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nf-core / kmermaid

k-mer similarity analysis pipeline
https://nf-co.re/kmermaid
MIT License
19 stars 12 forks source link

Update sourmash version #65

Closed olgabot closed 4 years ago

olgabot commented 4 years ago

Update sourmash version to avoid this error:

executor >  local (710)
[77/67e4ad] process > get_software_versions          [100%] 1 of 1 ✔
[f5/8ba6cb] process > tenx_tgz_extract_bam           [100%] 2 of 2 ✔
[a8/ba802c] process > samtools_fastq_aligned         [100%] 2 of 2 ✔
[9a/01375b] process > samtools_fastq_unaligned       [100%] 2 of 2 ✔
[7d/a16253] process > count_umis_per_cell            [100%] 2 of 2 ✔
[d8/bfbe7f] process > extract_per_cell_fastqs        [100%] 3 of 3 ✔
[6a/5eb2f2] process > fastp                          [100%] 276 of 276 ✔
[29/5f384e] process > sourmash_compute_sketch_fas... [ 38%] 421 of 1103, fail...
[-        ] process > sourmash_compare_sketches      [  0%] 0 of 2
[0;35m[nf-core/kmermaid] Pipeline completed with errors
WARN: Killing pending tasks (1)
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'sourmash_compute_sketch_fastx_nucleotide (mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_molecule-dna_ksize-3_log2sketchsize-2_trackabundance-false)'
Caused by:
  Process `sourmash_compute_sketch_fastx_nucleotide (mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_molecule-dna_ksize-3_log2sketchsize-2_trackabundance-false)` terminated with an error exit status (1)
Command executed:
  sourmash compute \
    --num-hashes $((2**2)) \
    --ksizes 3 \
    --dna \
     \
    --output mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_molecule-dna_ksize-3_log2sketchsize-2_trackabundance-false.sig \
    mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_R1_trimmed.fastq.gz
Command exit status:
  1
Command output:
  (empty)
Command error:

  == This is sourmash version 2.0.0a10.dev121+ged5be32. ==

  == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

  computing signatures for files: mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_R1_trimmed.fastq.gz

  Computing signature for ksizes: [3]

  Computing only nucleotide (and not protein) signatures.

  Computing a total of 1 signature(s).

  ... reading sequences from mouse_brown_fat_ptprc_plus_unaligned__aligned__CCATGTCCAAGCGATG_R1_trimmed.fastq.gz
  Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-kmermaid-1.0.0dev/bin/sourmash", line 8, in <module>
      sys.exit(main())
    File "/opt/conda/envs/nf-core-kmermaid-1.0.0dev/lib/python3.7/site-packages/sourmash/__main__.py", line 14, in main
      return mainmethod(args)
    File "/opt/conda/envs/nf-core-kmermaid-1.0.0dev/lib/python3.7/site-packages/sourmash/cli/compute.py", line 141, in main
      return compute(args)
    File "/opt/conda/envs/nf-core-kmermaid-1.0.0dev/lib/python3.7/site-packages/sourmash/command_compute.py", line 210, in compute
      notify('...{} {} sequences', filename, n, end='')
  UnboundLocalError: local variable 'n' referenced before assignment

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