Question: Denovo assembly of Putative Plasmid
1
gravatar for jigarnt
4.0 years ago by
jigarnt30
Canada
jigarnt30 wrote:

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 spades.support@bioinf.spbau.ru 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???

snp next-gen software error • 1.2k views
ADD COMMENTlink written 4.0 years ago by jigarnt30

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.

ADD REPLYlink written 4.0 years ago by Adrian Pelin2.4k

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

ADD REPLYlink written 4.0 years ago by jigarnt30

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

--pe1-1 /path/to/European_plasmid_tube_labelled_UB_R1.fastq
ADD REPLYlink written 4.0 years ago by h.mon29k

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

ADD REPLYlink written 4.0 years ago by jigarnt30
1

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.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by h.mon29k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2166 users visited in the last hour