Hi All, I am running nf-core/mag v 5.4.0 on Nextflow v 25.10.2 to build MAGs using long read PacBio HIFI data. When I use the following input code, sample sheet and custom configuration file,

nextflow run nf-core/mag -r 5.4.0 -profile apptainer -c mag-wall-time-increase.yaml -resume 263aef71-55e3-4ffe-a6fe-3a1f39f6574d \
--input 'KB1_long_read_sample_list_20260212.csv' \
--outdir KB1_long_read_MAGs_nf_core \
--min_contig_size 1500 \
--skip_spades \
--refine_bins_dastool \
--postbinning_input refined_bins_only \
--run_checkm2 \
--checkm2_db '/files/home/dgregoire/databases/CheckM2_database/uniref100.KO.1.dmnd' \
--gtdb_db '/datastore/researchdata/gtdbtk/release220'

the pipeline interrupts at the Prodigal and Metabat2 JGI Summarize contig depth steps with the following error message:

-[nf-core/mag] Pipeline completed with errors-
WARN: Killing running tasks (1)
ERROR ~ Could not find which method load() to invoke from this list:
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.InputStream)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.Reader)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.lang.String)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.File)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.nio.file.Path)

 -- Check script '/files/home/dgregoire/.nextflow/assets/nf-core/mag/subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 82 or see '.nextflow.log' file for more details

After doing some initial research, I suspect the problem may be an incompatibility between my nextflow version creating issues reading my custom config file (which is fine, to the best of my knowledge). This strikes me as strange, given that the run initiated and nextflow is caching the files properly based on my custom config file. I wanted to run it by the community first before I test downgrading to less recent nextflow version. Thanks in advance for any help.

For one thing, nextflow config files are not

yaml

files, so you shouldn't name it that (convention is

.conf

), but generaly that shouldn't make a difference

Do you think trying to manually pull the .sif for minimap may help here? I can also try switching the file extension to .config to see if that clears it up. I tried re-running a fresh instance of it as well after clearing the cache to see if that helps.

I don't think the error is related to the container

When I tried calling it using the following input code:

nextflow run nf-core/mag -r minimap2-yaml-issue -profile apptainer -c mag-wall-time-increase.yaml \
--input 'KB1_long_read_sample_list_20260212.csv' \
--outdir KB1_long_read_MAGs_nf_core \
--min_contig_size 1500 \
--skip_spades \
--refine_bins_dastool \
--postbinning_input refined_bins_only \
--run_checkm2 \
--checkm2_db '/files/home/dgregoire/databases/CheckM2_database/uniref100.KO.1.dmnd' \
--gtdb_db '/datastore/researchdata/gtdbtk/release220'

It returned an error message immediately:

Launching `<https://github.com/nf-core/mag>` [high_hypatia] DSL2 - revision: 9aefaa1f00 [minimap2-yaml-issue]

ERROR ~ Module compilation error
- file : /files/home/dgregoire/.nextflow/assets/nf-core/mag/subworkflows/local/hostremoval_longread/main.nf
- cause: Unexpected input: '}' @ line 56, column 1.
   }
   ^

1 error


 -- Check script '/files/home/dgregoire/.nextflow/assets/nf-core/mag/subworkflows/local/preprocessing_longread/main.nf' at line: 16 or see '.nextflow.log' file for more details

Oops, I may have made a typo, give me amoment

Ended up with the same error message using the following input code:

nextflow run nf-core/mag -r minimap2-yaml-issue -profile apptainer -c mag-wall-time-increase.yaml \
--input 'KB1_long_read_sample_list_20260212.csv' \
--outdir KB1_long_read_MAGs_nf_core \
--min_contig_size 1500 \
--skip_spades \
--refine_bins_dastool \
--postbinning_input refined_bins_only \
--run_checkm2 \
--checkm2_db '/files/home/dgregoire/databases/CheckM2_database/uniref100.KO.1.dmnd' \
--gtdb_db '/datastore/researchdata/gtdbtk/release220'

Error message:

-[nf-core/mag] Pipeline completed with errors-
WARN: Killing running tasks (2)
ERROR ~ Could not find which method load() to invoke from this list:
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.InputStream)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.Reader)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.lang.String)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.File)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.nio.file.Path)

 -- Check script '/files/home/dgregoire/.nextflow/assets/nf-core/mag/subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 82 or see '.nextflow.log' file for more details

Ugh that's frustrating...

So it looks like running it with 5.3.0 moved past the step causing the error originally. Run is still going, but it looks like it is going to finish okay. Maybe something updated in 5.4.0 that led to an incompatibility?

OK that helps narrow things down

Okay, troubleshooting run with 5.3.0 completed successfully after 5 days. Re-running with the minimap2-yaml-issue noted above and I’ll post the results once its done or interrupts again, thanks for catching this

I would greatly appreciate it, thank you!

Running with minimap2-yaml-issue with --checkm2 works!

Ahh fantastic! @Diego Alvarez Saravia fYI!

Fantastic! Your intuition was right on point @James Fellows Yates! Should we merge it then o should I try to reproduce the issue anyway (I could most probably on monday or tuesday)?

Same on my end, just waiting for the GTDB step to wrap but it looks like everything worked

I think you can merge @Diego Alvarez Saravia As we have two confirmed successful runs

So what version should we be calling for future runs that contains the bug fix? Has this been merged with 5.4.0?

It will be 5.4.1 (I assume @Diego Alvarez Saravia?), but we are just trying to finalise the release now

Yes, 5.4.1 will have this fixed!