samtools: command not found
cailiangliang765 opened this issue · 3 comments
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` [irreverent_pasteur] - 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`
A better text formatting would be appreciated.
A better text formatting would be appreciated.
Thanks for your reminder. I had reformatted this issue.
I guess it does not found because you are running it without enabling docker. Add the -with-docker option on the run command.