Comments (4)
Hi @CaiBiotech ,
Thanks for using the pipeline and for sharing.
The error is super odd, specially comming from the dump sofwares, with such message:
Traceback (most recent call last):
File ".command.sh", line 101, in <module>
main()
File ".command.sh", line 69, in main
raise AssertionError(
AssertionError: We assume that software versions are the same between all modules. If you see this error-message it means you discovered an edge-case and should open an issue in nf-core/tools.
Can you share the contents of the following directory so I can try to find the culprit?
--> /share/home/dw_user0001/easy_genome/job20240429/work/67/de629a449b02e7d503777c6a1087bb
.
I believe github allows you to share compressed files.
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That would be very helpful because, when trying to reproduce it, using the test case file you mentioned, which is the same one in the Quickstart
section of the pipeline's online manual.
When using the commands from there to run it, it finished successfully:
nextflow run fmalmeida/mpgap \
--output _ASSEMBLY \
--max_cpus 5 \
--skip_spades \
--input "samplesheet.yml" \
--unicycler_additional_parameters ' --mode conservative ' \
-profile docker --hybrid_strategy both -r master -latest
So, having the directory mentioned would be helpful to try to understand what happened. But, meanwhile, I would suggest you try running again to check if it reproduces.
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Updating Nextflow to version 23.10.1 seems to have resolved the issue. Thank you!
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Awesome!
I should consider then increasing the “minimum version” required to avoid it in the future.
Many thanks for reporting!
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Related Issues (20)
- update tool versions
- add homopolish tool HOT 1
- Add skip parameter for sreads polishers and fix multiqc report names HOT 1
- Incomplete pipeline and different errors when using nanopore reads files with different sizes (900 mb vs 11Gb) HOT 18
- Add hifiasm for long reads assemble HOT 5
- 100% missing in Busco HOT 4
- Enhance documentation (paper review) HOT 2
- Add example of non-bacterial dataset analysis (paper review) HOT 1
- problem with longreads_only assembly HOT 4
- Add a simple parameter to handle starting memory settings HOT 1
- add automatic samplesheet for bacannot
- add the possibility of running directly from SRA IDs
- When not giving `--genome_size` for long reads, message goes to log and not console HOT 1
- allow hifiasm to use hi-c and parental data
- should hifiasm be executed only when user says reads are high quality? HOT 1
- Enhance polishing and downstream as hybracter
- ERROR ~ Error executing process > 'HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2)' HOT 3
- NOTE: Process `HYBRID:strategy_2_pilon (aspergillus_terreus:strategy_2)` terminated with an error exit status (137) -- Execution is retried (1) HOT 9
- Quast report generated different columns and break MultiQC module HOT 1
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