Question: An error while running Velvet
0
gravatar for El Niño
3 months ago by
El Niño10
El Niño10 wrote:

Hi guys,

I am now running Velvet to do genome assembly, however at the very first step when I do

shuffleSequences_fastq.pl file_1.fastq file_2.fastq merged.fastq

I came across this error which reads:

syntax error at shuffleSequences_fastq.pl line 10, near "<"
Excessively long <> operator at shuffleSequences_fastq.pl line 21.

Can anybody help me with this?

Thanks a lot!

assembly • 184 views
ADD COMMENTlink modified 7 weeks ago by Biostar ♦♦ 20 • written 3 months ago by El Niño10

A small educational note: I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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ADD REPLYlink written 3 months ago by lieven.sterck5.8k

Thank you very much. That's exatly what I've been looking for.

ADD REPLYlink written 3 months ago by El Niño10

Can you post this line 10 of that perl script? (and perhaps a few lines above and below that line).

My first thought would be that there might be something wrong with your input. Can (did?) you check the integrity of your input fastq files?

ADD REPLYlink written 3 months ago by lieven.sterck5.8k

Here is the script:

https://github.com/dzerbino/velvet/blob/master/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl
ADD REPLYlink written 3 months ago by El Niño10
1

hmm, there does not seem to be a '<' at line 10 :/

is the command you provide here the exact same one as you try to run? are you using a humongously long path to the files as input for instance?

ADD REPLYlink written 3 months ago by lieven.sterck5.8k

It is likely that the script is not wrong, but that this error is thrown because of faulty input files. Are you sure the files are correctly paired-end? What preprocess is done on the files?

ADD REPLYlink written 7 weeks ago by Benn7.7k
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