fastq_quality_trimmer: Premature End-Of-File

Question

[blur]

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!

[WouterDeCoster]

Can you check the end of your file using e.g tail - n 12 yourfile?

Answer 1

[Charles Plessy]

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.

[SanEm]

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.