epi2me-labs/wf-cnv failed during analysis

[Ligerd5]

Hello, I am new to epi2melabs. I want to analysis CNV in CYP2D6 in chromosome 22. I followed the example on the epi2me/wf-cnv website.

nextflow run epi2me-labs/wf-cnv --fastq /srv/nabi/EPIMOL_Malaria/FASTQ_CYPD6/fastq_pass/COMBINED/isolate01-COMBINED.fastq.gz --reference /srv/nabi/EPIMOL_Malaria/copy_number/hg38.fa.gz --bin_size 500

Here is the error message I got and I do not understand how to go about it. Please can I get help on this

|||||||||| _ __ _ __ ____ |||||||||| | ____| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-cnv v0.0.9-g956b861

Core Nextflow options revision : master runName : modest_coulomb containerEngine: docker launchDir : /srv/nabi/EPIMOL_Malaria/copy_number workDir : /srv/nabi/EPIMOL_Malaria/copy_number/work projectDir : /home/nabi/.nextflow/assets/epi2me-labs/wf-cnv userName : nabi profile : standard configFiles : /home/nabi/.nextflow/assets/epi2me-labs/wf-cnv/nextflow.config

Input Options fastq : /srv/nabi/EPIMOL_Malaria/FASTQ_CYPD6/fastq_pass/COMBINED/isolate01-COMBINED.fastq.gz reference : /srv/nabi/EPIMOL_Malaria/copy_number/hg38.fa.gz

Advanced Options map_threads : 4

!! Only displaying parameters that differ from the pipeline defaults !!

If you use epi2me-labs/wf-cnv for your analysis please cite:

• The nf-core framework https://doi.org/10.1038/s41587-020-0439-x

---

This is epi2me-labs/wf-cnv v0.0.9-g956b861.

ERROR ~ wf-cnv is now deprecated and will no longer receive updates, please use wf-human-variation

-- Check '.nextflow.log' file for details Checking fastq input. Single file input detected. executor > local (3) [8d/acadf5] process > pipeline:getVersions [ 0%] 0 of 1 [1b/4e5fc0] process > pipeline:getParams [ 0%] 0 of 1 [69/9f749c] process > pipeline:getGenome [ 0%] 0 of 1 ✔ [- ] process > pipeline:concatenateReads - [- ] process > pipeline:alignment - [- ] process > pipeline:samtoolsIndex - [- ] process > pipeline:callCNV - [- ] process > pipeline:makeReport - [- ] process > output - ERROR ~ Error executing process > 'pipeline:getGenome'

Caused by: Process pipeline:getGenome terminated with an error exit status (127)

Command executed:

faSize -detailed -tab hg38.fa.gz > hg38.fa.gz_genome.txt workflow-glue get_genome --chr_counts hg38.fa.gz_genome.txt -o output.txt genome_string=cat output.txt

Command exit status: 127

Command output: (empty)

Command error: .command.run: line 290: docker: command not found

Work dir: /srv/nabi/EPIMOL_Malaria/copy_number/work/69/9f749c4fb6d59b8cfd7f5256c9cf98

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 ~ The genome build detected is not compatible with this workflow. Please check the reference sequence and try again.

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

I honestly do not knw how to troubleshoot this message. Any help please. Thank you

[rarthur-eicc]

This is the viralrecon repo. Did you mean to go here ?

[Ligerd5]

I followed the example from https://github.com/epi2me-labs/wf-cnv website. I did not use the sample sheet this time. I used it before and still got an error message.

[Ligerd5]

I do not understand what this phrase in the error message mean

Caused by: Process pipeline:getGenome terminated with an error exit status (127) Command executed:

faSize -detailed -tab hg38.fa.gz > hg38.fa.gz_genome.txt workflow-glue get_genome --chr_counts hg38.fa.gz_genome.txt -o output.txt genome_string=cat output.txt

Command exit status: 127

If I understand then I might try to troubleshoot.

[rarthur-eicc]

Dude, you’re on the wrong GitHub… wrong software package.

[Ligerd5]

Oh. Thank you so much. Will go the right one.

[maxulysse]

@Ligerd5 I closed your issue

[Ligerd5]

Great. Thank you.