How to assemble the bacterial genome; spades

Question

[dogdif]

I'm a new user and have no background of computer and genome stuff. I try to assembly the genome. This is what I try to run. I have no idea what I'm doing wrong.

Apples-MacBook-Pro:bin apple$ ./spades.py -k 21,33,55,77 --careful --only-assembler -1-1 11-0910_S7_L001_R1_001.fastq.gz -1-2 11-0910_S7_L001_R2_001.fastq.gz\ -o 11_0911

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: --only-assembler, 11-0910_S7_L001_R1_001.fastq.gz, 11-0910_S7_L001_R2_001.fastq.gz -o, 11_0911

In case you have troubles running SPAdes, you can write to [e-mail] Please provide us with params.txt and spades.log files from the output directory

Thanks

[dogdif]

Sorry about the topic. I try to run according to your suggestion but it's still the same.

Apples-MacBook-Pro:bin apple$ ./spades.py -k 21,33,55,77 --careful --only-assembler -1 11-0910_S7_L001_R1_001.fastq.gz -2 11-0910_S7_L001_R2_001.fastq.gz -o 11_0911

== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths: --only-assembler

[Adrian Pelin]

Ah I didn't notice you have a typo. Try --only-assembler instead of —only-assembler. I modified my answer to have the corrected version.

Answer 1

[Adrian Pelin]

This is not a tutorial, just a regular question. Try:

./spades.py -k 21,33,55,77 --careful --only-assembler -1 11-0910_S7_L001_R1_001.fastq.gz -2 11-0910_S7_L001_R2_001.fastq.gz -o 11_0911

[dogdif]

Oh Thank you. It's working now.

[dogdif]

Oh Thank you. It's working now.