renekat

Hello, I'm having this issue too.

Guillaume, Turns out that I had a wrong path to some data, which was causing my NullPointer Exception error. When I removed the -da option from my code I was able to see the assertion error which told me what the exact issue was. Not sure if this feedback will help with your error, but wanted to share. Best, René

Hello Guillaume, I am getting this "Exception in thread "main" java.lang.NullPointerException" error message too. Exception in thread "main" java.lang.NullPointerException at jgi.BBDuk.<init>(BBDuk.java:964) at jgi.RQCFilter2.ktrim(RQCFilter2.java:1808) at jgi.RQCFilter2.process(RQCFilter2.java:974) at jgi.RQCFilter2.main(RQCFilter2.java:71)</init> My code is: rqcfilter2.sh \ in=Illumina_reads.fq.gz \ rqcfilterdata=/RQCFilterData path=/Results/2019.09.10 \ int=t qtrim=rl removehuman=t removedog=t...

Hello! I have a directory of genomes (fasta files), each fasta file having multiple sequences. My question are: 1. Do I need to concatonate the sequences in each file in order for randomreads to work? Or, will it automatically detect multiple sequences in the file and make reads from all of them? 2. What is the best way to specify a list of sequence files? In the manual under basic parameters, it is written that no reference file is needed if already indexed. What does that mean? 3. What does the...

Hello! I have a directory of genomes (fasta files), each fasta file having multiple sequences. My question is two parts: 1. Do I need to concatonate the sequences in each file in order for randomreads to work? Or, will it automatically detect multiple sequences in the file and make reads from all of them? 2. What is the best way to specify a list of sequence files? In the manual under basic parameters, it is written that no reference file is needed if already indexed. What does that mean? Thank you...