?missing space from nullarbor.pl line 271 for trimmomatic

[ajmerritt1]

Hi Torsten, I switched on --trim and added CROP:200 to nullarbor.conf but on execution got error:

Exception in thread "main" java.io.FileNotFoundException: 
/dev/null/ILLUMINACLIP:/home/nullarbor/nullarbor/conf/trimmomatic.fa:1:30:11 (No such file or directory)

adding an extra space at column 107 of line 271 to produce .../dev/null ".($cfg... resolved it. new bug? known bug? old bug?

thx Adam

[tseemann]

@ajmerritt1 I think that bug was fixed long ago. the current conf has the space: @reads $id/$R1 /dev/null $id/$R2 /dev/null ".($cfg->{trimmomatic} || '') ]

What version are you using?

% nullarbor.pl --version
nullarbor.pl 2.0.20191013

FYI - nullarbor is now fully in bioconda. Might be easier way to keep up to date.

PS. the trimming would normally happen on the Illumina instrument. do you have this in your SampleSheet.csv ?

[Settings]
Adapter,CTGTCTCTTATACACATCT

Do you use Basespace or run bcl2fastq to generate the FASTQ ?

[ajmerritt1]

cool - am running version 2.0.20181010 on base env. was a hybrid-'ish install with github v. plus conda deps.

and am playing with bioconda 2.0.20191013 in a // env, confirmed the space is there the bioconda v.

I was less concerned about adapter trimming, just wanted to drop the last 100bp of my 2x300 reads and look at impact on quality & assembly. would be using basespace for fastq I'd think.

thx

Adam

[tseemann]

Yeah, it's interesting to see how things perform when going from 300bp to 150bp PE. We found Miseq 250/300 PE is usually wasted due to over-fragementation with Nextera XT, and the reads both totally overlap. It's an expensive way to do 250bp SE reads :-)