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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Error when annotating sample data #84

Open NBKingsley opened 8 years ago

NBKingsley commented 8 years ago

After getting dammit and all of the dependencies installed onto my Ubuntu machine, I tried following the annotation tutorial with the sample data, but the program failed after about four hours with the following error message:

'''

--- Running annotate!

      Transcriptome file: cdna_nointrons_utrs.fa

      Output directory: /home/nbkingsley/dammit_test/cdna_nointrons_utrs.fa.dammit

      [x] cdna_nointrons_utrs.fa

      [x] transcriptome_stats:cdna_nointrons_utrs.fa

      [x] busco:cdna_nointrons_utrs.fa-eukaryota

      [x] TransDecoder.LongOrfs:cdna_nointrons_utrs.fa

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

      [ ] remap_hmmer:longest_orfs.pep.pfam.tbl

      [ ] TransDecoder.Predict:cdna_nointrons_utrs.fa

      [ ] cmscan:cdna_nointrons_utrs.fa.x.Rfam.cm

      [ ] lastal:cdna_nointrons_utrs.fa.x.orthodb.maf

      [ ] sanitize_fasta:pep.fa

      [ ] crb-blast:cdna_nointrons_utrs.fa.x.pep.fa

      [ ] maf_best_hits:cdna_nointrons_utrs.fa.x.orthodb.maf-
      cdna_nointrons_utrs.fa.x.orthodb.maf.best.csv

Some tasks failed![dammit.annotate:ERROR] TaskError - taskid:maf_best_hits:cdna_nointrons_utrs.fa.x.orthodb.maf-cdna_nointrons_utrs.fa.x.orthodb.maf.best.csv[dammit.annotate:ERROR] PythonAction Error Traceback (most recent call last): File "/home/nbkingsley/dammitENV/local/lib/python2.7/site-packages/doit/action.py", line 383, in execute returned_value = self.py_callable(*self.args, **kwargs) File "/home/nbkingsley/dammitENV/local/lib/python2.7/site-packages/dammit/tasks.py", line 327, in cmd df = maf.MafParser(maf_fn).read() File "/home/nbkingsley/dammitENV/local/lib/python2.7/site-packages/dammit/fileio/maf.py", line 16, in read return pd.concat(self, ignore_index=True) File "/home/nbkingsley/dammitENV/local/lib/python2.7/site-packages/pandas/tools/merge.py", line 1334, in concat copy=copy) File "/home/nbkingsley/dammitENV/local/lib/python2.7/site-packages/pandas/tools/merge.py", line 1367, in init raise ValueError('No objects to concatenate') ValueError: No objects to concatenate [dammit.annotate:ERROR] ''' Any insights as to the cause of this error?

AdamStuckert commented 7 years ago

Did you figure this out @NBKingsley ? I'm getting the same error.

camillescott commented 7 years ago

I believe the answer was that she is running version 0.3, and that this is fixed in the 1.0 release candidate. There are instructions here for getting that (I need to update the README)

AdamStuckert commented 7 years ago

Excellent, that worked. Thanks Camille!