[Bug]: Verkko 2.2.1 not found error

[Kincekara]

What container were you trying to use, and how were you attempting to use it?

verkko --help returns not found error.

Relevant log output

/opt/conda/bin/verkko: 21: [[: not found
/opt/conda/bin/verkko: 25: [[: not found
/opt/conda/bin/verkko: 29: [[: not found
/opt/conda/bin/verkko: 29: linux: not found
/opt/conda/bin/verkko: 33: [[: not found
/opt/conda/bin/verkko: 37: [[: not found
/opt/conda/bin/verkko: 41: [[: not found
/opt/conda/bin/verkko: 45: [[: not found
/opt/conda/bin/verkko: 49: [[: not found
/opt/conda/bin/verkko: 60: [[: not found
/opt/conda/bin/verkko: 64: [[: not found
/opt/conda/bin/verkko: 68: [[: not found
/opt/conda/bin/verkko: 68: linux: not found
/opt/conda/bin/verkko: 73: [[: not found
/opt/conda/bin/verkko: 77: [[: not found
/opt/conda/bin/verkko: 81: [[: not found

[erinyoung]

Does it not print out the rest of the help message?

Below is the expectation:

#9 [test 1/5] RUN verkko --help
#9 0.052 /opt/conda/bin/verkko: 21: [[: not found
#9 0.052 /opt/conda/bin/verkko: 25: [[: not found
#9 0.052 /opt/conda/bin/verkko: 29: [[: not found
#9 0.052 /opt/conda/bin/verkko: 29: linux: not found
#9 0.052 /opt/conda/bin/verkko: 33: [[: not found
#9 0.052 /opt/conda/bin/verkko: 37: [[: not found
#9 0.052 /opt/conda/bin/verkko: 41: [[: not found
#9 0.052 /opt/conda/bin/verkko: 45: [[: not found
#9 0.052 /opt/conda/bin/verkko: 49: [[: not found
#9 0.054 /opt/conda/bin/verkko: 60: [[: not found
#9 0.054 /opt/conda/bin/verkko: 64: [[: not found
#9 0.054 /opt/conda/bin/verkko: 68: [[: not found
#9 0.054 /opt/conda/bin/verkko: 68: linux: not found
#9 0.054 /opt/conda/bin/verkko: 73: [[: not found
#9 0.054 /opt/conda/bin/verkko: 77: [[: not found
#9 0.054 /opt/conda/bin/verkko: 81: [[: not found
#9 0.087 usage: /opt/conda/bin/verkko -d <output-directory> --hifi <hifi-reads ...> --nano <nanopore-reads ...>
#9 0.087   MANDATORY PARAMETERS:
#9 0.087     -d <output-directory>    Directory to use for verkko intermediate and final results.
#9 0.087                              Will be created if needed.
#9 0.087     --hifi <files ...>       List of files containing PacBio HiFi reads.
#9 0.087                              Input reads can be any combination of FASTA/FASTQ,
#9 0.087                              uncompressed or gzip/bzip2/xz compressed.  Any
#9 0.087                              number of files can be supplied; *.gz works.
#9 0.087     --nano <files ...>       List of files containing Oxford Nanopore reads.
#9 0.087 
#9 0.087                              Input reads can be any combination of FASTA/FASTQ/SAM/BAM,
#9 0.087                              uncompressed or gzip/bzip2/xz compressed.  Any
#9 0.087                              number of files can be supplied; *.gz works.
#9 0.087 
#9 0.087   ALGORITHM PARAMETERS:
#9 0.087     --no-correction          Do not perform Canu correction on the HiFi reads.
#9 0.087     --no-nano                Assemble without ONT data.
#9 0.087 
#9 0.087     --hap-kmers h1 h2 type   Use rukki to assign paths to haplotypes.  'h1' and 'h2
#9 0.087                              must be Meryl databases of homopolymer-compressed parental
#9 0.087                              kmers.  'type' must be 'trio', 'hic' or 'strandseq'.
#9 0.087 
#9 0.087     --hic1 <files ...>       List of files containing left hic reads.
#9 0.087     --hic2 <files ...>       List of files containing right hic reads.
#9 0.087                              Order of left and right files should be same, no interlaced files allowed.
#9 0.087                              Input reads can be any combination of FASTA/FASTQ/SAM/BAM,
#9 0.087                              uncompressed or gzip/bzip2/xz compressed.  Any
#9 0.087                              number of files can be supplied; *.gz works.
#9 0.087 
#9 0.087     --porec <files>          List of files containing Pore-C reads.
#9 0.087                              Input reads can be any combination of FASTA/FASTQ/SAM/BAM,
#9 0.087                              uncompressed or gzip/bzip2/xz compressed.  Any
#9 0.088                              number of files can be supplied; *.gz works.
#9 0.088 
#9 0.088     --no-rdna-tangle         Switch off option that helps to proceed large rDNA tangles which may connect multiple chromosomes.
#9 0.088     --telomere-motif         Switch to user-supplied telomere motif, automatically searched in fwd/revcomp version.
#9 0.088                              By default, the cannonical vertebrate 'CCCTAA' motif is used during Hi-C scaffolding.
#9 0.088     --ref <path>             Path to optional reference. It is used only as a guidance during scaffolding.
#9 0.088     --uneven-depth           Disable coverage-based heuristics in homozygous nodes detection for Hi-C/PoreC phasing.
#9 0.088     --haplo-divergence       Estimation on maximum divergence between haplotypes, is used only with Hi-C/PoreC data.
