SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Repost: tophat-fusion outputs empty result mrfox Bioinformatics 31 10-13-2016 07:03 AM
bowtie2 outputs empty file leontp587 Bioinformatics 1 08-12-2014 06:51 AM
Tophat2 returns empty junction file: Warning: junction database is empty! sachitad Bioinformatics 4 02-15-2013 12:40 AM
bwa question on file outputs/inputs ikrier Bioinformatics 12 10-12-2012 08:22 AM
Aligner that outputs H2 flag in SAM file phalaenopsis Bioinformatics 0 08-04-2010 05:14 AM

Reply
 
Thread Tools
Old 09-11-2014, 06:01 PM   #1
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default Trimmomatic Keeps All Reads But Outputs An Empty File

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 ?
Dario1984 is offline   Reply With Quote
Old 09-12-2014, 04:08 AM   #2
tonybolger
Senior Member
 
Location: berlin

Join Date: Feb 2010
Posts: 156
Default

Quote:
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.
tonybolger is offline   Reply With Quote
Reply

Tags
bugs, trimmomatic

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO