search

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
Other
28 stars 3 forks source link

dammit step fails after rerunning assembly #78

Open ctb opened 5 years ago

ctb commented 5 years ago

if I remove the assembly, and then run_eelpond trinity default, the dammit step fails. output below.

I can get it to work properly by removing the annotation directory. I suspect that there is a stale indexed file or another dammit intermediate file in there. not sure if this is a dammit but or an eelpond bug - seems like a dammit bug?

- [ ] TransDecoder.Predict:lab4_trinity.fasta:
    * Cmd: `/home/diblions/eelpond/.snakemake/conda/9149e0c4/bin/TransDecoder.Pr
edict -t /home/diblions/eelpond/lab4_out_exp1/annotation/lab4_trinity.fasta.damm
it/lab4_trinity.fasta`
TaskFailed - taskid:TransDecoder.Predict:lab4_trinity.fasta
Command failed: '/home/diblions/eelpond/.snakemake/conda/9149e0c4/bin/TransDecoder.Predict -t /home/diblions/eelpond/lab4_out_exp1/annotation/lab4_trinity.fasta.dammit/lab4_trinity.fasta' returned 25

########################################
TaskFailed - taskid:TransDecoder.Predict:lab4_trinity.fasta
TransDecoder.Predict:lab4_trinity.fasta <stderr>:

#####################
Counts of kept entries according to attributes:
FRAMESCORE      39
FRAMESCORE|LONGORF      29
########################

-indexing [Gene.34::Transcript_9::g.34]  ]  
 Indexed Gene.34::Transcript_9::g.34::m.34 138
Error, no gene obj retrieved based on identifier Gene.2::Transcript_2::g.2::m.2 at /home/diblions/eelpond/.snakemake/conda/9149e0c4/opt/transdecoder/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 2.
        Gene_obj_indexer::get_gene(Gene_obj_indexer=HASH(0x1d44180), "Gene.2::Transcript_2::g.2::m.2") called at /home/diblions/eelpond/.snakemake/conda/9149e0c4/opt/transdecoder/util/gene_list_to_gff.pl line 29
Error, cmd: /home/diblions/eelpond/.snakemake/conda/9149e0c4/opt/transdecoder/util/gene_list_to_gff.pl lab4_trinity.fasta.transdecoder_dir/longest_orfs.cds.scores.selected lab4_trinity.fasta.transdecoder_dir/longest_orfs.gff3.inx > lab4_trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /home/diblions/eelpond/.snakemake/conda/9149e0c4/bin/TransDecoder.Predict line 379.
bluegenes commented 5 years ago

Hmm - my guess is that dammit is attempting to use a file generated with the previous assembly, and then getting an error when it runs into mismatched transcript names.

This means we need to change the way dammit is called (perhaps specify more targets) so that it properly reruns. Will look into it.