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donovan-h-parks / RefineM

A toolbox for improving metagenome-assembled genomes.
GNU General Public License v3.0
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TypeError: can only join an iterable #53

Open angelovaag opened 3 years ago

angelovaag commented 3 years ago

Dear @dparks1134 ,

I am trying to learn to use refineM as the description of its capacities sound really promising and useful to me. I ran it however, and got an error message (below) that even my IT support cannot help with. I was wondering if you have experienced this error and if you know what could be done to address it.

>refinem scaffold_stats -c 32 ../final.assembly.fasta -x fa . refinedBins ../final.assembly.bam
[2021-02-09 12:39:35] INFO: RefineM v0.1.2
[2021-02-09 12:39:35] INFO: refinem scaffold_stats -c 32 ../final.assembly.fasta -x fa . refinedBins ../final.assembly.bam
[2021-02-09 12:39:36] INFO: Calculating coverage profile for final.assembly.bam (1 of 1):
  Finished processing 324,037 of 324,037 (100.00%) reference sequences.

  # total reads: 32,833,238
    # properly mapped reads: 12,601,649 (38.38%)
    # duplicate reads: 0 (0.00%)
    # secondary reads: 0 (0.00%)
    # reads failing QC: 0 (0.00%)
    # reads failing alignment length: 1,538,698 (4.69%)
    # reads failing edit distance: 18,619,697 (56.71%)
    # reads not properly paired: 73,194 (0.22%)
[2021-02-09 12:41:03] INFO: Coverage profiles written to: refinedBins/coverage.tsv
[2021-02-09 12:41:03] INFO: Calculating tetranucleotide signature for each sequence:
  Finished processing 324,037 of 324,037 (100.00%) sequences.
[2021-02-09 12:42:10] INFO: Tetranucleotide signatures written to: refinedBins/tetra.tsv
[2021-02-09 12:43:03] INFO: Determining scaffold statistics.
Traceback (most recent call last):
  File "/opt/conda/envs/app3/lib/python3.6/site-packages/biolib/seq_io.py", line 351, in read_fasta_seq
    yield seq_id, ''.join(seq).replace(' ', '')
TypeError: can only join an iterable

[Error] Failed to process sequence file: ./bin.lowDepth.fa

  Controlled exit resulting from an unrecoverable error or warning.

Thank you