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preprocess:rename idle state #108

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Sanrrone opened this issue Jul 7, 2023 · 12 comments
Open

preprocess:rename idle state #108

Sanrrone opened this issue Jul 7, 2023 · 12 comments
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@mberacochea

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@Sanrrone
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Sanrrone commented Jul 7, 2023

Dears,
I'm trying to run a simple test with one of my fasta. But, in the step preprocess:rename never ends (11 hours of execution without progress).

the log:

Launching `https://github.com/EBI-Metagenomics/emg-viral-pipeline` [shrivelled_cantor] DSL2 - revision: aaf02d636a [v1.1]
 
Profile: local,singularity
 
Current User: valensan
Nextflow-version: 23.04.1
Starting time: 15-04-2023 06:51 UTC
Workdir location:
  /scratch/project_2007362/sandro/HeP_samples/6_tax_profile/phage/HeP-1003_tmp
Databases location:
  nextflow-autodownload-databases
 
Dev ViPhOG database: v3
Dev Meta database: v2
 
Only run annotation: false
 
[-        ] process > download_pprmeta:pprmetaGet    -
[-        ] process > download_virsorter_db:virso... -
[-        ] process > download_virfinder_db:virfi... -
[-        ] process > download_model_meta:metaGetDB  -
[-        ] process > download_viphog_db:viphogGetDB -
[-        ] process > download_ncbi_db:ncbiGetDB     -
[-        ] process > download_checkv_db:checkvGetDB -
[-        ] process > preprocess:rename              -
[-        ] process > preprocess:length_filtering    -
[-        ] process > detect:virsorter               -
[-        ] process > detect:virfinder               -
[-        ] process > detect:pprmeta                 -
[-        ] process > detect:parse                   -
[-        ] process > postprocess:restore            -
[-        ] process > annotate:prodigal              -
[-        ] process > annotate:hmmscan_viphogs       -
[-        ] process > annotate:hmm_postprocessing    -

[skipped  ] process > download_pprmeta:pprmetaGet    [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_virsorter_db:virso... [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_virfinder_db:virfi... [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_model_meta:metaGetDB  [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_viphog_db:viphogGetDB [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_ncbi_db:ncbiGetDB     [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_checkv_db:checkvGetDB [100%] 1 of 1, stored: 1 ✔
[-        ] process > preprocess:rename              [  0%] 0 of 1
[-        ] process > preprocess:length_filtering    -
[-        ] process > detect:virsorter               -
[-        ] process > detect:virfinder               -
[-        ] process > detect:pprmeta                 -
[-        ] process > detect:parse                   -
[-        ] process > postprocess:restore            -
[-        ] process > annotate:prodigal              -
[-        ] process > annotate:hmmscan_viphogs       -
[-        ] process > annotate:hmm_postprocessing    -
[-        ] process > annotate:ratio_evalue          -
[-        ] process > annotate:annotation            -
[-        ] process > annotate:plot_contig_map       -
[-        ] process > annotate:assign                -
[-        ] process > annotate:checkV                -
[-        ] process > annotate:write_gff             -
[-        ] process > plot:generate_krona_table      -
[-        ] process > plot:krona                     -
[-        ] process > plot:generate_sankey_table     -
[-        ] process > plot:sankey                    -
[skipping] Stored process > download_virsorter_db:virsorterGetDB
[skipping] Stored process > download_model_meta:metaGetDB
[skipping] Stored process > download_virfinder_db:virfinderGetDB
[skipping] Stored process > download_viphog_db:viphogGetDB
[skipping] Stored process > download_ncbi_db:ncbiGetDB
[skipping] Stored process > download_checkv_db:checkvGetDB
[skipping] Stored process > download_pprmeta:pprmetaGet

