3.13.0 Metaspades Markov Model Search for antibiotic resistance genes in environmental samples Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A., Prjibelski, A. D., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepanauskas, R., Clingenpeel, S. R., Woyke, T., McLean, J. S., Lasken, R., Tesler, G., Alekseyev, M. A., and Pevzner, P. A. Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A., Prjibelski, A. D., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepanauskas, R., Clingenpeel, S. R., Woyke, T., McLean, J. S., Lasken, R., Tesler, G., Alekseyev, M. A., and Pevzner, P. A. (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20, 714-737. 10.1089/cmb.2013.0084 Sequence Assembly metaspades_metamarc_xsede invocation perl "metamarc_wrapper_expanse" 1 metamarc_scheduler scheduler.conf perl $num_threads < 24 perl "threads_per_process=$num_threads\\n" . "node_exclusive=0\\n" . "mem=" . (int($num_threads*(248/32))) . "G\\n" . "nodes=1\\n" metamarc_scheduler2 scheduler.conf perl $num_threads > 23 perl "threads_per_process=24\\n" . "mem=" . (int(24*(248/32))) . "G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" inputfile1_fastq First fastq file inputfastq_R1.sub.fq.gz perl "spades.py -1 inputfastq_R1.sub.fq.gz" 2 command_line2 perl "--meta -t $num_threads" 16 metaspades_metamarc_workflow1 perl $run_metamarc perl "&& mkdir $name_spadesoutputdir" 0 44 metaspades_metamarc_workflow2 perl $run_metamarc perl "&& metamarc_wrapper_expanse mmarc -i spades_$name_spadesoutputdir/contigs.fasta" 0 45 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 12 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 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $runtime ne 0 perl "runhours=$value\\n" num_threads How many threads? 4 paired_end Files are paired end reads. 1 3 inputfastq2 Input fastq file2 (gzipped) inputfastq_R2.sub.fq.gz perl $paired_end 10 perl "-2 inputfastq_R2.sub.fq.gz" Please select the second fastq file perl $paired_end && !defined $inputfastq2 5 name_spadesoutputdir Name for the spades output directory perl "-o spades_$name_spadesoutputdir" output 15 specify_kmer Specify the kmer values for meta-spades perl "-k $value" 21,33,55,77,99,127 18 Please specify the kmer values for meta-spades perl !defined $specify_kmer run_metamarc Run Meta-Marc after meta-Spades 1 metamarc_filename Enter a name for the metamarc output file (-f) perl $run_metamarc metamarc_output 46 metamarc_filedirnames perl $run_metamarc perl "-o metamarc_$name_spadesoutputdir -f $metamarc_filename -t $num_threads" 46 all_outputfiles *