search

tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
134 stars 37 forks source link

samtools --version #274

Closed petroslad closed 3 years ago

petroslad commented 4 years ago

Hello there seems to be an issue with nullarbor using samtools: [20:26:50] This is snippy 4.4.3 [20:26:50] Written by Torsten Seemann [20:26:50] Obtained from https://github.com/tseemann/snippy [20:26:50] Detected operating system: linux [20:26:50] Enabling bundled linux tools. [20:26:50] Found bwa - /home/petros/anaconda3/envs/nullarbor/bin/bwa [20:26:50] Found bcftools - /home/petros/anaconda3/envs/nullarbor/bin/bcftools [20:26:50] Found samtools - /home/petros/anaconda3/envs/nullarbor/bin/samtools [20:26:50] Found java - /home/petros/anaconda3/envs/nullarbor/bin/java [20:26:50] Found snpEff - /home/petros/anaconda3/envs/nullarbor/bin/snpEff [20:26:50] Found samclip - /home/petros/anaconda3/envs/nullarbor/bin/samclip [20:26:50] Found seqtk - /home/petros/anaconda3/envs/nullarbor/bin/seqtk [20:26:50] Found parallel - /home/petros/anaconda3/envs/nullarbor/bin/parallel [20:26:50] Found freebayes - /home/petros/anaconda3/envs/nullarbor/bin/freebayes [20:26:50] Found freebayes-parallel - /home/petros/anaconda3/envs/nullarbor/bin/freebayes-parallel [20:26:50] Found fasta_generate_regions.py - /home/petros/anaconda3/envs/nullarbor/bin/fasta_generate_regions.py [20:26:50] Found vcfstreamsort - /home/petros/anaconda3/envs/nullarbor/bin/vcfstreamsort [20:26:50] Found vcfuniq - /home/petros/anaconda3/envs/nullarbor/bin/vcfuniq [20:26:50] Found vcffirstheader - /home/petros/anaconda3/envs/nullarbor/bin/vcffirstheader [20:26:50] Found gzip - /usr/bin/gzip [20:26:50] Found vt - /home/petros/anaconda3/envs/nullarbor/bin/vt [20:26:50] Found snippy-vcf_to_tab - /home/petros/anaconda3/envs/nullarbor/bin/snippy-vcf_to_tab [20:26:50] Found snippy-vcf_report - /home/petros/anaconda3/envs/nullarbor/bin/snippy-vcf_report [20:26:50] Need samtools --version >= 1.7 but you have 1.10 - please upgrade it.

The installed version is the latest one