Trimmomatic batch trimming 0.36 A flexible read trimming tool for Illumina NGS data Bolger, A. M., Lohse, M., and Usadel, B assembly http://www.usadellab.org/cms/index.php?page=trimmomatic http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf trimmomatic_batch_xsede inputfile1 The Input file is a zipped archive of all the strains 1 infile.txt inputfilename1 A hidden command that creates the command line perl (" " + str( inputfile1 ), " run "+ [str( inputfile1 ),"/mobyle_share/data/" + str( value )+'/'+str(inputfilename2)] [ inputfile1 is None] +' '+str( value ) ) [value is not None] 3 commandend1 commandend perl 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 10 batchoutfile batch outfile trimmomatic_batch.txt outfile Standard error file std.err runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Maximum Hours to Run must be 168 or less perl $runtime > 168 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 perl "runhours=$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 hours perl $specify_bootstraps && $bootstop < 50 && !$more_memory The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $specify_runs && $altrun_number < 50 && !$more_memory The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $specify_runs && $altrun_number >= 50 && !$more_memory The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $specify_bootstraps && $bootstop >= 50 && !$ancestral_states && !$fast_tree && !$bipartitions && !$startingtreeonly && !$log_likelihood && !$more_memory && !$morpho_weight_calibration && !$classify_into_reftree && !$compute_mr The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $use_bootstopping && !$more_memory The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl !$mulparambootstrap_seed && !$bootstrap_seed && !$specify_runs && !$more_memory The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $more_memory Estimate 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. general Program Settings inputfilename2 Specify your Strain List file stainlist.txt file_suffix File name suffix (Note paired files should be in one of these formats - the reverse file is determined automatically) 0 1 2 3 0 4 leading LEADING perl "" 5 30 trailing TRAILING 30 perl "" 6 slidingwindowsize SLIDINGWINDOW windowSize perl "" 7 4 requiredQuality SLIDINGWINDOW requiredQuality 20 perl "" 8 minlen MINLEN perl "" 36 9