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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Not running UniRef search #71

Closed carolinemdong closed 7 years ago

carolinemdong commented 8 years ago

dammit-all.log.txt Hi Camille,

We're having a little trouble with searching the UniRef database. All dependencies and databases requirements are satisfied, and it seems to run all of the steps successfully until it reaches the the last UniRef search. I've attached the dammit-all.log as well. We'd appreciate any help or pointers - thank you!

--- Running annotate!

      Transcriptome file: hybrid_490_clean_trinity.Trinity.fasta

      Output directory:
      /home/victaphanta/hybrid_490_clean_trinity.Trinity.fasta.dammit

      [ ] hybrid_490_clean_trinity.Trinity.fasta

      [ ] transcriptome_stats:hybrid_490_clean_trinity.Trinity.fasta

      [ ] busco:hybrid_490_clean_trinity.Trinity.fasta-vertebrata

      [ ] TransDecoder.LongOrfs:hybrid_490_clean_trinity.Trinity.fasta

      [ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

      [ ] remap_hmmer:longest_orfs.pep.pfam.tbl

      [ ] TransDecoder.Predict:hybrid_490_clean_trinity.Trinity.fasta

      [ ] cmscan:hybrid_490_clean_trinity.Trinity.fasta.x.Rfam.cm

      [ ] lastal:hybrid_490_clean_trinity.Trinity.fasta.x.orthodb.maf

      [ ] lastal:hybrid_490_clean_trinity.Trinity.fasta.x.uniref.maf

      [ ] maf_best_hits:hybrid_490_clean_trinity.Trinity.fasta.x.orthodb.maf-
      hybrid_490_clean_trinity.Trinity.fasta.x.orthodb.maf.best.csv

      [ ] maf-gff3:hybrid_490_clean_trinity.Trinity.fasta.x.orthodb.maf.gff3

      [ ] maf_best_hits:hybrid_490_clean_trinity.Trinity.fasta.x.uniref.maf-
      hybrid_490_clean_trinity.Trinity.fasta.x.uniref.maf.best.csv

Some tasks failed![dammit.annotate:ERROR] TaskError - taskid:maf_best_hits:hybrid_490_clean_trinity.Trinity.fasta.x.uniref.maf-hybrid_490_clean_trinity.Trinity.fasta.x.uniref.maf.best.csv[dammit.annotate:ERROR] PythonAction Error Traceback (most recent call last): File "/home/victaphanta/.local/lib/python2.7/site-packages/doit/action.py", line 383, in execute returned_value = self.py_callable(_self.args, *_kwargs) File "/home/victaphanta/.local/lib/python2.7/site-packages/dammit/tasks.py", line 343, in cmd df = maf.MafParser(maf_fn).read() File "/home/victaphanta/.local/lib/python2.7/site-packages/dammit/fileio/maf.py", line 16, in read return pd.concat(self, ignore_index=True) File "/home/victaphanta/.local/lib/python2.7/site-packages/pandas/tools/merge.py", line 845, in concat copy=copy) File "/home/victaphanta/.local/lib/python2.7/site-packages/pandas/tools/merge.py", line 878, in init raise ValueError('No objects to concatenate') ValueError: No objects to concatenate [dammit.annotate:ERROR]

carolinemdong commented 7 years ago

Hi Camille,

No worries, found the problem and fixed it. UniRef90 is just quite a large database so my virtual machine was running out of memory and wasn't building the lastdb. Thanks!

Caroline