search

magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
6 stars 3 forks source link

TrimReads for popoolation error #534

Open r-mashoodh opened 2 years ago

r-mashoodh commented 2 years ago

Hello,

I am trying to run the following

java -jar software/ReadTools.jar TrimReads --minReadLength 30 --disable5pTrim --input raw_data/S1_L2_1.fq --output S1_trimmed_1.fq

to mimic the Popoolation manual

however I get the following error:

A USER ERROR has occurred: Invalid output format for S1_trimmed_1.fq: extension should match one of .sam, .bam, .cram

Shouldn't the output be fq?

Thanks so much