cdna_alignment_orf_to_genome_orf.pl #181

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1. brianjohnhaas commented on Aug 30, 2023

   

   brianjohnhaas

   on Aug 30, 2023 via email

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   Hi, The best thing to do is to look at some of the example / sample data included with transdecoder. It looks like taco is probably not compatible with the current formatting.

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   On Wed, Aug 30, 2023 at 8:58 AM isnmn ***@***.***> wrote: Hi, I'm trying to combine my TACO output and TD output within this command but it returns error: $TD_PATH/util/cdna_alignment_orf_to_genome_orf.pl longest_orfs.cds.transdecoder.gff3 ../TACO/output/assembly.gtf TransDecoder_out.fa Error, cannot parse ID from info [tss_id "TSS45"; locus_id "L3"; abs_frac "1.00000"; rel_frac "1.00000"; expr "0.466"; transcript_id "TU45"; gene_id "G45"; ] of line chr1 taco transcript 170165 449773 1000 - . tss_id "TSS45"; locus_id "L3"; abs_frac "1.00000"; rel_frac "1.00000"; expr "0.466"; transcript_id "TU45"; gene_id "G45"; Could you help please? — Reply to this email directly, view it on GitHub <#181>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2QKFVF5HWINWHPK3DXX42INANCNFSM6AAAAAA4EPM5O4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
2. isnmn commented on Aug 30, 2023

   

   isnmn

   on Aug 30, 2023

   Last edited by isnmn

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   I noticed that TransDecoder.Predict produced empty pep file with this error:

   cds.transdecoder_dir/longest_orfs.cds --genetic_code Universal > longest_orfs.cds.transdecoder.pep Making pep file: longest_orfs.cds.transdecoder.pep Error, no sequence for TU10 at /export/home4/2762262d/MAIN/tools/TransDecoder-TransDecoder-v5.7.0/util/gff3_file_to_proteins.pl line 82. Error, cmd: /export/home4/2762262d/MAIN/tools/TransDecoder-TransDecoder-v5.7.0/util/gff3_file_to_proteins.pl --gff3 longest_orfs.cds.transdecoder.gff3 --fasta longest_orfs.cds.transdecoder_dir/longest_orfs.cds --genetic_code Universal > longest_orfs.cds.transdecoder.pep died with ret 65280 No such file or directory at /export/home4/2762262d/MAIN/tools/TransDecoder-TransDecoder-v5.7.0/PerlLib/Pipeliner.pm line 187. Pipeliner::run('Pipeliner=HASH(0x15ad520)') called at /export/home4//2762262d/MAIN/tools/TransDecoder-TransDecoder-v5.7.0//TransDecoder.Predict line 372

   Well nevermind, I solved this problem. I'll try cufflinks not TACO for the previous issue:
   Error, cannot parse ID from info [ID=TU45;geneID=G45 ] of line chr1 taco transcript 170165 449773 1000 - . ID=TU45;geneID=G45