executor >  local (1)
[skipped  ] process > download_pprmeta:pprmetaGet    [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_virsorter_db:virso... [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_virfinder_db:virfi... [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_model_meta:metaGetDB  [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_viphog_db:viphogGetDB [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_ncbi_db:ncbiGetDB     [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > download_checkv_db:checkvGetDB [100%] 1 of 1, stored: 1 ✔
[7c/d224ad] process > preprocess:rename (1)          [  0%] 0 of 1
[-        ] process > preprocess:length_filtering    -
[-        ] process > detect:virsorter               -
[-        ] process > detect:virfinder               -
[-        ] process > detect:pprmeta                 -
[-        ] process > detect:parse                   -
[-        ] process > postprocess:restore            -
[-        ] process > annotate:prodigal              -
[-        ] process > annotate:hmmscan_viphogs       -
[-        ] process > annotate:hmm_postprocessing    -
[-        ] process > annotate:ratio_evalue          -
[-        ] process > annotate:annotation            -
[-        ] process > annotate:plot_contig_map       -
[-        ] process > annotate:assign                -
[-        ] process > annotate:checkV                -
[-        ] process > annotate:write_gff             -
[-        ] process > plot:generate_krona_table      -
[-        ] process > plot:krona                     -
[-        ] process > plot:generate_sankey_table     -
[-        ] process > plot:sankey                    -
[skipping] Stored process > download_virsorter_db:virsorterGetDB
[skipping] Stored process > download_model_meta:metaGetDB
[skipping] Stored process > download_virfinder_db:virfinderGetDB
[skipping] Stored process > download_viphog_db:viphogGetDB
[skipping] Stored process > download_ncbi_db:ncbiGetDB
[skipping] Stored process > download_checkv_db:checkvGetDB
[skipping] Stored process > download_pprmeta:pprmetaGet
slurmstepd: error: *** JOB 17698767 ON r06c28 CANCELLED AT 2023-07-07T04:26:41 DUE TO TIME LIMIT ***

Additionally, I looked into .command.err and .command.log there is almost no output just:

INFO:    Convert SIF file to sandbox...

what could I do?

thanks in advance
@mberacochea mberacochea self-assigned this Jul 7, 2023
@mberacochea
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Hi @Sanrrone

That is seems to be a problem with your singularity setup. Can you try with Docker instead?

Cheers

@Sanrrone
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Hi!,
unfortunately I am under a HPC so I cannot use Docker.

@hoelzer
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hoelzer commented Jul 10, 2023

Hi @Sanrrone!

Ah, but when you are on a HPC please use the available job scheduler, e.g. if it is SLURM:

-profile slurm,singularity

I think you used local which will run all processes on the current node you are (probably the login node, where no calculations should run).

Besides, on some HPCs there are latency issues. If this still happens, please let us know and we can maybe give some further guidance.

@Sanrrone
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Hi,
I'm using local but inside a slurm job just to test it.
if I use the slurm profile I got:
sbatch: error: AssocMaxSubmitJobLimit which is a missconfiguration in the profile. How can I edit the slurm profile?

@hoelzer
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hoelzer commented Jul 10, 2023

So you submit the whole pipeline run command as a SLURM job? Hm, should also work I think.

To edit the Nextflow SLURM profile, you could clone the GitHub repository and edit the nextflow.config file (there is a SLURM part, https://github.com/EBI-Metagenomics/emg-viral-pipeline/blob/master/nextflow.config#L99). Then, run the pipeline via specifying the nextflow run virify.nf ...

There is also a way to inject an additional configuration via the -c flag that can overwrite pipeline defaults. But maybe it's easier to first try the other way.

@Sanrrone
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Sanrrone commented Jul 11, 2023 •
edited

Hi,
I used the slurm profile with the local virify.nf with no success, still the process doesn't finish.

N E X T F L O W  ~  version 23.04.1
Launching `/scratch/project_2007362/software/emg-viral-pipeline/virify.nf` [nice_planck] DSL2 - revision: 20ab8a0de7
 
Profile: slurm,singularity
 
Current User: valensan
Nextflow-version: 23.04.1
Starting time: 15-04-2023 06:51 UTC
Workdir location:
  /scratch/project_2007362/sandro/HeP_samples/6_tax_profile/phage/HeP-1003_tmp
Databases location:
  nextflow-autodownload-databases
 
Dev ViPhOG database: v3
Dev Meta database: v2
 
Only run annotation: false
 
[-        ] process > preprocess:rename           -
[-        ] process > preprocess:length_filtering -
[-        ] process > detect:virsorter            -
[-        ] process > detect:virfinder            -
[-        ] process > detect:pprmeta              -
[-        ] process > detect:parse                -
[-        ] process > postprocess:restore         -
[-        ] process > annotate:prodigal           -
[-        ] process > annotate:hmmscan_viphogs    -
[-        ] process > annotate:hmm_postprocessing -
[-        ] process > annotate:ratio_evalue       -
[-        ] process > annotate:annotation         -
[-        ] process > annotate:plot_contig_map    -

