Trimmomatic batch trimming0.36A flexible read trimming tool for Illumina NGS dataBolger, A. M., Lohse, M., and Usadel, Bassemblyhttp://www.usadellab.org/cms/index.php?page=trimmomatichttp://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdftrimmomatic_batch_xsedeinputfile1The Input file is a zipped archive of all the strains1infile.txtinputfilename1A hidden command that creates the command lineperl(" " + str( inputfile1 ), " run "+
[str( inputfile1 ),"/mobyle_share/data/" + str( value )+'/'+str(inputfilename2)]
[ inputfile1 is None]
+' '+str( value ) )
[value is not None]3commandend1commandendperl
java -jar /usr/local/apps/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trim_missing_log __repl__.1.fastq.gz __repl__.2.fastq.gz __repl__.1.paired.fq.gz __repl__.1.unpaired.fq.gz __repl__.2.paired.fq.gz __repl__.2.unpaired.fq.gz
CROP:280 HEADCROP:20 LEADING:$leading TRAILING:$trailing SLIDINGWINDOW:$slidingwindowsize:$requiredQuality MINLEN:$minlen,
java -jar /usr/local/apps/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trim_missing_log __repl__.1.fq.gz __repl__.2.fq.gz __repl__.1.paired.fq.gz __repl__.1.unpaired.fq.gz __repl__.2.paired.fq.gz __repl__.2.unpaired.fq.gz
CROP:280 HEADCROP:20 LEADING:$leading TRAILING:$trailing SLIDINGWINDOW:$slidingwindowsize:$requiredQuality MINLEN:$minlen ,
java -jar /usr/local/apps/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trim_missing_log __repl___R1_001.fastq.gz __repl___R2_001.fastq.gz __repl__.1.paired.fq.gz __repl__.1.unpaired.fq.gz __repl__.2.paired.fq.gz __repl__.2.unpaired.fq.gz
CROP:280 HEADCROP:20 LEADING:$leading) TRAILING:$trailing SLIDINGWINDOW:$slidingwindowsize:$requiredQuality MINLEN:$minlen,
java -jar /usr/local/apps/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trim_missing_log __repl___R1_001.fq.gz __repl___R2_001.fq.gz __repl__.1.paired.fq.gz __repl__.1.unpaired.fq.gz __repl__.2.paired.fq.gz __repl__.2.unpaired.fq.gz
CROP:280 HEADCROP:20 LEADING:$leading TRAILING:$trailing SLIDINGWINDOW:$slidingwindowsize:$requiredQuality MINLEN:$minlen $file_suffix 10batchoutfilebatch outfiletrimmomatic_batch.txtoutfileStandard error filestd.errruntime1scheduler.confMaximum Hours to Run (click here for help setting this correctly)0.25Maximum Hours to Run must be 168 or lessperl$runtime > 168Maximum Hours to Run must be greater than 0.1perl$runtime < 0.1perl"runhours=$value\\n"The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hoursperl$specify_bootstraps && $bootstop < 50 && !$more_memoryThe job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hoursperl$specify_runs && $altrun_number < 50 && !$more_memoryThe job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hoursperl$specify_runs && $altrun_number >= 50 && !$more_memoryThe job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hoursperl$specify_bootstraps && $bootstop >= 50 && !$ancestral_states && !$fast_tree && !$bipartitions && !$startingtreeonly && !$log_likelihood && !$more_memory && !$morpho_weight_calibration && !$classify_into_reftree && !$compute_mrThe job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hoursperl$use_bootstopping && !$more_memoryThe job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hoursperl!$mulparambootstrap_seed && !$bootstrap_seed && !$specify_runs && !$more_memoryThe job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hoursperl$more_memoryEstimate the maximum time your job will need to run. We recommend testimg initially with a time less than 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue.
Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may
run sooner than jobs configured for the full 168 hours.
generalProgram Settingsinputfilename2Specify your Strain List filestainlist.txtfile_suffixFile name suffix (Note paired files should be in one of these formats - the reverse file is determined automatically)012304leadingLEADINGperl""530trailingTRAILING30perl""6slidingwindowsizeSLIDINGWINDOW windowSizeperl""74requiredQualitySLIDINGWINDOW requiredQuality20perl""8minlenMINLENperl""369