-[nf-core/viralrecon] Pipeline completed with errors- Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518)' Caused by: Process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518) terminated with an error exit status (20)

[dejenie21]

Description of the bug

It is my first time running nf-core/viralrecon pipeline using a sequence from nanopore (Minion). I used the following script but th Pipeline completed with errors. Is there anyone who can help me in troubleshooting the problem?
when I try to view the complete command output by changing to the process work dir and entering the command cat .command.out, nothing is shown.

Command used and terminal output

The script I used:
#!/bin/bash

nextflow run nf-core/viralrecon \
  --input /home/dej/SARS/data105/samplesheet.csv \
  --outdir results105 \
  --platform nanopore \
  --protocol amplicon \
  --genome 'MN908947.3' \
  --primer_set artic \
  --primer_set_version 3 \
  --skip_assembly \
  --fastq_dir data105/fastq_pass/ \
  --artic_minion_caller medaka \
  --artic_minion_medaka_model r941_min_fast_g303 \
  -profile singularity -resume



-[nf-core/viralrecon] Pipeline completed with errors-
Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518)'

Caused by:
  Process `NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12373518)` terminated with an error exit status (20)

Command executed:

  export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin

  artic \
      minion \
      --normalise 500 --medaka --minimap2 \
      --threads 12 \
      --read-file SRX12373518.fastq.gz \
      --scheme-directory ./primer-schemes \
      --scheme-version 3 \
      --medaka-model r941_min_fast_g303 \
       \
       \
      nCoV-2019 \
      SRX12373518

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION":
      artic: 1.2.3
  END_VERSIONS

Command exit status:
  20

Command output:
  (empty)

Command error:
                      insertion -> insertion:  0.353

                      Emission Probabilities:
                      match (equal):           0.966
                      match (not equal):       0.011
                      insertion:               1.000
                      deletion:                1.000

  2023-03-31 06:25:23 Reading potential variants from input VCF...
  2023-03-31 06:25:23 77 potential variants identified.
  2023-03-31 06:25:23 Generating haplotype fragments from reads...
  2023-03-31 06:25:23    10% of variants processed...
  2023-03-31 06:25:23    20% of variants processed...
  2023-03-31 06:25:23    30% of variants processed...
  2023-03-31 06:25:23    40% of variants processed...
  2023-03-31 06:25:23    50% of variants processed...
  2023-03-31 06:25:23    60% of variants processed...
  2023-03-31 06:25:23    70% of variants processed...
  2023-03-31 06:25:23    80% of variants processed...
  2023-03-31 06:25:23    90% of variants processed...
  2023-03-31 06:25:23    100% of variants processed.
  2023-03-31 06:25:23 Calling initial genotypes using pair-HMM realignment...
  Note: the --sample option not given, applying all records regardless of the genotype
  The site MN908947.3:11332 overlaps with another variant, skipping...
  The site MN908947.3:16466 overlaps with another variant, skipping...
  The fasta sequence does not match the REF allele at MN908947.3:22288:
     REF .vcf: [TGCTTTA]
     ALT .vcf: [T]
     REF .fa : [TGCTTNN]CATAGAAGTTATTTGACTCCTGGTGATTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCNNNNTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
  Running: minimap2 -a -x map-ont -t 12 ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta SRX12373518.fastq.gz | samtools view -bS -F 4 - | samtools sort -o SRX12373518.sorted.bam -
  Running: samtools index SRX12373518.sorted.bam
  Running: align_trim --normalise 500 ./primer-schemes/nCoV-2019/V3/nCoV-2019.scheme.bed --start --remove-incorrect-pairs --report SRX12373518.alignreport.txt < SRX12373518.sorted.bam 2> SRX12373518.alignreport.er | samtools sort -T SRX12373518 - -o SRX12373518.trimmed.rg.sorted.bam
  Running: align_trim --normalise 500 ./primer-schemes/nCoV-2019/V3/nCoV-2019.scheme.bed --remove-incorrect-pairs --report SRX12373518.alignreport.txt < SRX12373518.sorted.bam 2> SRX12373518.alignreport.er | samtools sort -T SRX12373518 - -o SRX12373518.primertrimmed.rg.sorted.bam
  Running: samtools index SRX12373518.trimmed.rg.sorted.bam
  Running: samtools index SRX12373518.primertrimmed.rg.sorted.bam
  Running: medaka consensus --model r941_min_fast_g303 --threads 12 --chunk_len 800 --chunk_ovlp 400 --RG 1 SRX12373518.trimmed.rg.sorted.bam SRX12373518.1.hdf
  Running: medaka variant ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta SRX12373518.1.hdf SRX12373518.1.vcf
  Running: medaka consensus --model r941_min_fast_g303 --threads 12 --chunk_len 800 --chunk_ovlp 400 --RG 2 SRX12373518.trimmed.rg.sorted.bam SRX12373518.2.hdf
  Running: medaka variant ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta SRX12373518.2.hdf SRX12373518.2.vcf
  Running: artic_vcf_merge SRX12373518 ./primer-schemes/nCoV-2019/V3/nCoV-2019.scheme.bed 2> SRX12373518.primersitereport.txt 1:SRX12373518.1.vcf 2:SRX12373518.2.vcf
  Running: bgzip -f SRX12373518.merged.vcf
  Running: tabix -f -p vcf SRX12373518.merged.vcf.gz
  Running: longshot -P 0 -F -A --no_haps --bam SRX12373518.primertrimmed.rg.sorted.bam --ref ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta --out SRX12373518.merged.vcf --potential_variants SRX12373518.merged.vcf.gz
  Running: artic_vcf_filter --medaka SRX12373518.merged.vcf SRX12373518.pass.vcf SRX12373518.fail.vcf
  Running: bgzip -f SRX12373518.pass.vcf
  Running: tabix -p vcf SRX12373518.pass.vcf.gz
  Running: artic_make_depth_mask --store-rg-depths ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta SRX12373518.primertrimmed.rg.sorted.bam SRX12373518.coverage_mask.txt
  Running: artic_mask ./primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta SRX12373518.coverage_mask.txt SRX12373518.fail.vcf SRX12373518.preconsensus.fasta
  Running: bcftools consensus -f SRX12373518.preconsensus.fasta SRX12373518.pass.vcf.gz -m SRX12373518.coverage_mask.txt -o SRX12373518.consensus.fasta
  Command failed:bcftools consensus -f SRX12373518.preconsensus.fasta SRX12373518.pass.vcf.gz -m SRX12373518.coverage_mask.txt -o SRX12373518.consensus.fasta