[-        ] process > preprocess:rename           -
[-        ] process > preprocess:length_filtering -
[-        ] process > detect:virsorter            -
[-        ] process > detect:virfinder            -
[-        ] process > detect:pprmeta              -
[-        ] process > detect:parse                -
[-        ] process > postprocess:restore         -
[-        ] process > annotate:prodigal           -
[-        ] process > annotate:hmmscan_viphogs    -
[-        ] process > annotate:hmm_postprocessing -
[-        ] process > annotate:ratio_evalue       -
[-        ] process > annotate:annotation         -
[-        ] process > annotate:plot_contig_map    -
[-        ] process > annotate:assign             -
[-        ] process > annotate:checkV             -
[-        ] process > annotate:write_gff          -
[-        ] process > plot:generate_krona_table   -
[-        ] process > plot:krona                  -
[-        ] process > plot:generate_sankey_table  -
[-        ] process > plot:sankey                 -

executor >  slurm (1)
[df/c2eed8] process > preprocess:rename (1)       [  0%] 0 of 1
[-        ] process > preprocess:length_filtering -
[-        ] process > detect:virsorter            -
[-        ] process > detect:virfinder            -
[-        ] process > detect:pprmeta              -
[-        ] process > detect:parse                -
[-        ] process > postprocess:restore         -
[-        ] process > annotate:prodigal           -
[-        ] process > annotate:hmmscan_viphogs    -
[-        ] process > annotate:hmm_postprocessing -
[-        ] process > annotate:ratio_evalue       -
[-        ] process > annotate:annotation         -
[-        ] process > annotate:plot_contig_map    -
[-        ] process > annotate:assign             -
[-        ] process > annotate:checkV             -
[-        ] process > annotate:write_gff          -
[-        ] process > plot:generate_krona_table   -
[-        ] process > plot:krona                  -
[-        ] process > plot:generate_sankey_table  -
[-        ] process > plot:sankey                 -

executor >  slurm (1)
[df/c2eed8] process > preprocess:rename (1)       [  0%] 0 of 1
[-        ] process > preprocess:length_filtering -
[-        ] process > detect:virsorter            -
[-        ] process > detect:virfinder            -
[-        ] process > detect:pprmeta              -
[-        ] process > detect:parse                -
[-        ] process > postprocess:restore         -
[-        ] process > annotate:prodigal           -
[-        ] process > annotate:hmmscan_viphogs    -
[-        ] process > annotate:hmm_postprocessing -
[-        ] process > annotate:ratio_evalue       -
[-        ] process > annotate:annotation         -
[-        ] process > annotate:plot_contig_map    -
[-        ] process > annotate:assign             -
[-        ] process > annotate:checkV             -
[-        ] process > annotate:write_gff          -
[-        ] process > plot:generate_krona_table   -
[-        ] process > plot:krona                  -
[-        ] process > plot:generate_sankey_table  -
[-        ] process > plot:sankey                 -
slurmstepd: error: *** JOB 17780187 ON r18c08 CANCELLED AT 2023-07-11T15:31:30 DUE TO TIME LIMIT ***

the strange thing is I have no log about it so I cannot track the issue at all.

@hoelzer
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hoelzer commented Jul 12, 2023

Ok, this is indeed strange.

Can you run other Nextflow pipelines (e.g. try smt from https://nf-co.re/)? I want to figure out if this is a specific problem with VIRify or a general problem with your architecture and Nextflow installation.

