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Another question: It seem that the pipeline is stu...
# mag
r
Another question: It seem that the pipeline is stuck when adding 
--run_checkm2
Copy code
# Run nf-core/mag starting from assemblies
nextflow run nf-core/mag \
  -profile apptainer \
  --input /project2/ckenkel_26/liruiqi/mag_out_project2/samplesheet.csv \
  --assembly_input /project2/ckenkel_26/liruiqi/mag_out_project2/checkm2_nohost/assembly_input.csv \
  --outdir /project2/ckenkel_26/liruiqi/mag_out_project2/checkm2_nohost \
  --gtdb_db /project2/ckenkel_26/liruiqi/mag_out_project2/gtdb226/release226 \
  --run_checkm2 \
  --refine_bins_dastool \
  --postbinning_input both \
  --email <mailto:liruiqi@usc.edu|liruiqi@usc.edu> \
  -resume
error message in the log:
Copy code
executor >  local (1)
[-        ] NFC…PREPROCESSING:NANOPLOT_RAW -
[37/9a37b3] NFC…IT-CR180008.contigs.fa.gz) | 2 of 2, cached: 2 ✔
[78/4d5e3b] NFC…G:QUAST (MEGAHIT-CR180008) | 2 of 2, cached: 2 ✔
[a2/bd139b] NFC…AG:MAG:PRODIGAL (CR180008) | 0 of 2
[e8/a14e08] NFC…LY_BUILD (SPAdes-CR180008) | 2 of 2, cached: 2 ✔
[-        ] NFC…ION:BOWTIE2_ASSEMBLY_ALIGN -
[-        ] NFC…ON:MINIMAP2_ASSEMBLY_INDEX -
[-        ] NFC…ON:MINIMAP2_ASSEMBLY_ALIGN -
[-        ] NFCORE_MAG:MAG:ALE             -
[-        ] NFC…ZEBAMCONTIGDEPTHS_LONGREAD -
[-        ] NFC…EBAMCONTIGDEPTHS_SHORTREAD -
[-        ] NFC…MAG:BINNING:CONVERT_DEPTHS -
[-        ] NFC…:BINNING:METABAT2_METABAT2 -
[-        ] NFCORE_MAG:MAG:BINNING:MAXBIN2 -
[-        ] NFC…BINNING:ADJUST_MAXBIN2_EXT -
[-        ] NFC…CONCOCT:CONCOCT_CUTUPFASTA -
[-        ] NFC…NCOCT_CONCOCTCOVERAGETABLE -
[-        ] NFC…NG_CONCOCT:CONCOCT_CONCOCT -
[-        ] NFC…NCOCT_MERGECUTUPCLUSTERING -
[-        ] NFC…T:CONCOCT_EXTRACTFASTABINS -
[-        ] NFC…:MAG:GTDBTK:GTDBTK_SUMMARY | 0 of 1
Plus 28 more processes waiting for tasks…
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 '/home1/liruiqi/.nextflow/assets/nf-core/mag/subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 82 or see '.nextflow.log' file for more details
It won't fail or exit, but will eventually time out on slurm. I am very confused by this issue now. It won't even produce a html report under 
pipeline_info
j
OK interesting, this is the same problem as @Daniel Gregoire reported here! https://nfcore.slack.com/archives/CE9MS66BS/p1771291151300719
Could you send me your 
.nextflow.log
file
Even though I don't know the issue yet, I've made a random stab in the dark of a fix: Could you run 
nextflow pull
, and then run your command again but with 
-r minimap2-yaml-issue
r
nextflow.log.4,nextflow.log.5
Can you elaborate how exact should I do it with slurm? Do I put 
nextflow pull
in the script, and then put the real command again below with 
-r minimap2-yaml-issue
, like:
Copy code
nextflow pull
# Run nf-core/mag starting from assemblies
nextflow run nf-core/mag \
  -profile apptainer \
  -r minimap2-yaml-issue \
  --input /project2/ckenkel_26/liruiqi/mag_out_project2/samplesheet.csv \
  --assembly_input /project2/ckenkel_26/liruiqi/mag_out_project2/checkm2_nohost/assembly_input.csv \
  --outdir /project2/ckenkel_26/liruiqi/mag_out_project2/checkm2_nohost \
  --gtdb_db /project2/ckenkel_26/liruiqi/mag_out_project2/gtdb226/release226 \
  --run_checkm2 \
  --refine_bins_dastool \
  --postbinning_input both \
  --email liruiqi@usc.edu \
  -resume
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