#9 0.088                              Should be increased for species with divergence significantly higher than in human. Default: 0.05, min 0, max 0.2
#9 0.088 
#9 0.088     --screen <contaminant_name> </full/path/to/contaminant.fasta>
#9 0.088                              Screens contaminant from provided file. Multiple screen commands are allowed and are additive.
#9 0.088                              To screen typical contaminants of human assemblies one can use --screen-human-contaminants option with no parameters, which removes rDNA, mitochondria and EBV.
#9 0.088 
#9 0.088     --paths <paths.gaf>      Option required to generate fasta file from user-provided paths through assembly graph.
#9 0.088                              Requires an existing assembly specified by '--assembly <path_to_assembly>' and input reads.
#9 0.088                              Output is specified as '-d <output_dir>' (<output_dir> should  not be equal to <path_to_assembly>).
#9 0.088                              The gaf file must be formatted as follows: 'name >utig4-1<utig4-2 HAPLOTYPE1' with one path per line,
#9 0.088                              where utig4-1 is in fwd orientation and utig4-2 is in reverse complement.
#9 0.088 
#9 0.088   COMPUTATIONAL PARAMETERS:
#9 0.088     --python <interpreter>   Path or name of a python interpreter.  Default: 'python'.
#9 0.088     --perl <interpreter>     Path of name of a perl interpreter.  Default: 'perl'.
#9 0.088     --mbg <path>             Path to MBG.             Default for all three
#9 0.088     --graphaligner <path>    Path to GraphAligner.    one packaged with verkko.
#9 0.088     --mashmap <path>         Path to MashMap.
#9 0.088     --seqtk <path>           Path to seqtk.
#9 0.088     --winnowmap <path>       Path to Winnowmap.
#9 0.088     --minimap   <path>       Path to minimap2.
#9 0.088     --bwa <path>             Path to BWA.
#9 0.088     --samtools <path>        Path to Samtools.
#9 0.088 
#9 0.088     --cleanup                Remove intermediate results.
#9 0.088     --no-cleanup             Retain intermediate results (default).
#9 0.088 
#9 0.088     --local                  Run on the local machine (default).
#9 0.088     --local-memory           Specify the upper limit on memory to use, in GB, default 64
#9 0.088     --local-cpus             Specify the number of CPUs to use, default 'all'
#9 0.088 
#9 0.088     --grid                   Enable Grid support (SGE, Slurm, PBS, and LSF are supported).
#9 0.088 
#9 0.088     --snakeopts <string>     Append snakemake options in "string" to the
#9 0.088                              snakemake command.  Options MUST be quoted.
#9 0.088 
#9 0.088     --sto-run                Set resource limits for various stages.
#9 0.088     --ovb-run                Format: number-of-cpus memory-in-gb time-in-hours
#9 0.088     --ovs-run                  --cns-run 8 32 2
#9 0.088     --red-run
#9 0.088     --mbg-run
#9 0.088     --utg-run
#9 0.088     --spl-run
#9 0.088     --ali-run
#9 0.088     --pop-run
#9 0.088     --utp-run
#9 0.088     --lay-run
#9 0.088     --sub-run
#9 0.088     --par-run
#9 0.088     --cns-run
#9 0.088     --ahc-run
#9 0.088     --fhc-run
#9 0.088     --shc-run
#9 0.088 
#9 0.088 ADVANCED MODULE PARAMETERS (expert users):
#9 0.088 HiFi read correction:
#9 0.088     --correct-k-mer-size           Set the k-mer size to use for finding overlaps (425)
#9 0.088     --correct-k-mer-window         Set the window size for sketching reads when finding overlaps (19)
#9 0.088     --correct-k-mer-coverage       Set the maximum count of kmer to use for finding overlaps (1000)
#9 0.088     --correct-min-read-length      Set the overall minimum read length (4000)
#9 0.088     --correct-min-overlap-length   Set the minimum overlap length (1000)
#9 0.088     --correct-batch-size           Set the RED batch size, in Mbp (30000)
#9 0.088                                    (might also need to adjust --red-run)
#9 0.088     
#9 0.088 MBG:
#9 0.088     --base-k
#9 0.088     --max-k
#9 0.088     --window
#9 0.088     --threads
#9 0.088     --unitig-abundance
#9 0.088     --hifi-coverage
#9 0.088     
#9 0.088 ONT splitting:
#9 0.088     --split-bases
#9 0.088     --split-reads
#9 0.088     --min-ont-length
#9 0.088     
#9 0.088     
#9 0.088 GraphAligner:
#9 0.088     --seed-min-length
#9 0.088     --seed-max-length
#9 0.088     --align-bandwidth
#9 0.088     --score-fraction
#9 0.088     --min-identity
#9 0.088     --min-score
#9 0.088     --end-clipping
#9 0.088     --incompatible-cutoff
#9 0.088     --max-trace
#9 0.088     --haploid                      Better ONT alignment for haploid genomes
#9 0.088 
#9 0.088   Verkko module path: /opt/conda/lib/verkko/

[Kincekara]

@erinyoung It prints the rest of the help message after the errors as you shared.