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snostrip's Introduction

snoStrip - an automatic snoRNA annotation pipeline

Current release: v2.0

Installation

Instruction for installation and configuration of "snoStrip" on Linux/Unix machines.

REQUIRED PROGRAMS

The snoStrip pipeline utilizes several open source programs for detection and property extraction of putative snoRNAs. Please ensure that the following programs are correctly installed:

  1. snoRNA detection:

    • blastall version 2.2.26 or newer
    • infernal version 1.1 or newer

  2. property extraction:

    • MUSCLE version 3.7 or newer

    • RNAsubopt version 2.1.9 or newer

    • fastacmd version 2.2.26 or newer

CONFIGURATION OF SNOSTRIP

The configuration file, the snoStrip pipeline, all necessary packages, and additional scripts are located in the folder 'bin'.

Please move into the snoStrip directory and start the configuration script by

cd bin/
./configure.sh

The configure.sh script will search for all necessary programs and additional scripts. Several snoStrip scripts will be adapted to find the path required modules.

Once the configuration process is finished, the snoStrip pipeline should work properly.

Run snoStrip

Plase read the help page of the snoStrip pipeline.

./snoStrip.pl -h

snostrip's People

Contributors

boll3 avatar janleipzig avatar

Stargazers

Guosong Jia avatar Joerg Fallmann avatar avatar

Watchers

Sven Findeiß avatar James Cloos avatar Christian Hoener zu Siederdissen avatar avatar Joerg Fallmann avatar

snostrip's Issues

BioPerl should be removed from packages

The required BioPerl packages should be made available using an existing BioPerl installation and not being part of the snoStrip source code: packages/Bio

Failed when running the conda version

Dear developers:
Thanks for developing the software!
It's hard to obtain the blastall nowadays because it was discarded from ncbi-blast. So I installed the software using Anaconda.
The commends used for software installation are attached below:

$ conda create -n snostrip python=3.6
$ conda activate snostrip
(snostrip)$ conda install -c bioconda snostrip

The software was installed successfully. However, an error occurred when running the following commands:

(snostrip)$ snoStrip.pl -d /data/a/jiaguosong/jiaguosong/reference_genome_panel/DY45019_hifi/01_smallRNA_ncRNA_annotation/smallRNA_searching/snostrip_try -k fun -g DY45019_hifiasm_final.chr.fasta -n Schizosaccharomyces osmophilus -j
Smartmatch is experimental at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1766.
Smartmatch is experimental at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1775.
Name "CONFIG::PROTOSTOMIA_FASTA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1919.
Name "CONFIG::FUNGI_FASTA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1914.
Name "CONFIG::DEUTEROSTOMIA_TARGET_RNA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1901.
Name "CONFIG::DEUTEROSTOMIA_FASTA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1929.
Name "CONFIG::FUNGI_TARGET_RNA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1904.
Name "CONFIG::PROTOSTOMIA_TARGET_RNA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1902.
Name "CONFIG::PLANT_TARGET_RNA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1903.
Name "CONFIG::PLANT_FASTA_PATH" used only once: possible typo at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1924.
Use of uninitialized value $CONFIG::FUNGI_FASTA_PATH in concatenation (.) or string at /data/a/jiaguosong/anaconda3/envs/snostrip/bin/snoStrip.pl line 1914.
ERROR:
Did not find multifasta!

Can anyone help me to solve this error?
Thanks~
Guo-Song

Illegal division by zero at searchForTargetSites.pm line 338

Hi, I was looking into using this tool to annotate snoRNA in a newly-assembled plant genome but I am unable to get it to work. This is the error I am getting:

(/homes/epi/adam/conda/snostrip) [adam@epi snoRNA]$ snoStrip.pl -g final.fasta -d Tarvense -k pla -n Thlaspi arvense
Smartmatch is experimental at bin/snoStrip/bin/snoStrip.pl line 1765.
Smartmatch is experimental at bin/snoStrip/bin/snoStrip.pl line 1774.
current snoRNA family: CD_1

Name "CONFIG::RSCRIPT" used only once: possible typo at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/scripts/blastRelatives.pl line 33.

analyze Thlaspi arvense (blast) ... ... ERROR - no blasthits found
current snoRNA family: CD_10

Name "CONFIG::RSCRIPT" used only once: possible typo at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/scripts/blastRelatives.pl line 33.

analyze Thlaspi arvense (blast) ... ... ERROR - no blasthit with sufficient score found!

current snoRNA family: CD_100

Name "CONFIG::RSCRIPT" used only once: possible typo at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/scripts/blastRelatives.pl line 33.

analyze Thlaspi arvense (blast)substr outside of string at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/scripts/blastRelatives.pl line 519.
Use of uninitialized value in concatenation (.) or string at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/scripts/blastRelatives.pl line 431.
 ... ... 1 sequence(s) found

        sequence: 1
                check for conserved target sites ...... Illegal division by zero at /scr/episan/RP03/thlaspi/RNA/snoRNA/bin/snoStrip/bin/packages/searchForTargetSites.pm line 338, <GEN0> line 87.

It seems that this normalisation step is dividing by zero in my case at L388

Remove R from snoStrip

scripts/clusterChains.R should be exchanged with a perl version (or maybe bedtools)
It's the only reason R and genomeIntervals are needed.

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