Question: Trimmomatic couldn't generate output file
0
gravatar for leukippus0116
10 weeks ago by
leukippus01160 wrote:

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?

trimmomatic software error • 216 views
ADD COMMENTlink modified 7 weeks ago by swbarnes29.6k • written 10 weeks ago by leukippus01160

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.
code_formatting

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by GenoMax96k

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...

ADD REPLYlink written 10 weeks ago by leukippus01160
0
gravatar for swbarnes2
7 weeks ago by
swbarnes29.6k
United States
swbarnes29.6k wrote:

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.

ADD COMMENTlink written 7 weeks ago by swbarnes29.6k
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