bbduk can't read file

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

bbduk

• 2,473 views • link

updated 4.9 years ago by lieven.sterck

• written 4.9 years ago by Frank •

1 answer

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

• 0 views • link

written 4.9 years ago by lieven.sterck

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!

• 0 views • link

written 4.9 years ago by Frank •

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