Snippy --check , Need to upgrade snpEff?? URGENT PLEASE

[FabioMiglioransa]

dear all,

Im having problems to run snippy 4.6.0 When I --check dependencies, I receive the following message:

[11:09:57] This is snippy 4.6.0 [11:09:57] Written by Torsten Seemann [11:09:57] Obtained from https://github.com/tseemann/snippy [11:09:57] Detected operating system: linux [11:09:57] Enabling bundled linux tools. [11:09:57] Found bwa - /home/fabio/miniconda3/envs/snippy2/bin/bwa [11:09:57] Found bcftools - /home/fabio/miniconda3/envs/snippy2/bin/bcftools [11:09:57] Found samtools - /home/fabio/miniconda3/envs/snippy2/bin/samtools [11:09:57] Found java - /home/fabio/miniconda3/envs/snippy2/bin/java [11:09:57] Found snpEff - /home/fabio/miniconda3/envs/snippy2/bin/snpEff [11:09:58] Found samclip - /home/fabio/miniconda3/envs/snippy2/bin/samclip [11:09:58] Found seqtk - /home/fabio/miniconda3/envs/snippy2/bin/seqtk [11:09:58] Found parallel - /home/fabio/miniconda3/envs/snippy2/bin/parallel [11:09:58] Found freebayes - /home/fabio/miniconda3/envs/snippy2/bin/freebayes [11:09:58] Found freebayes-parallel - /home/fabio/miniconda3/envs/snippy2/bin/freebayes-parallel [11:09:58] Found fasta_generate_regions.py - /home/fabio/miniconda3/envs/snippy2/bin/fasta_generate_regions.py [11:09:59] Found vcfstreamsort - /home/fabio/miniconda3/envs/snippy2/bin/vcfstreamsort [11:09:59] Found vcfuniq - /home/fabio/miniconda3/envs/snippy2/bin/vcfuniq [11:09:59] Found vcffirstheader - /home/fabio/miniconda3/envs/snippy2/bin/vcffirstheader [11:09:59] Found gzip - /usr/bin/gzip [11:09:59] Found vt - /home/fabio/miniconda3/envs/snippy2/bin/vt [11:10:00] Found snippy-vcf_to_tab - /home/fabio/miniconda3/envs/snippy2/bin/snippy-vcf_to_tab [11:10:00] Found snippy-vcf_report - /home/fabio/miniconda3/envs/snippy2/bin/snippy-vcf_report [11:10:00] Checking version: samtools --version is >= 1.7 - ok, have 1.12 [11:10:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.12 [11:10:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.5 [11:10:01] Need snpEff -version >= 4.3 but you have 3.7 - please upgrade it.

I have noticed though, that while installing in a conda environment, it appeared [ snpEff--5.0] version. So Im not sure why Im receiving this warning. Everything else seems fine.

is there anything I can do to solve this issue? How can I check the current version of snpEff and/or update/upgrade it??

I would really appreciate some help.

Thanks in advance

[FabioMiglioransa]

update

I used this line of code:

parse_version('snpEff --version', 5.0, qr/snpEff\s(\d+.\d+)/ms)

in /miniconda3/envs/snippy/bin/snpEff and it seems to have worked well, as now I read that ' dependencies look good'.

but now Im getting this message in the log file:

parse_version( 'snpEff --version', 5.0, qr/snpEff\s(\d+.\d+)/ms) ^ SyntaxError: unexpected character after line continuation character

:/ any ideas?

[biobrad]

when you are in your conda environment, you can try: conda install -c bioconda snpEff=4.3

see how that goes.