: /lustre/project/usvl_vect or/TransDecoder/util/PWM/buildatgPWM+-.pl --transcripts transdecoder/longest_ orfs.pep --selected_orfs transdecoder/longest_orfs.cds.top_500_longest --out_p refix transdecoder/start_refinement --pwm_left 20 --pwm_right 10 Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91. substr outside of string at /lustre/project/usvl_vector/TransDecoder/util/PWM/bu ildatgPWM+-.pl line 99. Use of uninitialized value $start_codon in string ne at /lustre/project/usvl_vec tor/TransDecoder/util/PWM/buildatgPWM+-.pl line 100. Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91. substr outside of string at /lustre/project/usvl_vector/TransDecoder/util/PWM/bu ildatgPWM+-.pl line 99. Use of uninitialized value $start_codon in string ne at /lustre/project/usvl_vec tor/TransDecoder/util/PWM/buildatgPWM+-.pl line 100. Use of uninitialized value within %seqs in uc at /lustre/project/usvl_vector/Tra nsDecoder/util/PWM/buildatgPWM+-.pl line 91.

-

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/feature_scoring .+-.pl --features_plus transdecoder/start_refinement.+.features --features_min us transdecoder/start_refinement.-.features --atg_position 20 > transdecoder/s tart_refinement.feature.scores Use of uninitialized value $pwm_length in subtraction (-) at /lustre/project/usv l_vector/TransDecoder/util/PWM/feature_scoring.+-.pl line 82. -round: 1 -round: 2 -round: 3 -round: 4 -round: 5

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/featurescores to_ROC.pl transdecoder/start_refinement.feature.scores > transdecoder/start_refi nement.feature.scores.roc -parsing scores Use of uninitialized value $min_val in subtraction (-) at /lustre/project/usvl_v ector/TransDecoder/util/PWM/feature_scores_to_ROC.pl line 46. Use of uninitialized value $max_val in subtraction (-) at /lustre/project/usvl_v ector/TransDecoder/util/PWM/feature_scores_to_ROC.pl line 46.

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/plot_ROC.Rscrip t transdecoder/start_refinement.feature.scores.roc || : /usr/bin/env: Rscript: No such file or directory

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/compute_AUC.pl transdecoder/start_refinement.feature.scores.roc Can't exec "Rscript": No such file or directory at /lustre/project/usvl_vector/T ransDecoder/util/PWM/compute_AUC.pl line 82.

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/make_seqLogo.Rs cript transdecoder/start_refinement.+.pwm || : /usr/bin/env: Rscript: No such file or directory

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/make_seqLogo.Rs cript transdecoder/start_refinement.-.pwm || : /usr/bin/env: Rscript: No such file or directory

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/deplete_feature _noise.pl --features_plus transdecoder/start_refinement.+.features --pwm_minus transdecoder/start_refinement.-.pwm --out_prefix transdecoder/start_refinement .enhanced num features: 0 num_incorporate: 0 -num feature swaps: 0

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/feature_scoring .+-.pl --features_plus transdecoder/start_refinement.enhanced.+.features --fea tures_minus transdecoder/start_refinement.-.features --atg_position 20

trans decoder/start_refinement.enhanced.feature.scores Use of uninitialized value $pwm_length in subtraction (-) at /lustre/project/usv l_vector/TransDecoder/util/PWM/feature_scoring.+-.pl line 82. -round: 1 -round: 2 -round: 3 -round: 4 -round: 5

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/featurescores to_ROC.pl transdecoder/start_refinement.enhanced.feature.scores > transdecoder/s tart_refinement.enhanced.feature.scores.roc -parsing scores Use of uninitialized value $min_val in subtraction (-) at /lustre/project/usvl_v ector/TransDecoder/util/PWM/feature_scores_to_ROC.pl line 46. Use of uninitialized value $max_val in subtraction (-) at /lustre/project/usvl_v ector/TransDecoder/util/PWM/feature_scores_to_ROC.pl line 46.

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/plot_ROC.Rscrip t transdecoder/start_refinement.enhanced.feature.scores.roc || : /usr/bin/env: Rscript: No such file or directory

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/compute_AUC.pl transdecoder/start_refinement.enhanced.feature.scores.roc Can't exec "Rscript": No such file or directory at /lustre/project/usvl_vector/T ransDecoder/util/PWM/compute_AUC.pl line 82.

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/PWM/make_seqLogo.Rs cript transdecoder/start_refinement.enhanced.+.pwm || : /usr/bin/env: Rscript: No such file or directory

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/start_codon_refinem ent.pl --transcripts transdecoder/longest_orfs.pep --gff3_file transdecoder/long est_orfs.cds.bestcandidates.gff3 --workdir transdecoder > transdecoder/longest orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections.Use of uninitialized value $pwm_range_left in su btraction (-) at /lustre/project/usvl_vector/TransDecoder/util/start_codon_refin ement.pl line 105. Use of uninitialized value $pwm_range_right in addition (+) at /lustre/project/u svl_vector/TransDecoder/util/start_codon_refinement.pl line 105.

Running CMD: cp transdecoder/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 longest_orfs.pep.transdecoder.gff3 copying output to final output file: longest_orfs.pep.transdecoder.gff3* Running CMD: /lustre/project/usvl_vector/TransDecoder/util/gff3_file_to_bed.pl longest_orfs.pep.transdecoder.gff3 > longest_orfs.pep.transdecoder.bed Making bed file: longest_orfs.pep.transdecoder.bed

Running CMD: /lustre/project/usvl_vector/TransDecoder/util/ gff3_file_to_proteins.pl --gff3 longest_orfs.pep.transdecoder.gff3 --fasta transdecoder/longest_orfs.pep --genetic_code Universal > longest_orfs.pep.transdecoder.pep Making pep file: longest_orfs.pep.transdecoder.pep Error, no sequence for TRINITY_DN0_c0_g1_i1 at /lustre/project/usvl_vector/TransDecoder/util/gff3_file_to_proteins.pl line 82. Error, cmd: /lustre/project/usvl_vector/TransDecoder/util/ gff3_file_to_proteins.pl --gff3 longest_orfs.pep.transdecoder.gff3 --fasta transdecoder/longest_orfs.pep --genetic_code Universal > longest_orfs.pep.transdecoder.pep died with ret 65280 No such file or directory at /lustre/project/usvl_vector/TransDecoder/PerlLib/Pipeliner.pm line 185. Pipeliner::run('Pipeliner=HASH(0x21b3448)') called at /project/usvl_vector/TransDecoder/TransDecoder.Predict line 379`

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--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

zjlahey commented 2 years ago

I'm not sure why I was running predict with the pep file. Thanks for clearing this up!