Denovo assembly of Putative Plasmid

Question

[jigarnt]

Hi All,

I have illumina sequenced a putative plasmid with paired end library. Through sequencing I fetched two files, namely Plasmid_R1.fastq and Plasmid_R2.fastq. I am trying to run SPADES with this command:

European_plasmid lindakohn$ /Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 --careful --only-assembler \ --pe1-1 European_plasmid_tube_labelled_UB_R1.fastq --pe1-2 European_plasmid_tube_labelled_UB_R2.fastq \ -o spades_output

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: --pe1-1, European_plasmid_tube_labelled_UB_R1.fastq, -o, spades_output

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. lindas-mac-pro:European_plasmid lindakohn$ /Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 \ --careful --only-assembler --pe1-1 European_plasmid_tube_labelled_UB_R1.fastq --pe1-2 European_plasmid_tube_labelled_UB_R2.fastq \ -o spades_output

What is the possible solution for this???

[Adrian Pelin]

You have posted variations of this question as answers to other question at least 4 times (jigarnt) please do not do that.

Instead of --pe1-1 or --pe1-2, try -1 and -2. Sometimes that resolves the error.

[jigarnt]

Hi Adrian,

Sorry for posting it many times, but my intention was to get a quick and prompt response from the experts in the community.

It is important to me to figure this out as quick as possible. I tried what you suggested but it is showing same error. Also, I do not think there is something wrong with the software itself because I ran TEST and it works fine.

Thanks, Jigar

[h.mon]

You probably need to write the whole path to the fastq files:

--pe1-1 /path/to/European_plasmid_tube_labelled_UB_R1.fastq

[jigarnt]

Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 \ --careful --only-assembler \ --pe1-1 /Users/lindakohn/Desktop/PD/European_plasmid/European_plasmid_tube_labelled_UB_R1.fastq --pe2-2 /Users/lindakohn/Desktop/PD/European_plasmid_tube_labelled_UB_R2.fastq \ -o European_plasmid_fasta

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: --careful, --pe1-1, /Users/lindakohn/Desktop/PD/European_plasmid/European_plasmid_tube_labelled_UB_R1.fastq, -o, European_plasmid_fasta

Getting same error

[h.mon]

My only suggestion at this point is for you to type all the command from the beginning (do not copy / paste), and use tab completion where appropriate to avoid errors.