samtools: command not found

[cailiangliang765]

nextflow run CRG-CNAG/CalliNGS-NF --gatk /home/cllcentosvm/GenomeAnalysisTK.jar

N E X T F L O W ~ version 19.04.1 Launching CRG-CNAG/CalliNGS-NF` [irreverentpasteur] - revision: e9e0fcf [master] C A L L I N G S - N F v 1.0 genome : /home/cllcentosvm/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/genome.fa reads : /home/cllcentosvm/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/reads/rep1{1,2}.fq.gz variants : /home/cllcentosvm/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/known_variants.vcf.gz blacklist: /home/cllcentosvm/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/blacklist.bed results : results gatk : /home/cllcentosvm/GenomeAnalysisTK.jar [warm up] executor > local executor > local (4) [22/5f3c38] process > 1C_prepare_star_genome_index [100%] 1 of 1, failed: 1 [5c/fed7e8] process > 1A_prepare_genome_samtools [100%] 1 of 1, failed: 1 ✘ [db/b888c0] process > 1B_prepare_genome_picard [100%] 1 of 1, failed: 1 [13/3808c1] process > 1D_prepare_vcf_file [200%] 2 of 1, failed: 2 ✘ WARN: Killing pending tasks (3) ERROR ~ Error executing process > '1A_prepare_genome_samtools (genome)'

Caused by: Process 1A_prepare_genome_samtools (genome) terminated with an error exit status (127)

Command executed:

samtools faidx genome.fa

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 2: samtools: command not found

Work dir: /home/cllcentosvm/work/5c/fed7e8c936daf9d7177e140378b822

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

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

[pditommaso]

A better text formatting would be appreciated.

[cailiangliang765]

A better text formatting would be appreciated.

Thanks for your reminder. I had reformatted this issue.

[pditommaso]

I guess it does not found because you are running it without enabling docker. Add the -with-docker option on the run command.