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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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