Error running version 2.6.0 with Nanopore data in process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION

[AdrianMBarrera]

Description of the bug

Hi, everyone!

Our team have been using the latest version (2.6.0) of ViralRecon to process Illumina data for a while without any issues. However, if we try to test it with Nanopore data some errors arised during the execution of ARTIC_MINION subworkflow.

Change to version 2.5 seems to fix it and all process ended successfully.

Thank you in advance,
Adrián Muñoz

Command used and terminal output

# Activate conda environment:
conda activate nf-core

# Command:
nextflow run nf-core/viralrecon -r 2.6.0 \
  --input SampleSheet.csv \
  --platform nanopore \
  --protocol amplicon \
  --outdir results \
  --genome MN908947.3 \
  --primer_set artic \
  --primer_set_version 1200 \
  --fastq_dir ../../fastq_pass \
  --fast5_dir ../../fast5_pass \
  --sequencing_summary ../../sequencing_summary.txt \
  -profile docker

# Error message:
-[nf-core/viralrecon] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (150421716)'

Caused by:
  Process `NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (150421716)` 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  --minimap2 \
      --threads 12 \
      --read-file SAMPLE_1.fastq.gz \
      --scheme-directory ./primer-schemes \
      --scheme-version 1200 \
       \
      --fast5-directory fast5_pass \
      --sequencing-summary sequencing_summary.txt \
      nCoV-2019 \
      150421716
  
  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:
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
  [M::mm_idx_stat::0.010*3.53] distinct minimizers: 5587 (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332; total length: 29903
  [M::worker_pipeline::11.199*3.92] mapped 222915 sequences
  [M::main] Version: 2.24-r1122
  [M::main] CMD: minimap2 -a -x map-ont -t 12 ./primer-schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 150421716.fastq.gz
  [M::main] Real time: 11.206 sec; CPU: 43.963 sec; Peak RSS: 0.366 GB
  HDF5-DIAG: Error detected in HDF5 (1.10.6) thread 139721650939648:
    #000: H5Dio.c line 199 in H5Dread(): can't read data
      major: Dataset
      minor: Read failed
    #001: H5Dio.c line 603 in H5D__read(): can't read data
      major: Dataset
      minor: Read failed
    #002: H5Dchunk.c line 2293 in H5D__chunk_read(): unable to read raw data chunk
      major: Low-level I/O
      minor: Read failed
    #003: H5Dchunk.c line 3658 in H5D__chunk_lock(): data pipeline read failed
      major: Dataset
      minor: Filter operation failed
    #004: H5Z.c line 1301 in H5Z_pipeline(): required filter 'vbz' is not registered
      major: Data filters
      minor: Read failed
    #005: H5PLint.c line 270 in H5PL_load(): search in path table failed
      major: Plugin for dynamically loaded library
      minor: Can't get value
    #006: H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in path /usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin encountered an error
      major: Plugin for dynamically loaded library
      minor: Can't get value
    #007: H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin
      major: Plugin for dynamically loaded library
      minor: Can't open directory or file
  The fast5 file is compressed with VBZ but the required plugin is not loaded. Please read the instructions here: https://github.com/nanoporetech/vbz_compression/issues/5
  HDF5-DIAG: Error detected in HDF5 (1.10.6) thread 139721551283968:
    #000: H5T.c line 1754 in H5Tclose(): not a datatype
      major: Invalid arguments to routine
      minor: Inappropriate type
  HDF5-DIAG: Error detected in HDF5 (1.10.6) thread 139721551283968:
    #000: H5T.c line 1754 in H5Tclose(): not a datatype
      major: Invalid arguments to routine
  
      minor: Inappropriate type
  Running: nanopolish index -s sequencing_summary.txt -d fast5_pass SAMPLE_1.fastq.gz
  Running: minimap2 -a -x map-ont -t 12 ./primer-schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta SAMPLE_1.fastq.gz | samtools view -bS -F 4 - | samtools sort -o SAMPLE_1.sorted.bam -
  Running: samtools index SAMPLE_1.sorted.bam
  Running: align_trim --normalise 500 ./primer-schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --start --remove-incorrect-pairs --report SAMPLE_1.alignreport.txt < SAMPLE_1.sorted.bam 2> SAMPLE_1.alignreport.er | samtools sort -T SAMPLE_1 - -o SAMPLE_1.trimmed.rg.sorted.bam
  Running: align_trim --normalise 500 ./primer-schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --remove-incorrect-pairs --report SAMPLE_1.alignreport.txt < SAMPLE_1.sorted.bam 2> SAMPLE_1.alignreport.er | samtools sort -T SAMPLE_1 - -o SAMPLE_1.primertrimmed.rg.sorted.bam
  Running: samtools index SAMPLE_1.trimmed.rg.sorted.bam
  Running: samtools index SAMPLE_1.primertrimmed.rg.sorted.bam
  Running: nanopolish variants --min-flanking-sequence 10 -x 1000000 --progress -t 12 --reads SAMPLE_1.fastq.gz -o SAMPLE_1.vcf -b SAMPLE_1.trimmed.rg.sorted.bam -g ./primer-schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta -w "MN908947.3:1-29904" --ploidy 1 -m 0.15 --read-group 2 
  Command failed:nanopolish variants --min-flanking-sequence 10 -x 1000000 --progress -t 12 --reads SAMPLE_1.fastq.gz -o SAMPLE_1.2.vcf -b SAMPLE_1.trimmed.rg.sorted.bam -g ./primer-schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta -w "MN908947.3:1-29904" --ploidy 1 -m 0.15 --read-group 2 

Work dir:
  ./work/91/1e0d7ccd56770126e42995155e9181

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

Relevant files

No response

System information

• Nextflow version: 23.10.0.5889
• Hardware: Desktop server
• Executor: local
• Container engine: Docker
• OS: CentOS 7
• Version of nf-core/viralrecon: 2.6.0