@Sanrrone
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I tried to run viroprofiler, and yes, Also with an error but this time related with singularity:

-[ViroProfiler] Pipeline completed with errors-

[-        ] process > VIROPROFILER:SETUP:DB_CHECKV   -
[-        ] process > VIROPROFILER:SETUP:DB_VIBRANT  -
[-        ] process > VIROPROFILER:SETUP:DB_VIRSO... -
[-        ] process > VIROPROFILER:SETUP:DB_DRAM     -
[-        ] process > VIROPROFILER:SETUP:DB_IPHOP    -
[-        ] process > VIROPROFILER:SETUP:DB_VREFSEQ  -
Pulling Singularity image docker://denglab/viroprofiler-virsorter2:v0.2.5 [cache /scratch/project_2007362/software/singularity/cache/denglab-viroprofiler-virsorter2-v0.2.5.img]
Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /scratch/project_2007362/software/singularity/cache/denglab-viroprofiler-geneannot-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-vibrant:v0.2 [cache /scratch/project_2007362/software/singularity/cache/denglab-viroprofiler-vibrant-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-host:v0.1 [cache /scratch/project_2007362/software/singularity/cache/denglab-viroprofiler-host-v0.1.img]
Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /scratch/project_2007362/software/singularity/cache/denglab-viroprofiler-base-v0.2.img]

ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIRSORTER2'
Caused by:
  Failed to pull singularity image
  command: singularity pull  --name denglab-viroprofiler-virsorter2-v0.2.5.img.pulling.1689159264399 docker://denglab/viroprofiler-virsorter2:v0.2.5 > /dev/null
  status : 255
  message:
    INFO:    Converting OCI blobs to SIF format
    WARNING: 'nodev' mount option set on /scratch, it could be a source of failure during build process
    INFO:    Starting build...
    Getting image source signatures
    Copying blob sha256:7a6db449b51b92eac5c81cdbd82917785343f1664b2be57b22337b0a40c5b29d
    Copying blob sha256:b51904ca3834848d576e609bab4b382028643e662db724a58edb9401f9af220c
    Copying blob sha256:16f76cf3882a90e2e7969b03b7d0147c189cfb3966d14800091466f2d5fc0a51
    Copying blob sha256:377cc88d7c7e949460cc24d07979f2e428f2482e0b360d72860ff1df404208e0
    Copying blob sha256:7a15ae76cb488a6adde55d23dfd5571c57bf02206168b7795f7b473b1dc7c218
    Copying blob sha256:d0e88a31bdb313b5fab1a325bc79ad5c487cb722dbf65b1561fd4810ebd7b717
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:301aa5df7f62dcf710fc30e41d585887f918992bc71dba116c7edc267a3c3422
    Copying blob sha256:26142b6b2c1ea5de9b7566a9862ea2e9beb02b1a059295cd221ec89c75aac1e8
    Copying blob sha256:a7c07239fd155305c23fdbe3cb67838b8d57e0d5922d01b643ec5da4dbf7c7d7
    Copying blob sha256:a540153f7d72ad59b0b5d01a2425f0a8aa59bcd9fe6d0784aaeb43301f903aff
    Copying blob sha256:c0f68707fa83ac4d248c81ac27d1dd5d378fed88ddf1e6edb8d9fb1f549d75bd
    Copying blob sha256:66cbca5e11012c5b367f8b2cf18f81ec91b1780abcc9a34ba008a4ecb197f3a4
    Copying config sha256:ef836e11d9dcca820a285d003fb8af9a8e7051282bd5158c1eaa645da4ba00b7
    Writing manifest to image destination
    Storing signatures
    FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: Error initializing source oci:/scratch/project_2007362/software/singularity/cache/cache/blob:88d200bb0a32556fa99b4af044d0224b2ddf3c25d05fe56976067b5eaab5eb60: EOF

but at least in this case I have the error to do some tracking.
What do you think?

@hoelzer
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hoelzer commented Jul 12, 2023

Maybe smt is wrong with the singularity image that was pulled and converted for VIRify, causing the latency issue.

Can you remove the singularity images that were already stored for VIRify, and then run the pipeline again with -profile local,singularity and also define --cores 1 --max_cores 1. You can use some small test FASTA as input. By that, the pipeline should go through each process step by step and pull the images. Once all the images are stored, you can run the full pipeline.

@Sanrrone
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Hi,
Still the same error, after a clean installation, and using the parameters you specified. I also think something is wrong with the archiquecture of the HPC. But, how can I figure out it?

@hoelzer
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hoelzer commented Jul 14, 2023

Hm, do you have some admin to ask for help?

