Browco
commented
4 years ago Hi,
I know this issue is 4months old but I had the same "problem" and I found the solution, so if it can helps someone with the same error..
Based on the README (https://github.com/pmelsted/pizzly) :
So, kallisto quant creates an "output" directory and some files like fusion.txt with :
kallisto quant -i index.idx --fusion -o output r1.fastq.gz r2.fastq.gz
and then this directory is used by pizzly with
pizzly -k 31 --gtf transcripts.gtf --cache index.cache.txt --align-score 2 \ --insert-size 400 --fasta transcripts.fa.gz --output test output/fusion.txt <-- here
What I didn't understand was the role of "test" in --output argument, which is just a prefix for output files, and must be written by the user.
So don't forget to write this prefix AND to specify the kallisto quant output directory.
Hello - not sure what I am doing wrong to get this error despite providing all necessary files in correct format with correct arguments. After running pizzly, I get "pizzly: Not enough arguments were provided". The fusion.txt was generated in kallisto quant step (did not get a fusion.json).