Out of date spades may be causing errors with assemblies

[cahuparo]

Description of the bug

Traceback (most recent call last):
  File "/nfs7/BPP/Chang_Lab/paradarc/ps_pipeline_validation/scripts/pathogensurveillance/work/conda/spades-ca8fa9996df717ef1077978990e85dd1/bin/spades.py", l>
    import support
  File "/nfs7/BPP/Chang_Lab/paradarc/ps_pipeline_validation/scripts/pathogensurveillance/work/conda/spades-ca8fa9996df717ef1077978990e85dd1/share/spades/spad>
    from distutils.version import LooseVersion
ModuleNotFoundError: No module named 'distutils'

Spades keep throwing this error. I checked and the conda environment is out of date (bioconda::spades=3.15.5) when compared to the one in nf-core tools: (bioconda::spades=4.0.0)

Command used and terminal output

No response

Relevant files

No response

System information

No response

[zachary-foster]

Could it be a failed conda environemnt build? If it is consistent after remaking the env, can you try updating the conda env and seeing if that fixes the problem?

[cahuparo]

I updated spades conda to 4.0.0 in the yml file. It works for a while but I got a new error:

Caused by:
  Process `PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FILTER_ASSEMBLY (pinf_mx_P6634)` terminated with an error exit status (1)


Command executed:

  gzip -dc pinf_mx_P6634.scaffolds.fa.gz > pinf_mx_P6634_unzipped.fasta
  
  process_spades_assem.py \
      --verbose \
      --summary pinf_mx_P6634.summary \
      --cov_cutoff 1 --len_cutoff 100 \
      pinf_mx_P6634_unzipped.fasta > pinf_mx_P6634_filtered.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FILTER_ASSEMBLY":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/nfs7/BPP/Grunwald_Lab/home/paradarc/crispr_dx/pinf/scripts/pathogensurveillance/bin/process_spades_assem.py", line 3, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /nfs7/BPP/Grunwald_Lab/home/paradarc/crispr_dx/pinf/scripts/pathogensurveillance/work/c7/fc91e79d9f5fad890c9c3ad80dbbb6