Sometimes, on HPC with Singularity, it also helps to specify some environment variables, see here:

export SINGULARITY_TMPDIR=/path/to/some/singularity_tmpdir

E.g. see the discussion here: nextflow-io/nextflow#2786

Or see here https://www.nextflow.io/docs/latest/config.html#config-singularity and scroll down to

Environment variables

Can you try another pipeline I am heavily involved (maybe I then know better what's going on if it also fails or works): https://github.com/replikation/poreCov

nextflow run replikation/poreCov -profile test_fastq,slurm,singularity -r 1.8.3 --update

It might be that you have to define some additional parameters based on your infrastructure. Per default, the pipeline will store downloaded singularity images to a folder ./singularity and also intermediate files to .work.

I would be curious if this runs or you get again an error (e.g. the same as for viroprofiler.

@Sanrrone
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Hi,
I always use the cache dir env variable (its a good practice). Also I tried the new software to test. I got some errors but they are different:

the run code

export SINGULARITY_CACHEDIR="/scratch/sandro/HeP_samples/6_tax_profile/phage/tmpfolder"
nextflow run replikation/poreCov -profile "test_fastq,local,singularity" -r 1.8.3 --max-cores 16 --update --cachedir $SINGULARITY_CACHEDIR

N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/replikation/poreCov` [magical_torvalds] DSL2 - revision: b86c57c384 [1.8.3]

________________________________________________________________________________
    
poreCov | A Nextflow SARS-CoV-2 workflow for nanopore data
    
 
  Latest available poreCov release: 1.8.3
  If neccessary update via: nextflow pull replikation/poreCov
________________________________________________________________________________
 Using 4/16 CPU threads per process for a local run [--max_cores]
 

WARNING: Singularity image building sometimes fails!
Multiple resumes (-resume) and --max_cores 1 --cores 1 for local execution might help.

Warning: Running --update might not be poreCov compatible!
Found latest pangolin container, using: nanozoo/pangolin-v4:4.3--1.21 
Found latest nextclade2 container, using: nanozoo/nextclade2:2.14.0--2023-06-16 

.
Profile:             test_fastq,local,singularity
Current User:        valensan
Nextflow-version:    23.04.1
poreCov-version:     1.8.3

Pathing:
Workdir location [-work-Dir]:
    /scratch/project_2007362/sandro/HeP_samples/6_tax_profile/phage/work/nextflow-poreCov-valensan
Output dir [--output]: 
    results
Databases location [--databases]:
    /scratch/project_2007362/software/singularity/cache
Singularity cache dir [--cachedir]: 
    /scratch/project_2007362/software/singularity/cache
______________________________________
Parameters:
Medaka model:         r941_min_hac_g507 [--medaka_model]
Min depth nucleotide: 20 [--min_depth]
Latest Pangolin/Nextclade?: true [--update]
CPUs to use:          4 [--cores]
Memory in GB:         12 [--memory]
______________________________________


Primerscheme:        V1200 [--primerV]
Min read-length set to: 400 [--minLength]
Max read-length set to: 1500 [--maxLength]
______________________________________


RKI output for german DESH upload:
Output stored at:      results/4.RKI-summary  
Min Identity to NC_045512.2: 0.90 [--seq_threshold]
Min Depth used:        20 [--min_depth]
   Min Depth should be 20 or more for RKI upload
Proportion cutoff N:   0.05 [--n_threshold]
______________________________________

[-        ] process > get_nanopore_fastq -

[-        ] process > get_nanopore_fastq             -
[-        ] process > read_qc_wf:nanoplot            -
[-        ] process > filter_fastq_by_length         -
[-        ] process > read_classification_wf:down... -
[-        ] process > read_classification_wf:kraken2 -
[-        ] process > read_classification_wf:krona   -
[-        ] process > artic_ncov_wf:artic_medaka     -
[-        ] process > artic_ncov_wf:covarplot        -
[-        ] process > determine_lineage_wf:pangolin  -
[-        ] process > determine_mutations_wf:next... -
[-        ] process > genome_quality_wf:president    -
[-        ] process > genome_quality_wf:seqrs        -
[-        ] process > rki_report_wf:rki_report       -
[-        ] process > align_to_reference             -
[-        ] process > create_summary_report_wf:ge... -
[-        ] process > create_summary_report_wf:pl... -
[-        ] process > create_summary_report_wf:su... -

