Error of fast_quality_trimmer input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)

Question

[jolin0701-dy]

Here is what I do.

1. Download *.fastq.gz files.

2. Uncompress the *.fastq.gz files by double-clicking on them in the finder window.

3. head *.fastq files

$ head YZ1_S1_L001_R1_001.fastq

@NS500704:50:HFLKTBGXX:1:11101:5770:1047 1:N:0:GTTAAA

ATGGCNTTTTCATGAACTTTCAAATATGAATCTTACAGTGTATACTTGGTGAATATTAGAAGCATGGAAGAGATC

+

AAAAA#EEEEEEEEEAEEEEAEEEEAEAE6A<aaeea e="" ee="" ee6e="" a="" aeeea<="" ea="" a="" <a="" e="" ae&lt;<="" p="">

@NS500704:50:HFLKTBGXX:1:11101:16873:1047 1:N:0:GTGAAA

AACTGNCGCTGCGGGATGAACCGAACGCCGGGTTAAGGCGCCCGATGCCGACGCTCATCAGACCCCAGAAAAGGT

+

AAAAA#EEEEEEEEEEEEEEEEE/EEEEEAEEEEEEAEEEEEEEAEEEEE/EAEEE6EEAEAEEEEEA/EEEEEE

@NS500704:50:HFLKTBGXX:1:11101:7523:1047 1:N:0:GTGAAA

GCTACNGGCGTACACTAGCGTCTCCAAAGCTTCACTTAGCCTTGCAGATCACAGAGAACCTGGAAAGATCGGAAG

1. Run fastq_quality_trimmer

$ fastq_quality_trimmer -Q33 -v -t 20 - l 20 -i YZ1_S1_L001_R1_001.fastq -o YZ1_S1_L001_R1_001.trimmed.fastq

fastq_quality_trimmer: input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)

Any suggestions would be greatly appreciated!!

Answer 1

[GenoMax]

You have an extra space in your fastq_quality_trimmer command before l 20

Try

$ fastq_quality_trimmer -Q33 -v -t 20 -l 20 -i YZ1_S1_L001_R1_001.fastq -o YZ1_S1_L001_R1_001.trimmed.fastq

[jolin0701-dy]

Thanks~~~~ Your reply is so fast!! It works!!!!