Error when run TransDecoder.Predict

[Huyen Phan]

Hi Brian,

I am trying to run TransDecoder.Predict on my Trinity de novo assembly to predict ORF on a very big data set of 2.9mil transcripts. I am using TransDecoder v5.5.0. The 'TransDecoder.LongOrfs' was working fine. For the 2nd step, I run this code :

transdecoder$ TransDecoder.Predict -t all_t1to5_final.fa_cdhit97

and alway run into this error message:

'-- Skipping CMD: /usr/lib/transdecoder/util/get_top_longest_fasta_entries.pl all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds 5000 5000 > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_longest_5000, checkpoint exists.

-- Skipping CMD: /usr/lib/transdecoder/util/exclude_similar_proteins.pl all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_longest_5000 > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr, checkpoint exists.

-- Skipping CMD: /usr/lib/transdecoder/util/get_top_longest_fasta_entries.pl all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_500_longest, checkpoint exists.

PCT_GC: 50.4

-- Skipping CMD: /usr/lib/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.top_500_longest all_t1to5_final.fa_cdhit97.transdecoder_dir/base_freqs.dat > all_t1to5_final.fa_cdhit97.transdecoder_dir/hexamer.scores, checkpoint exists.

-- Skipping CMD: /usr/lib/transdecoder/util/score_CDS_likelihood_all_6_frames.pl all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds all_t1to5_final.fa_cdhit97.transdecoder_dir/hexamer.scores > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.scores, checkpoint exists.

* Running CMD: /usr/lib/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.gff3 --cds_scores all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 797  > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.best_candidates.gff3

-indexing [TRINITY_DN66701_c0_g1::TRINITY_DN66701_c0_g1_i1::g.2150025]  Killed

Error, cmd: /usr/lib/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.gff3 --cds_scores all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 797  > all_t1to5_final.fa_cdhit97.transdecoder_dir/longest_orfs.cds.best_candidates.gff3  died with ret 35072 at /usr/lib/transdecoder/PerlLib/Pipeliner.pm line 166.

        Pipeliner::run(Pipeliner=HASH(0x564344bd4320)) called at /usr/bin/TransDecoder.Predict line 291'

 Would you be able to give me some advice on what the problem would be and how to fix it? 

Thank you very much for your time and help. It is much appreciated.

Kind regards

Huyen

[Brian Haas]

hi,

the error message: 

  -indexing [TRINITY_DN66701_c0_g1::TRINITY_DN66701_c0_g1_i1::g.2150025]  Killed

suggests that you either exceeded the allowed RAM allocation or the process ran out of time on a grid submission.

best,

~b

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--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Huyen Phan]

Hi Brian,

 

Thank you for your suggestions. I have split my big file into 3 smaller ones and they work perfectly.

 

I appreciate your help to our community too.

 

Thanks and kind regards

Huyen