Megahit Assembly - command line error

Question

[yuki4208]

I am new to bioinformatics and I need help:((

I have downloaded megahit and working in the 'bin' directory

1. I don't know where I am supposed to put my samples

2. Even if I run the files with the specific directory from bin/Input/R1 and R2 nothing happens

   bin$ ./megahit -1 Input/Input-1_S6_L001_R1_001.fastq.gz -2 Input/Input-1_S6_L001_R2_001.fastq.gz -o A_Input

What is wring with my command line?

[Asaf]

Do you get an error?

Answer 1

[Mensur Dlakic]

This part of your command ./megahit means that you have a megahit executable in the present directory. If that's not the case, it won't work.

This part of your command Input/Input-1_S6_L001_R1_001.fastq.gz means that in that same directory you have a sub-directory called Input, and in that sub-directory a file called Input-1_S6_L001_R1_001.fastq.gz. Same for your other paired-end file.

These are possible errors that I can point out without actually knowing the error message. It would help if you post what that error message is.