Process Radtags on XSEDE 1.44 Checks that the barcode and the RAD cut site are intact, and then demultiplexes the data. Make sure barcode files have LINUX line endings - upload barcode files. Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., and Cresko, W. A. Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., and Cresko, W. A. (2013) Stacks: an analysis tool set for population genomics. Molecular ecology 22, 3124-3140 Phylogeny/Alignment http://catchenlab.life.illinois.edu/stacks/manual/ stacks_xsede inputfile1_fastq First fastq file inputfastq1.zip perl "-1 inputfastq1.zip" 4 stacks_scheduler scheduler.conf perl "threads_per_process=1\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 invocation perl "/projects/ps-ngbt/opt/comet/stacks/1.44/process_radtags -r " 1 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Estimate the maximum time your job will need to run. We recommend testing initially with a < 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. Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl $runtime ne 0 perl "runhours=$value\\n" paired_end Files are paired( -P ). perl ($value) ? "-P": "" 0 3 inputfastq2 Input fastq file2 inputfastq2.zip perl $paired_end perl "-2 inputfastq2.zip" Please select the second fastq file perl $paired_end && !defined $inputfastq2 5 general Program Settings barcode_file Input barcode file barcode.data perl "-b barcode.data" Please select the barcode file perl !defined $barcode_file 7 barcode_options Barcode options: --inline_null --index_null --inline_inline --index_index --inline_index --index_inline --inline_null perl $value 8 inputfiletype Specify the input file type (-i) bustard bam fastq gzfastq gzfastq perl "-i $value" 9 scoring Specify how quality scores are encoded. (-E) phred33 phred64 phred33 perl " -E $value" 10 restr_enzyme1 Provide the restriction enzyme used (cut site occurs on single-end read).(--renz1) apeKI bamHI dpnII ecoRI ecoT22I hindIII mluCI mseI mspI ndeI nlaIII notI nsiI pstI sau3AI sbfI sexAI sgrAI sphI xbaI mspI perl " --renz_1 $value" 11 restr_enzyme2 If a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).(--renz2) notset apeKI bamHI dpnII ecoRI ecoT22I hindIII mluCI mseI mspI ndeI nlaIII notI nsiI pstI sau3AI sbfI sexAI sgrAI sphI xbaI perl defined $value ? "--renz_2 $value":"" 12 adaptersequence1 Adaptor sequence that may occur on the single-end read for filtering.(--adapter_1) perl defined $value "--adapter_1 $value" 13 adaptersequence2 Adaptor sequence that may occur on the paired-read for filtering.(--adapter_2) perl defined $value "--adapter_2 $value" 14 mismatches Number of mismatches allowed in the adapter sequence (--adapter_mm) perl defined $value "--adapter_mm $value" 15 low_qual Discard low quality reads. (-q) perl ($value) ? " -q " : "" 16 trim_read Trim reads to length (-t) perl (defined $value) ? "-t $value" : "" 17 commandend3 commandend perl " % cp inputstrainfile.data strainfile.txt" 50 strainfile strainfile strainfile.txt logfile log file std.err output_name Name for your output output Please enter a value for the output file name perl !defined $output_name all_outputfiles *