Trimmomatic Keeps All Reads But Outputs An Empty File

[Dario1984]

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.

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

I use version 0.32. Is it a bug ?

[tonybolger]

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.