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