Entering edit mode
4.9 years ago
El Niño
▴
10
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!
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Thank you very much. That's exatly what I've been looking for.
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?
Here is the script:
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?
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?