i am running a pipeline to clean the reads
there was an error
Error in add(raw()) : record does not start with '@'
Calls: trimRead -> yield -> yield -> <anonymous> -> add -> .Call
Execution halted
i never met it before,i think that is maybe due to data problem?
one fastq record start without '@'
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shan gao
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On 01/23/2013 07:55 PM, Wang Peter wrote:
> i am running a pipeline to clean the reads
>
> there was an error
> Error in add(raw()) : record does not start with '@'
> Calls: trimRead -> yield -> yield -> <anonymous> -> add -> .Call
> Execution halted
>
> i never met it before,i think that is maybe due to data problem?
> one fastq record start without '@'
maybe sequence and quality length mismatch, or maybe a programming
error on my
part. I guess you have a FastqStreamer() or FastqSampler, and you can
print the
streamer after the error to find out about where in the file the error
is
occurring. To illustrate after
example(FastqStreamer)
we get a file 'fl' that is a fastq file, and create a streamer
> strm = FastqStreamer(fl, 100)
and yield twice
> yield(strm)
class: ShortReadQ
length: 100 reads; width: 36 cycles
> yield(strm)
class: ShortReadQ
length: 100 reads; width: 36 cycles
and then find that the current buffer holds 100 records, and we've
already added
200.
> strm
class: FastqStreamer
file: s_1_sequence.txt
status: n=100 current=100 added=200 total=200
You could print out your streamer after the error to find the
approximate place
in the file where the error occurs. Also if it is a programming error
on my
part, then you can perhaps work around this by choosing a different
yield size
or 'readerBlockSize'; making these prime numbers might be particularly
effective
at avoiding the error (but I'd rather fix the bug).
It would help to have more code to see what you are doing. If it is
not clear
that there is an error in the fastq file, then it would help to make a
reproducible example (simple code and sample data file) available to
me.
Martin
>
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