executor >  local (2)
[49/7cd4aa] process > get_nanopore_fastq             [  0%] 0 of 1
[-        ] process > read_qc_wf:nanoplot            -
[-        ] process > filter_fastq_by_length         -
[b5/1e2c57] process > read_classification_wf:down... [  0%] 0 of 1
[-        ] process > read_classification_wf:kraken2 -
[-        ] process > read_classification_wf:krona   -
[-        ] process > artic_ncov_wf:artic_medaka     -
[-        ] process > artic_ncov_wf:covarplot        -
[-        ] process > determine_lineage_wf:pangolin  -
[-        ] process > determine_mutations_wf:next... -
[-        ] process > genome_quality_wf:president    -
[-        ] process > genome_quality_wf:seqrs        -
[-        ] process > rki_report_wf:rki_report       -
[-        ] process > align_to_reference             -
[-        ] process > create_summary_report_wf:ge... -
[-        ] process > create_summary_report_wf:pl... -
[-        ] process > create_summary_report_wf:su... -

executor >  local (3)
[49/7cd4aa] process > get_nanopore_fastq             [100%] 1 of 1, failed: 1 ✔
[-        ] process > read_qc_wf:nanoplot            -
[-        ] process > filter_fastq_by_length         -
[43/c564d7] process > read_classification_wf:down... [ 50%] 1 of 2, failed: 1...
[-        ] process > read_classification_wf:kraken2 -
[-        ] process > read_classification_wf:krona   -
[-        ] process > artic_ncov_wf:artic_medaka     -
[-        ] process > artic_ncov_wf:covarplot        -
[-        ] process > determine_lineage_wf:pangolin  -
[-        ] process > determine_mutations_wf:next... -
[-        ] process > genome_quality_wf:president    -
[-        ] process > genome_quality_wf:seqrs        -
[-        ] process > rki_report_wf:rki_report       -
[-        ] process > align_to_reference             -
[-        ] process > create_summary_report_wf:ge... -
[-        ] process > create_summary_report_wf:pl... -
[-        ] process > create_summary_report_wf:su... -
Not enough reads in all samples, please investigate results/1.Read_quality
Could not generate any genomes, please check your reads results/1.Read_quality
[49/7cd4aa] NOTE: Process `get_nanopore_fastq` terminated with an error exit status (255) -- Error is ignored
[b5/1e2c57] NOTE: Process `read_classification_wf:download_database_kraken2` terminated with an error exit status (255) -- Execution is retried (1)

executor >  local (4)
[49/7cd4aa] process > get_nanopore_fastq             [100%] 1 of 1, failed: 1 ✔
[-        ] process > read_qc_wf:nanoplot            -
[-        ] process > filter_fastq_by_length         -
[43/c564d7] process > read_classification_wf:down... [ 50%] 1 of 2, failed: 1...
[-        ] process > read_classification_wf:kraken2 -
[-        ] process > read_classification_wf:krona   -
[-        ] process > artic_ncov_wf:artic_medaka     -
[-        ] process > artic_ncov_wf:covarplot        -
[-        ] process > determine_lineage_wf:pangolin  -
[-        ] process > determine_mutations_wf:next... -
[-        ] process > genome_quality_wf:president    -
[-        ] process > genome_quality_wf:seqrs        -
[-        ] process > rki_report_wf:rki_report       -
[-        ] process > align_to_reference             -
[4f/832cc7] process > create_summary_report_wf:ge... [100%] 1 of 1, failed: 1 ✔
[-        ] process > create_summary_report_wf:pl... -
[-        ] process > create_summary_report_wf:su... -
Not enough reads in all samples, please investigate results/1.Read_quality
Could not generate any genomes, please check your reads results/1.Read_quality
[49/7cd4aa] NOTE: Process `get_nanopore_fastq` terminated with an error exit status (255) -- Error is ignored
[b5/1e2c57] NOTE: Process `read_classification_wf:download_database_kraken2` terminated with an error exit status (255) -- Execution is retried (1)
[4f/832cc7] NOTE: Process `create_summary_report_wf:get_variants_classification` terminated with an error exit status (255) -- Error is ignored
slurmstepd: error: *** JOB 17855474 ON r02c22 CANCELLED AT 2023-07-17T13:44:54 DUE TO TIME LIMIT ***

in this case I give the run 30min (which doesn't end).
at least the there are tracking files and it doesn't seems an singularity error.

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