fastq_quality_trimmer: Premature End-Of-File
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4.6 years ago
blur ▴ 220

Hi, I am running FASTX and got this error: fastq_quality_trimmer: Premature End-Of-File Does anyone know what it means? could my file be truncated?

thanks!

fastq_quality_trimmer fastx • 2.8k views
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Can you check the end of your file using e.g tail - n 12 yourfile?

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4.6 years ago
Charles Plessy ★ 2.8k

A query to the source code of FASTX Toolkit shows that this error messages is printed when FASTX tools are given an empty file. Indeed:

$ touch empty # creates an empty file called "empty" (if there was no such file)

$ fastq_quality_trimmer -t 10 -i empty
fastq_quality_trimmer: Premature End-Of-File (filename ='empty')

$ echo -n | fastq_quality_trimmer -t 10
fastq_quality_trimmer: Premature End-Of-File (filename ='-')

Therefore, your input was most likely an empty file or an empty stream.

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Absolutely, this turned out to be my problem. I had just upgrade from 0.0.13 to 0.0.14 as recommended in another post and still got the same error. This has clarified my problem.

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