Shovill batch assemblies
Hi,
I am trying to write a bash for loop in order to assemble a group of illumina reads (R1 and R2) with shovill (by T. Seemann). I have activated the conda environment where the shovill package is installed and I have 'cd'ed to the folder where my reads are. I have tried to modify a loop I found here for Spades:
for file1 in *R1*fastq
do
file2=${file1/R1/R2}
out=${file1%%.fastq}_output
shovill --R1 $file1 --R2 $file2 --outdir/Users/laura/Desktop/Pdd-Pdp/shovill --depth 0
done
but of course it doesn't work :(
Could someone help me please? Maybe also explaining how each command is used?
Thank you!
Laura
1 answer
Log in to answer this question.
More posts like this
-
How to merge multiple paired fastq files using BBmerge?
written by Princy •
-
Run STAR on .fastq files I1, R1 and R2
written by PianoEntropy •
-
How to run SPAdes assembler with bam files?
written by marongiu.luigi
-
Bash Script Loop Help
written by V
-
Error: reads file does not look like a FASTQ file
written by AHW •
-
BWA mem output inconsistent on same but re-ordered FASTQ input
written by ramy •
-
Using trimmomatic on multiple paired-end read files
written by bioinformaticssrm2011
-
Error with SRA downloaded reads and SPAdes 3.1.0
written by jlimenitakis •
-
SPAdes --restart-from error
written by chapmansm13 •
-
bash loop for alignment RNA-seq data
written by Paul
I cleaned up your code a little.
Does your code have
--outdir/Users/...or--outdir /Users/...? The space is important.Right, that was silly of me, thank you! :) However, I think I also need to add some code to create a subdirectory in '/Users/laura/Desktop/Pdd-Pdp/shovill' for each assembly - ideally called with the same name of the input - because after the first assembly, I get the following error:
Folder '/Users/laura/Desktop/Pdd-Pdp/shovill' already exists. Try using --force
the flag --force would overwrite the content of the folder though.