bbduk can't read file

Question

[Frank]

Hi all,

When trying to filter reads using bbduk, I get the following error message:

maskMiddle was disabled because useShortKmers=true Exception in thread "main" java.lang.RuntimeException: Can't read file '/home/bioinf/TrainingData/SRR6197336/SRR6197336_1.fastq' at shared.Tools.testInputFiles(Tools.java:185) at jgi.BBDuk.<init>(BBDuk.java:912) at jgi.BBDuk.main(BBDuk.java:78)

This is my code:

~/Downloads/bbmap/bbduk.sh in1=~/TrainingData/SRR6197336/SRR6197336_1.fastq in2=~/TrainingData/SRR6197336/SRR6197336_2.fastq out1=~/TrainingData/reads/bbduk/SRR6197336_1_bbduk.fastq out2=~/TrainingData/reads/bbduk/SRR6197336_2_bbduk.fastq ktrim=r k=23 mink=11

I am not really sure what is going wrong here. Any help would be appreciated!

Thanks

Answer 1

[lieven.sterck]

can you verify that the files are in the location you think they are? (/home/bioinf/TrainingData/SRR6197336/) and have the correct name?

[Frank]

thanks for your note. despite having checked the paths carefully, I must have had a typo somewhere. copying the file location into the code did the trick. Thank you!