Work dir:
  /home/dej/SARS/data105/work/0d/6b75867a93eeaffdaa78c9e3fd8ef2

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

WHEN i RE-RUN THE COMMAND USING THE FOLLOWING SCRIPT

#!/bin/bash

nextflow run nf-core/viralrecon -profile singularity
--max_memory '32.GB' --max_cpus 12
--input /home/dej/SARS/data105/samplesheet.csv
--outdir results_105/viralrecon
--platform nanopore
--protocol amplicon
--genome 'MN908947.3'
--primer_set artic
--primer_set_version 3
--skip_assembly
--fastq_dir data105/fastq_pass/
--artic_minion_caller medaka
--artic_minion_medaka_model r941_min_fast_g303

ERROR:

-[nf-core/viralrecon] Pipeline completed with errors-
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 1) -- Cause: github.com
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 1) -- Cause: github.com
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 2) -- Cause: github.com
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 2) -- Cause: github.com
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 3) -- Cause: github.com
WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 3) -- Cause: github.com
Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12622371)'

Caused by:
Can't stage file https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed -- reason: github.com

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Relevant files

No response

System information

No response

[Sam-Sims]

I think this is a similar issue I outlined in more detail here artic-network/fieldbioinformatics#125 with the artic minion step.

You could examine your vcf files and see if it seems similar.

Essentially it seems there are overlapping variants in the fail.vcf and pass.vcf which causes preconsensus fasta file to be masked and thus bcftools complains when applying the "pass" variant as it expects the reference but instead finds the masked "N".

Typically I have seen this happen in indels when an amplicon drops out - when medaka variant is run on the pool containing the dropped amplicon it prodcues variants that should be filtered out - but dont seem to be.

I was wondering if it was something odd/bug happening with the longshot annotation and dropped amplicons (as it doesnt happen when medaka annotate is used via the --no-longshot flag in minion) causing the artifact variants to be kept from the dropped amplicon. Unforunately I havent had to time to look further.

One way around the issue is to run minion manually using the --no-longshot flag or use bcftools norm with the --check-ref x flag to exclude those sites.

[maxulysse]

@dejenie21 I think that @Sam-Sims might be onto something.

BTW, the second script you run seems to have issue accessing file on github given the errors

[MOISECHRIST]

-[nf-core/viralrecon] Pipeline completed with errors-
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (nCoV-2019.reference.fasta)'

Caused by:
Process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (nCoV-2019.reference.fasta) terminated with an error exit status (127)

Command executed:

samtools faidx nCoV-2019.reference.fasta
cut -f 1,2 nCoV-2019.reference.fasta.fai > nCoV-2019.reference.fasta.sizes

cat <<-END_VERSIONS > versions.yml
"NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES":
getchromsizes: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
127

Command output:
(empty)

Command error:
.command.sh: ligne 2: samtools : commande introuvable

Work dir:
/home/lnsp/nfcore-tools/work/32/59e65c87859c1ac572477c409d97a9

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details
ERROR ~ Invalid method invocation call with arguments: [[MN908947.3]] (nextflow.util.ArrayBag) on _closure10 type

-- Check '.nextflow.log' file for details