error assembly megahit

Question

[fernandoavila3428]

Hi,

I'm trying to make an assembly of several sequences with next command but I have an error

My samples

sample1_1.fq
sample1_2.fq
sample2_1.fq
sample2_2.fq

---

for i in *.fq ; do /home/fernado/megahit/megahit -1 $i\_1.fq -2 $i\_2.fq  -o assembly$i ; done

16Gb memory in total.

Using: 12Gb.

megahit: Cannot find file assembly_sample1_1.fq_1.fq

I hope you can help

Answer 1

[Fabio Marroni]

You are sending the wrong file names. From the error message I understand that megahit is looking for the file "assembly_sample1_1.fq_1.fq", which doesn't exist

Try this:

for i in *_1.fq
do 
read1=${i/.fq/}
read2=${read1/_1/_2}
/home/fernado/megahit/megahit -1 $read1 -2 $read2  -o assembly$i
done

[fernandoavila3428]

Hi, I try as you suggest but it seems that not recognize the key in the script, therefore I have a error

./assembly.sh ./assembly.sh:6: ./assembly.sh: Bad substitution

This the script

 for i in *_1.fq  
 do  
 read1=${i/.fq/} 
 read2=${read1/_1/_2}   
 /home/fernado/megahit/megahit  -1  $read1  -2 $read2 -o assembly$i 
 done

[fernandoavila3428]

When I changed the key by parentheses it works but does not recognize the files

 for i in *_1.fq 
 do           
 read1=$(i/.fq/)
 read2=$(read1/_1/_2) 
 home/fernado/megahit/megahit  -1  $read1  -2 $read2 -o assembly$i 
 done

For example this the error

/assembly.sh: 6: ./assembly.sh: i/.fq/: not found
/assembly.sh: 7: ./assembly.sh: read1/_1/_2: not found

[Fabio Marroni]

Sorry... I don't understand what you mean by "it seems that you do not recognize the key and change it by parentheses, but I have a error" Let's debug step by step: try this and let me know if this gives an error.

mkdir test_dir
cd test_dir    
touch sample1_1.fq sample1_2.fq sample2_1.fq sample2_2.fq
    for i in *_1.fq
    do 
    read1=${i/.fq/}
    read2=${read1/_1/_2}
    echo "/home/fernado/megahit/megahit -1 $read1 -2 $read2  -o assembly$i"
    done

[fernandoavila3428]

copy the script exactly, but there is an error

./assembly.sh                                                                      
./assembly.sh: 6: ./assembly.sh: Bad substitution

And the lines 6 is this:

read1=${i/.fq/}

[Fabio Marroni]

I am sorry... I don't know what to do. For me it works :-(

However, try to change the way you feed the read name to megahit. Maybe, if you have a few files, you can start by feeding the names by hand and then when you will have figured out the correct way to feed the names you can use automated scripts.

As far as the Bad substitution, try to give a look here

[fernandoavila3428]

I think my shell is the problem because don´t recognize "{ }", I try to use the script in other computer

Answer 2

[fernandoavila3428]

already worked in this way

#!/bin/bash
for  f1 in *_1.fq 
do            
f2=${fi%%_1.fq}"_2.fq"
/home/fernado/megahit/megahit  -1  $f1  -2 $f2 -o "assembly$fi.out" 
done

Thanks