Error running TransDecoder.Predict #199
Description
Hello,
I encountered this error:
-- Skipping CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/get_top_longest_fasta_entries.pl /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000, checkpoint [/home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/__checkpoints_TDpredict/get_longest_orfs.ok] exists.
-- Skipping CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/exclude_similar_proteins.pl /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr, checkpoint [/home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/__checkpoints_TDpredict/nr.ok] exists.
-- Skipping CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/get_top_longest_fasta_entries.pl /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest, checkpoint [/home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/__checkpoints_TDpredict/top_train_select.ok] exists.
PCT_GC: 46.2
-- Skipping CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/base_freqs.dat > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/hexamer.scores, checkpoint [/home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/__checkpoints_TDpredict/hexamer_scores.ok] exists.
* [Fri Mar 22 10:56:47 2024] Running CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/score_CDS_likelihood_all_6_frames.pl /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/hexamer.scores > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.scores
* [Fri Mar 22 12:18:15 2024] Running CMD: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 --pfam_hits annotations/pfam_orfs.out --blast_hits annotations/sprotblastp_orfs.out > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3
Selecting best orfsblastp output found (annotations/sprotblastp_orfs.out) and processing...
PFAM output found (annotations/pfam_orfs.out) and processing...
Error, cmd: /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/util/select_best_ORFs_per_transcript.pl --gff3_file /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 --pfam_hits annotations/pfam_orfs.out --blast_hits annotations/sprotblastp_orfs.out > /home2/komornikova/Lana_try/transXpress/transdecoder/transcriptome.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 died with ret 35072 No such file or directory at /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/opt/transdecoder/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x561b2948c308)) called at /home2/komornikova/Lana_try/transXpress/.snakemake/conda/50cd150fcf9782446eeddc6e4ba57026_/bin/TransDecoder.Predict line 369
when I ran this command:
TransDecoder.Predict -t transcriptome.fasta --output_dir transdecoder --retain_pfam_hits annotations/pfam_orfs.out --retain_blastp_hits annotations/sprotblastp_orfs.out &> logs/transdecoder_predict.log
From the error message I suppose one of those files is missing but all of them are present and non-empty.
I would appreciate any kind of help. Thank you!