Bowtie --quiet not found when using sRNAbench from the container

[RuBBiT-hj]

Hi,

I encountered some errors when using sRNAbench from the srnatoolbox container. It says "bowtie --quiet was not found to be installed. Please install first. Will quit now!." When I checked the packages in the container, it seems that bowtie2 is present but bowtie is not.

I tried to build a new container by adding bowtie, this error disappeared and the preprocessing went well. However, the mapping part still failed as it skips all the libraries. For example:

     The following library Rnor_6_0_RNAcentral seems not to be in fasta format (*.fa, *.fasta, *.mfa). Will skip this library.

######################################################################

######################################################################

     No mappings found for Rnor_6_0_RNAcentral .Probably something is wrong with the bowtie index.

I re-ran my analysis on the webpage version, and it seemed good.

The parameters from the webpage:

Input File:Library_03.fastq
 ---- Mapping parameters and Annotations ---- 
Number of allowed mismatches: 1 (mm=1) 
Alignment type: seed alignment (alignType=n) 
Length of the seed: 20 (seed=20)  
Used genome assembly bowtie1 index: Rnor_6_0_mp 
Minimum number of reads: 2 
Minimum read length: 15 
No maximum read length:   
---- ANNOTATIONS ----  
Used miRNAs reference species from MirGeneDB v2 
Used miRNAs for species: Rno 
Used ncRNA annotations:  libs=Rnor_6_0_RNAcentral (RNAcentral database 20.0) 
libs=Rnor_6_0_ncRNA (ncRNA from Ensembl release 104 (51 for Metazoan)) 
libs=Rnor_6_0_cdna (cDNA from Ensembl release 104 (51 for Metazoan)) 
 ---- Preprocessing and adapter trimming parameters: ----  
Unknown protocol: trimmed  
---No quality filtering was used (only reads with ambigous bases are filtered out- ---

The parameters I used in bash script:

mm=1
alignType=n
seed=20
species=NA
microRNA=rno
miRNA_ref=miRBase v22

libs=Rnor_6_0_RNAcentral
libs=Rnor_6_0_ncRNA
libs=Rnor_6_0_cdna
adapter=trimmed
kingdom=animal
qualityType=NA
input=sRNA/reads.fa
origInput=Library_03.fastq
inputType=fastq

I wonder if there are some potential issues about the sRNAbench part in the container, or if I uses it improperly. Thank you!

[klaasdewaele]

Hi RuBBit, I encountered a similar Bowtie error with the Docker container, which I resolved by copying installation files from /srv/bin/bin/bowtie to /usr/bin/local: sudo cp -r /srv/bin/bin/bowtie /usr/local/bin

I didn't encounter the RNAcentral error, however I did have issues in downloading the required genome reference files: 1) If I remember well, the populate script (for automated downloading of reference files) isn't in the path specified in the sRNAtoolbox manual (/opt/sRNAtoolboxDB/populate); I had to retrieve it using find. 2) Even when using the populate script, there was a persistent failure in populating the database with reference genomes, which stemmed from an error at the database/server side - only after email contact with the authors this was resolved, and perhaps this is also at play for your organism. Hope you get it solved!

[sarabioinfo]

Hi,

I had the same error. I solved it exporting Bowtie to $PATH.

I hope it can be useful to someone!