I am trying to use biobloom tool to categorize sequences of sample that I have. I have to use one command like below:
./biobloomcategorizer -e –p /output/prefix –f "filter1.bf filter2.bf filter3.bf" inputReads1_1.fq inputreads1_2.fq
Since I have so many files about 19000, I have to use bash scripting. The command I am using is like one-liner below. The fastq files and all
.bf files are in a same directory but when I am writing the script in this way, biobloomcategorizer is not working at all while there is no issue with the tool itself as I tried the command above for only a few files. Can anyone tell me how should I modify the script below to make the tool work for so many files that I have?
for i in *.bf; do biobloomcategorizer -e –p /output/prefix –f echo \"$i\" filename_1.fastq filename_2.fastq; done