Trimmomatic Keeps All Reads But Outputs An Empty File

Dario1984

Senior Member

Join Date: Jun 2011
Posts: 166

Trimmomatic Keeps All Reads But Outputs An Empty File

09-11-2014, 06:01 PM

Code:

TrimmomaticPE: Started with arguments: -threads 32 7975_UNSW_D1YM6ACXX_NoIndex_L002_R1_001.fastq.gz 7975_UNSW_D1YM6ACXX_NoIndex_L002_R2_001.fastq.gz -baseout L002Trimmed LEADING:20 TRAILING:20 MINLEN:75
Quality encoding detected as phred33
Input Read Pairs: 256616906 Both Surviving: 256616906 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

But when I check the output, I see an empty file.

Code:

-rw-r----- 1 dario   biostat            0 Sep 12 11:27 L002Trimmed

I use version 0.32. Is it a bug ?

Tags: bugs, trimmomatic

tonybolger

Senior Member

Join Date: Feb 2010

Posts: 156
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09-12-2014, 04:08 AM

Originally posted by Dario1984 View Post

I use version 0.32. Is it a bug ?

Yes, there is a bug with parsing the parameters which only allows certain orders - all the 'option' parameters (i.e those with the minus) must currently come before non-option parameters (explicit file names or trimming steps).

Thus if you use -basein or -baseout, you need to put these options _before_ the explicit file names - even if this means putting the templated output files (via -baseout) before the explicit input files.
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Trimmomatic Keeps All Reads But Outputs An Empty File

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