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mdshw5 / fastqp

Simple FASTQ quality assessment using Python
https://pypi.python.org/pypi/fastqp
MIT License
108 stars 14 forks source link

fastqp stuck with very long consensus fastq file #18

Closed peterdfields closed 8 years ago

peterdfields commented 8 years ago

I'm trying to generate a plot of fastq quality along a very long (800kb) assembly sequence. When I run fastqp I get the following and seemingly no non-stdout output:

At 1775681 bytes per read of 887828 length we estimate 1 reads in input file. Bin size (-s) set to 1.

It might be the case that this is simply not the appropriate tool. The goal is simply a summary of support of given nucleotide calls along the de novo reference. All advice is much appreciated!

mdshw5 commented 8 years ago

Yes, @peterdfields, I believe this is the wrong tool for your task. If there is only one sequence in the input file, fastqp will likely error when calculating base quality quantiles.

peterdfields commented 8 years ago

Makes sense. Thanks for your reply!