Comments (3)
Hi @PierreLyons Thanks for taking the time to report your issue!
Would you happen to be able to attach/copy-paste the contents of parse_influenza_blast_results.log
for this analysis?
The parse_influenza_blast_results.py
Python script makes use of Polars, Pandas and NumPy which may be trying to use functions that rely on certain CPU instructions. Or there could just be a bug in the script and the full stack trace might be helpful.
Have you tried Conda/Mamba instead of Podman/Docker?
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Hi @peterk87
Thanks for the quick response.
I haven't tried Conda yet, it's next on my list to try. I'll update once I do.
I'm also struggling to find the parse_influenza_black_results.log file, any ideas where it is stored? Thanks.
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Update regarding this issue:
Note: the same issue happens using either Docker or Conda/Mamba.
I've managed to isolate the issue to the use of polars, which seems to have been added to parse_influenza_blast_results.py in revision 3.2.0, which is when the pipeline breaks on my system. polars uses AVX, which my cpu doesn't support. The polars team has created a legacy version of polars (polars-lts-cpu) which was complied without AVX, and can be installed via pip (not available within conda-forge).
As a quick patch, I've manually created the conda env used by the subtyping_report.nf module with all dependencies except for polars, and then pip installed polars-lts-cpu within that environment. I then simply point the subtyping_report.nf module to the custom environment.
This is working well (almost, see below) now as a patch. I've also requested newer hardware, which I think is the most sensible solution to this issue.
The SUBTYPING_REPORT module completed successfully, but then the SOFTWARE_VERSIONS module threw an error.
I will describe it quickly here as well as my fix, but let me know if you'd like me to open a new issue. I'm not sure if my above fix caused this new issue.
dumpsoftwareversions.py caused this error (truncated for readability):
ERROR ~ Error executing process > 'NF_FLU:ILLUMINA:SOFTWARE_VERSIONS (1)'
Caused by:
Process NF_FLU:ILLUMINA:SOFTWARE_VERSIONS (1)
terminated with an error exit status (1)
Command executed [/home/vitalite/.nextflow/assets/CFIA-NCFAD/nf-flu/./workflows/../modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py]:
[ ... error truncated for readability ... ]
yaml.scanner.ScannerError: mapping values are not allowed here
in "collated_versions.yml", line 2, column 13
For reference, here are the first two lines of collated_versions.yml (second line truncated for readability):
"NF_FLU:ILLUMINA:CAT_ILLUMINA_FASTQ":
cat: Usage: cat [OPTION]... [FILE]... Concatenate FILE(s) to standard output. W [...]
This issue seems to be with the ":" after Usage.
My fix was to add a sed to remove colons from the echo commands at lines 103 and 104 in the nf-flu/modules/local/cat_illumina_fastq.nf file:
original:
cat:
gzip: $(echo $(gzip --help 2>&1) | sed 's/ (.//')
modified:
cat:
gzip: $(echo $(gzip --help 2>&1) | sed 's/ (.//' | sed 's/://')
This has solved the issue and now the pipeline runs (note: I can only run the pipeline with Conda).
Once again. let me know if I should open a new issue.
Thanks,
Pierre
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Related Issues (20)
- Error running newly installed pipeline HOT 1
- [BUG]: Conda and Mamba profiles broken in 3.3.0 HOT 1
- [BUG]: no H/N subtypes assigned in subtyping reports with user-specified sequences HOT 1
- [BUG]: The fasta sequence does not match the REF allele at OQ234674.1:1946 HOT 3
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- [BUG]: Mixed IAV and IBV run analysis reports all samples as IBV only HOT 4
- Optional dehosting
- Update README and docs for running nf-flu test profiles for Nanopore and Illumina platforms HOT 1
- [BUG]: ComputeError on SUBTYPING_REPORT HOT 4
- Read samplesheet.csv with fields as strong rather than inferred types
- Compatibility with cloud storage paths HOT 2
- Clair3 not variant calling ends of each segment HOT 4
- VADR Annotation HOT 4
- [BUG]: pull is only supported for shub URIs HOT 1
- Ability to output consensus sequences based on quality metrics (i.e., breadth and depth of coverage)
- [BUG]: nf-flu improperly labels segment ID for PB1 and PB2 for Influenza B HOT 3
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- [BUG]: CAT_ILLUMINA_FASTQ can mistakenly append 1:N:0:./2:N:0:. to quality score lines
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