Hello, I am working with nf-core/mag and keep ending up with the same error:

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_MAG:MAG:ANCIENT_DNA_ASSEMBLY_VALIDATION:PYDAMAGE_ANALYZE (SPAdes-22ds)'

Caused by:
  process hasn't exited

Here is my code:

nextflow pull nf-core/mag
nextflow run nf-core/mag -r 5.5.0 \
-c custom.config \
-profile singularity \
--input /projects/standard/mnievesc/zolik006/01_projects/01_PIALQ/02_analysis/03_Metagenomics/01_analysis/04_Denovo/sam$
--clip_tool adapterremoval \
--host_fasta /projects/standard/mnievesc/shared/ref_seqs/human_g1k_v37.fasta \
--host_fasta_bowtie2index /projects/standard/mnievesc/shared/ref_seqs \
--spades_fix_cpus 32 \
--megahit_fix_cpu_1 \
--reads_minlength 30 \
--binning_map_mode own \
--min_contig_size 500 \
--save_assembly_mapped_reads \
--exclude_unbins_from_postbinning \
--skip_prokka \
--run_checkm \
--run_busco \
--checkm_db /projects/standard/mnievesc/zolik006/02_refseqs/09_metaWARP/CheckM_DB \
--refine_bins_dastool \
--refine_bins_dastool_threshold 0.3 \
--postbinning_input refined_bins_only \
--run_gunc \
--gunc_db /projects/standard/mnievesc/zolik006/02_refseqs/11_gunc/gunc_db_progenomes2.1.dmnd \
--gtdb_db /projects/standard/mnievesc/zolik006/gtdbtk/share/gtdbtk-2.6.1/db \
--ancient_dna \
--outdir /projects/standard/mnievesc/zolik006/01_projects/01_PIALQ/02_analysis/03_Metagenomics/01_analysis/04_Denovo/

And my custom.config:

process {
        withName: GTDBTK_CLASSIFYWF {
                cpus = 32
                memory = 256.GB
        }
        withName: CHECKM_QC {
                cpus = 32
                memory = 256.GB
        }
        withName: PYDAMAGE_ANALYZE {
                cpus = 32
                memory = 256.GB
        }
}

When I look at the .command.log in the work-directory I can see that it completed analyzing all of the sequences. I am only putting in one ancient DNA sequencing file (22ds) that has about 18 million reads. I do not know what is causing it to get stuck on phydamage and would appreciate any advice on what I can do to fix this.

Hi, @Jaime Zolik! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Rike Hanssen for help.

--> #CE9MS66BS

Thank you so much! Just found the channel!

Hi Jaime, can you show the contents of your task workdir? And which executor are you using?