i am having trouble with the VIBRANT embedded in Viroprofiler

Question

[krmoon518]

Hi, I am trying to run the Viroprofiler, the new program to analyze viral metagenome data. Since the Viroprofiler encompasses multiple programs to run them all at once, I am facing error message after error message while running the command.

While I was running my command as suggested,

$nextflow run deng-lab/viroprofiler -r main -profile singularity --input my_samplesheet.csv --outdir viroprofile_contig -c example_custom.config -resume

I am constantly failing at the VIBRANT step:

iexecutor >  local (2)
[7a/cd37fc] process > VIROPROFILER:FASTQC (DNA1)           [100%] 1 of 1, cached: 1 V
[0f/d20086] process > VIROPROFILER:FASTP (DNA1)            [100%] 1 of 1, cached: 1 V
[1d/13e669] process > VIROPROFILER:SPADES (DNA1)           [100%] 1 of 1, cached: 1 V
[41/10bf58] process > VIROPROFILER:CONTIGLIB                         [100%] 1 of 1, cached: 1 V
[7c/e620a8] process > VIROPROFILER:CHECKV                            [100%] 1 of 1, cached: 1 V
[fb/2f4712] process > VIROPROFILER:CONTIGLIB_CLUSTER                 [100%] 1 of 1, cached: 1 V
[7c/37f9c3] process > VIROPROFILER:GENEPRED4CTG                      [100%] 1 of 1, cached: 1 V
[f3/3335a3] process > VIROPROFILER:NRPROT                            [100%] 1 of 1, cached: 1 V
[6a/63739d] process > VIROPROFILER:NRGENE                            [100%] 1 of 1, cached: 1 V
[14/70c324] process > VIROPROFILER:CONTIGINDEX                       [100%] 1 of 1, cached: 1 V
[22/13bc44] process > VIROPROFILER:MAPPING2CONTIGS2 (DNA1) [  0%] 0 of 1
[-        ] process > VIROPROFILER:ABUNDANCE                         -
[10/fc4cb3] process > VIROPROFILER:VIBRANT                           [100%] 1 of 1, failed: 1 X
[d6/32181e] process > VIROPROFILER:DVF                               [100%] 1 of 1, cached: 1 V
[-        ] process > VIROPROFILER:VIRCONTIGS_PRE                    -
[-        ] process > VIROPROFILER:VIRSORTER2                        -
[-        ] process > VIROPROFILER:DRAMV                             -
[-        ] process > VIROPROFILER:TAXONOMY_VCONTACT                 -
[-        ] process > VIROPROFILER:TAXONOMY_MMSEQS                   -
[-        ] process > VIROPROFILER:TAXONOMY_MERGE                    -
[-        ] process > VIROPROFILER:VIRALHOST_IPHOP                   -
[-        ] process > VIROPROFILER:BACPHLIP                          -
[-        ] process > VIROPROFILER:RESULTS_TSE                       -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS       -
[-        ] process > VIROPROFILER:MULTIQC                           -
Execution cancelled -- Finishing pending tasks before exit

The error message on the screen says:

ERROR ~ Error executing process > 'VIROPROFILER:VIBRANT'

Caused by:
Missing output file(s) "VIBRANT_contigs/VIBRANT_results_contigs/VIBRANT_genome_quality_contigs.tsv`expected by process`VIROPROFILER:VIBRANT"

and the log says,

VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py.

I have already installed the required version of VIBRANT with all the legitimate databases on my Linux.

I have no idea where and how to fix this error..

can someone please help me?

Thank you in advance!

Answer 1

[tahsinkhan570]

the database for vibrant is not installed, eventhough downloads successfully.

go to path/to/db/vibrant/database/

pip install matplotlib #required dependency for vibrant

python3 VIBRANT_setup.py 

it will download necessary files and uncompress using hmmer (hmmpress)

Best wishes