An error occured in TransDecoder.Predict v5.50
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Kun Fang
May 12, 2019, 7:10:37 AM5/12/19
to TransDecoder-users
Hello~
When I use TransDecoder.Predict to deal my data, this a error occured :
those are some details:
root@center:/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0# /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/TransDecoder.Predict -t Trinity.fasta
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000, checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/get_longest_orfs.ok] exists.
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/exclude_similar_proteins.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr, checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/nr.ok] exists.
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest, checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/top_train_select.ok] exists.
PCT_GC: 45
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/seq_n_baseprobs_to_loglikelihood_vals.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest Trinity.fasta.transdecoder_dir/base_freqs.dat > Trinity.fasta.transdecoder_dir/hexamer.scores, checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/hexamer_scores.ok] exists.
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/score_CDS_likelihood_all_6_frames.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds Trinity.fasta.transdecoder_dir/hexamer.scores > Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores, checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/score_cdss.ok] exists.
-- Skipping CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 , checkpoint [/usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/Trinity.fasta.transdecoder_dir.__checkpoints/select_best_orfs.691ea0ee1fcedf5fdce06fe9341cda97.ok] exists.
* Running CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement
Training start codon pattern recognition* Running CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10
* Running CMD: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores
-round: 1
Error, no non-zero probability value specified for char [C] at /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/PWM/../../PerlLib/PWM.pm line 371.
Error, cmd: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores died with ret 65280 No such file or directory at /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/../PerlLib/Pipeliner.pm line 185.
Pipeliner::run(Pipeliner=HASH(0x55f0ff015da8)) called at /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/train_start_PWM.pl line 141
Error, cmd: /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement died with ret 512 No such file or directory at /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/PerlLib/Pipeliner.pm line 185.
Pipeliner::run(Pipeliner=HASH(0x55decc199f28)) called at /usr/bioinformation/TransDecoder-TransDecoder-v5.5.0/TransDecoder.Predict line 379
and how to solve it？
thinks
Brian Haas
May 12, 2019, 8:30:10 AM5/12/19
to Kun Fang, TransDecoder-users
Hi,
You might need to turn off the start codon refinement. There's a command line parameter to do this.
~b
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Kun Fang
May 12, 2019, 9:27:37 AM5/12/19
to TransDecoder-users
Hello
Thank you for answering my question. It worked.
I have few more question:
Could you please tell me there is the differences between turning off and turing on this option?
How does turning off this function affect my final results?
在 2019年5月12日星期日 UTC+8下午8:30:10，Brian Haas写道：
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Brian Haas
May 12, 2019, 7:32:37 PM5/12/19
to Kun Fang, TransDecoder-users
it's better to have it on for more accurate start codon prediction. If you have little data or you're running it on a set of transcripts that lack 5' UTRs, then it'll show the sort of error that you described.
If you turn it off, you'll get the most 5' start position for each orf.
best,
~b
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