Open RuBBiT-hj opened 1 year ago
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!
Hi,
I had the same error. I solved it exporting Bowtie to $PATH.
I hope it can be useful to someone!
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:
I re-ran my analysis on the webpage version, and it seemed good.
The parameters from the webpage:
The parameters I used in bash script:
I wonder if there are some potential issues about the sRNAbench part in the container, or if I uses it improperly. Thank you!