tamburinif/StrainSifter

bash: bamtools: command not found

annarerra opened this issue · 0 comments

annarerra commented

Hello,

When I run the command snakemake {prefix}.tree.pdf i have an error bash: bamtools: command not found
and a bit later this:

Error in rule bwa_align:
jobid: 36
output: filtered_bam/sample2.filtered.bam
shell:
bwa mem -t 1 /site/ly/work/projects/Share/ESPRIOAC_FUI/WGSre/127_patient1_clones_metasamples_freqvar/DB/patient1_plvt_19004237701_clB1_21_ref.20201007.fasta /site/ly/work/projects/Share/ESPRIOAC_FUI/WGSre/127_patient1_clones_metasamples_freqvar/Raw/patient1_plvt_19004237701_clB1_23_S25_R1_001.fastq.gz /site/ly/work/projects/Share/ESPRIOAC_FUI/WGSre/127_patient1_clones_metasamples_freqvar/Raw/patient1_plvt_19004237701_clB1_23_S25_R2_001.fastq.gz | samtools view -b -q 60 | bamtools filter -tag 'NM:<=5' | samtools sort --threads 1 -o filtered_bam/sample2.filtered.bam
(exited with non-zero exit code)

Do you have an idea what can be the problem?
(bamtools & samtools (1.11) are already installed in the environment)

environment.yaml:
name: ssift
channels:

  • conda-forge
  • r
  • bioconda
  • defaults
    dependencies:
  • bwa
  • samtools
  • ncurses
  • bamtools
  • bedtools
  • MUSCLE
  • FastTree
  • r-ggplot2
  • bioconductor-ggtree
  • r-phangorn
  • snakemake=5.6.0

Thank you in advance :)