Someone has experience with KNIFE software for circRNA detection?

Question

[najibveto]

I am getting troubles to run KNIFE in my Linux box. Here is the command and the output of the system. Someone has experienced such kind of error?. Thanks in advance.

COMMAND:

./completeRun.sh /home/fenguita/work/Nuno_FA_circRNAs/raw/ complete /home/fenguita/work/Nuno_FA_circRNAs/results/ output 8

OUTPUT

./findCircularRNA.sh "/home/fenguita/work/Nuno_FA_circRNAs/raw/ complete /home/fenguita/work/Nuno_FA_circRNAs/results/ output 8"
./findCircularRNA.sh: 72: ./findCircularRNA.sh: [[: not found
./findCircularRNA.sh: 83: ./findCircularRNA.sh: [[: not found
cat: /home/fenguita/work/Nuno_FA_circRNAs/results//taskIdFiles/output.txt: No such file or directory
./findCircularRNA.sh: 144: ./findCircularRNA.sh: Syntax error: Bad for loop variable

Answer 1

[WouterDeCoster]

According to https://github.com/lindaszabo/KNIFE/tree/master/circularRNApipeline_Standalone you are missing an argument:

##########################
### USAGE
############################

sh completeRun.sh read_directory read_id_style alignment_parent_directory

[najibveto]

thanks a lot for your help.

[WouterDeCoster]

I moved my comment to an answer, if this indeed solved your question you can now also accept it.

[archana.bioinfo87]

Hi dear,

I did the same according to USAGE but still getting same error.

sh completeRun.sh /mnt/c/Users/ark446/Downloads/SRR_files/ complete /mnt/c/Users/ark446/Downloads/outfile_knife/

Please let me know where I have to correct. Its quite urgent for me.

Thanks

Answer 2

[jianxiangshi]

Please refer to this solution: https://github.com/lindaszabo/KNIFE/tree/master/testData

I have encountered the same error. But I get KNIFE to work after I disable dash for sh by re-configuring sh.

sudo dpkg-reconfigure dash