Optimizing the parameters k in Abyss

Question

[Maliha]

I want to do genome assembly of chicken. I am trying to optimize the kmer value for AByss using this tutorial and code -

#!/bin/bash
for k in `seq 50 8 90`; do
     mkdir k${k}
     abyss-pe np=16 -C k${k} name=chicken k=$k in= '/home/zsiddiki/
     BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/
     BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'
done
abyss-fac k*/chicken-scaffolds.fa

I am getting this error everytime -

make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k50' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k50' make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k58' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k58' make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k66' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k66' make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k74' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k74' make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k82' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k82' make: Entering directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k90' make: No rule to make target '/home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/ BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'. Stop. make: Leaving directory '/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/k90' error: `k*/chicken-scaffolds.fa': No such file or directory

What should I change in my code?

Answer 1

[colindaven]

Try putting your abyss command in one line, as it seems to be broken up. Also, the space after in= looks incorrect.

 abyss-pe np=16 -C k${k} name=chicken k=$k in='/home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s1.fastq /home/zsiddiki/BLRI_hilly_chicken/upload/soapnuke/clean/F5A/s2.fastq'