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mbhall88 / rasusa

Randomly subsample sequencing reads or alignments
https://doi.org/10.21105/joss.03941
MIT License
203 stars 17 forks source link

won't detect input file #63

Closed rmormando closed 11 months ago

rmormando commented 11 months ago

I'm trying to use rasusa to downsample some Illumina short reads to a smaller coverage using this command here:

docker run quay.io/mbhall88/rasusa -i P2B_R1.fastq.gz P2B_R2.fastq.gz --coverage 5 --genome-size 12m -o P2B_5x_r1.fq.gz P2B_5x_r2.fq.gz

However, I keep getting this error message:

error: Invalid value "P2B_R1.fastq.gz" for '--input <INPUT>...': "P2B_R1.fastq.gz" does not exist

I installed the latest version of rasusa through Docker - following the commands listed on the GitHub page. I used a path at first to find the input files but it gave me that error message so I moved the files to my home directory where I run docker images but that didn't work either. If someone could help me figure out how to fix this error that would be great!

rmormando commented 11 months ago

I got it to work! I went back and installed the tool through Git and was able to set the two files to 5x coverage! (I also had to unzip the files, but it worked!)