TransDecoder.Predict Error

[Clifton Lewis]

Hi,

I downloaded varioud transcriptomes from EBI and I am running them trhough TransDecoder and it fails for half the sequences. I'm unsure as to what the cause of the issue is. Anyone have any suggestions ? Thanks in advance.

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/get_top_longest_fasta_entries.pl Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest

PCT_GC: 56.6

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/seq_n_baseprobs_to_loglikelihood_vals.pl Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest Culex_tarsalis_GFDL01.fasta.transdecoder_dir/base_freqs.dat > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/hexamer.scores

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/score_CDS_likelihood_all_6_frames.pl Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds Culex_tarsalis_GFDL01.fasta.transdecoder_dir/hexamer.scores > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.scores

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 927  --blast_hits cult_blastp.outfmt6  > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 

Selecting best orfsblastp output found (cult_blastp.outfmt6) and processing...

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/train_start_PWM.pl --transcripts Culex_tarsalis_GFDL01.fasta --selected_orfs Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement

Training start codon pattern recognition* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/build_atgPWM_+-.pl  --transcripts Culex_tarsalis_GFDL01.fasta  --selected_orfs Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest  --out_prefix Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 

Error, feature_seq: NNNNNNNNNTGGGGCTCCGGATGGCCACCGTCC contains non-GATC chars... skipping

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/feature_scoring.+-.pl  --features_plus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.+.features  --features_minus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.-.features  --atg_position 20  > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.feature.scores

-round: 1

Error, feature_seq: NNNNNNNNNTGGGGCTCCGGATGGCCACCGTCC contains non-GATC chars... skipping

-round: 2

Error, feature_seq: NNNNNNNNNTGGGGCTCCGGATGGCCACCGTCC contains non-GATC chars... skipping

-round: 3

Error, feature_seq: NNNNNNNNNTGGGGCTCCGGATGGCCACCGTCC contains non-GATC chars... skipping

-round: 4

Error, feature_seq: NNNNNNNNNTGGGGCTCCGGATGGCCACCGTCC contains non-GATC chars... skipping

-round: 5

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/feature_scores_to_ROC.pl Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.feature.scores > Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.feature.scores.roc

-parsing scores

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/plot_ROC.Rscript Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.feature.scores.roc || :

/usr/bin/env: Rscript: No such file or directory

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/compute_AUC.pl Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.feature.scores.roc

Can't exec "Rscript": No such file or directory at /cm/shared/apps/transdecoder/5.5.0/util/PWM/compute_AUC.pl line 82.

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/make_seqLogo.Rscript Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.+.pwm || :

/usr/bin/env: Rscript: No such file or directory

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/make_seqLogo.Rscript Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.-.pwm || :

/usr/bin/env: Rscript: No such file or directory

* Running CMD: /cm/shared/apps/transdecoder/5.5.0/util/PWM/deplete_feature_noise.pl  --features_plus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.+.features  --pwm_minus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.-.pwm  --out_prefix Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.enhanced

num features: 3 num_incorporate: 0

Error, len(target_sequence)=33 and pwm length = 0 at /cm/shared/apps/transdecoder/5.5.0/util/PWM/../../PerlLib/PWM.pm line 337.

PWM::score_plus_minus_pwm('PWM=HASH(0x87faa8)', 'AGGTTAGCCAGAGTTCCCTCATGCTGGATGTTG', 'PWM=HASH(0x623bc0)') called at /cm/shared/apps/transdecoder/5.5.0/util/PWM/deplete_feature_noise.pl line 116

Error, cmd: /cm/shared/apps/transdecoder/5.5.0/util/PWM/deplete_feature_noise.pl  --features_plus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.+.features  --pwm_minus Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.-.pwm  --out_prefix Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement.enhanced died with ret 65280 No such file or directory at /cm/shared/apps/transdecoder/5.5.0/util/../PerlLib/Pipeliner.pm line 185.

Pipeliner::run('Pipeliner=HASH(0x623b90)') called at /cm/shared/apps/transdecoder/5.5.0/util/train_start_PWM.pl line 141

Error, cmd: /cm/shared/apps/transdecoder/5.5.0/util/train_start_PWM.pl --transcripts Culex_tarsalis_GFDL01.fasta --selected_orfs Culex_tarsalis_GFDL01.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Culex_tarsalis_GFDL01.fasta.transdecoder_dir/start_refinement died with ret 512 No such file or directory at /cm/shared/apps/transdecoder/5.5.0/PerlLib/Pipeliner.pm line 185.

Pipeliner::run('Pipeliner=HASH(0xe49188)') called at /cm/shared/apps/transdecoder/5.5.0/TransDecoder.Predict line 379

Thanks,

Clifton