Trimmomatic couldn't generate output file

Question

[leukippus0116]

Hello everyone, I am new to bioinformatic. I'm working on NGS data trimming using trimmomatic and have a problem dealing with this. Can anybody help me please?

I used PE mode in trimmomatic like this;

@naka-71-130 fastq % trimmomatic \
> PE -threads 2 -phred33 -trimlog log.txt \  
> 20-026_S1_L001_R1_001.fastq.gz \
> 20-026_S1_L001_R2_001.fastq.gz \
> paired_output_20-026_S1_L001_R1_001.fastq.gz \
> unpaired_output_20-026_S1_L001_R1_001.fastq.gz  \
> paired_output_20-026_S1_L001_R2_001.fastq.gz \
> unpaired_output_20-026_S1_L001_R2_001.fastq.gz \
> SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:80

and the output is OK.

TrimmomaticPE: Started with arguments:
 -threads 2 -phred33 -trimlog log.txt 20-026_S1_L001_R1_001.fastq.gz 20-026_S1_L001_R2_001.fastq.gz paired_output_20-026_S1_L001_R1_001.fastq.gz unpaired_output_20-026_S1_L001_R1_001.fastq.gz paired_output_20-026_S1_L001_R2_001.fastq.gz unpaired_output_20-026_S1_L001_R2_001.fastq.gz SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:80
Input Read Pairs: 127995 Both Surviving: 40728 (31.82%) Forward Only Surviving: 74524 (58.22%) Reverse Only Surviving: 1182 (0.92%) Dropped: 11561 (9.03%)
TrimmomaticPE: Completed successfully

but with next sample, the trimmomatic couldn't generate output file and the original fast.gz file became 0 kb.

@naka-71-130 fastq % trimmomatic \
> PE -threads 2 -phred33 -trimlog log2.txt \
> 20-027_S2_L001_R1_001.fastq.gz \
> 20-027_S2_L001_R2_001.fastq.gz \
> paired_output_20-027_S2_L001_R1_001.fastq.gz \
> unpaired_output_20-027_S2_L001_R1_001.fastq.gz \
> paired_output_20-027_S2_L001_R2_001.fastq.gz \
> unpaired_output_20-027_S2_L001_R2_001.fastq.gz \
> SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:80

Output is like this.

Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version

I don't understand why this could happen. Will somebody help me to solve this situation please?

[GenoMax]

When a program spits out built-in help, it almost always refers to a typo or an error in the command line in providing options. Check those out.

Please use the 101 code button on the edit toolbar to properly present your command lines.

[leukippus0116]

Thank you for your kind reply! I edited my previous post.

I actually copy and pasted the first command line for the next sample, and tried several times. so maybe not a typo error...

Answer 1

[swbarnes2]

For starters, I would not give your outputs the same name as your inputs! You need to keep inputs and outputs separate.

The simplest explanation is that not a single one of your 20-027 reads passes your filter, so you just overwrote your original file with nothing.