Hello, hello I am trying to run the seqinspector pipeline form the `add_long_reads` branch and having trouble with

toulligqc

. First I got a permission error (

ValueError: sort array is read-only

), but then I updated to the newest version of the toulligqc module, and got the following error:

-[nf-core/seqinspector] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SEQINSPECTOR:SEQINSPECTOR:TOULLIGQC (Undetermined_05)'

Caused by:
  Process `NFCORE_SEQINSPECTOR:SEQINSPECTOR:TOULLIGQC (Undetermined_05)` terminated with an error exit status (1)


Command executed:

  toulligqc \
      --fastq Undetermined_S0_L001_R1_001.fastq.gz \
      --output-directory Undetermined_05 \

Command exit status:
  1

Command output:
  ToulligQC version 2.7.1
  * Initialize extractors
  * Start Toulligqc info extractor
  * End of Toulligqc info extractor (done in 0m0.00s)
  * Start fastq extractor

Command error:
  Unable to find image '<http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>' locally
  f883b71bc5c8ba80: Pulling from library/toulligqc_huggingface_hub_matplotlib_numpy_pruned
  6e59cb05818e: Already exists
  dec6b097362e: Already exists
  5f20d5c36a06: Already exists
  4f4fb700ef54: Already exists
  5a47b42d3e8c: Already exists
  ad4a1cea1cef: Already exists
  c0287eaf45ee: Already exists
  4f4fb700ef54: Already exists
  b8a1a9b42924: Already exists
  57d1d9429ba0: Already exists
  a444aa1775d5: Already exists
  b9afb7fce560: Already exists
  a1bf15c61759: Pulling fs layer
  b13abb49f40a: Pulling fs layer
  a1bf15c61759: Verifying Checksum
  a1bf15c61759: Download complete
  a1bf15c61759: Pull complete
  b13abb49f40a: Verifying Checksum
  b13abb49f40a: Download complete
  b13abb49f40a: Pull complete
  Digest: sha256:7c72ded818ef3386a9baeb06e1770640d8fc536dbc513af39458f65849fd6cdb
  Status: Downloaded newer image for <http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>
  Traceback (most recent call last):
    File "/opt/conda/bin/toulligqc", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/toulligqc.py", line 426, in main
      extractor.init()
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 60, in init
      self.dataframe_1d = self._load_fastq_data()
                          ^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 253, in _load_fastq_data
  ToulligQC version 2.7.1
  * Initialize extractors
  * Start Toulligqc info extractor
  * End of Toulligqc info extractor (done in 0m0.00s)
  * Start fastq extractor
      run_info = self.check_fastq()
                 ^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 360, in check_fastq
      metadata = dict(x.split("=") for x in first_line.split(" ")[1:])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ValueError: dictionary update sequence element #0 has length 1; 2 is required

Work dir:
  /Users/franziska.franziska/workspace/seqinspector/work/28/b92f680318c3de080e707650ae0766

Container:
  <http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

My command was:

nextflow run <http://main.nf|main.nf> -profile docker,arm64,test --input ../../Desktop/seqinspector_input/test_data/samplesheet.csv --outdir /Users/franziska.franziska/Desktop/seqinspector_outdir_test/ --fastq_screen_references ../../Desktop/seqinspector_input/fastq_screen_refs_base.csv --fasta /Users/franziska.franziska/Desktop/seqinspector_input/sars_cov2_genome/ncbi_dataset\(1\)/ncbi_dataset/data/genomic.fna --tools toulligqc

@Maxime Garcia was able to run it on his linux computer without issues, but I am on a Mac, so I assume some problems due to the different structure

yeah, I assume that the recipe for arm is not working as expected

apple arm != linux arm

aha, ok! I’ll try!