3.13.0 SPAdes for de novo assembly Bankevich, A., Nurk, S., 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. Bankevich, A., Nurk, S., Antipov, D., et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19, 455-477 10.1089/cmb.2012.0021 de Novo Sequence Assembly spades_access invocation perl !$more_memory perl "spades_3.15.5_expanse -t 16" 1 invocation_more perl $more_memory perl "spades_3.15.5_expanse -t 128" 1 spaces_scheduler scheduler.conf perl !$more_memory perl "threads_per_process=16\\n" . "node_exclusive=0\\n" . "mem=32G\\n" . "nodes=1\\n" metamarc_scheduler2 scheduler.conf perl $more_memory perl "threads_per_process=128\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" inputfile1_fastq inputfastq_1.fq.gz 2 inputfile1S perl $specify_readtype eq "-s" perl "--s 1 inputfastq_1.fq.gz" 2 inputfile1_2 perl $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 1 inputfastq_1.fq.gz" 2 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 $runtime cpu hours perl !$more_memory The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $more_memory perl "runhours=$value\\n" specify_readtype My read files are: -s Single reads --pe Paired end reads --hqmp High quality mate-paired reads specify_inputtype My first input file is: 80 Single read file -12 Interleaved forward and reverse reads (-pe, -hqmp) -1 Forward reads only (-pe, -hqmp) -m File with merged forward and reverse reads (-pe, -hqmp) specify_librarynumber How many read libraries? 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 select_perlibs Additional Paired End Read Libraries inputfastq22 Select fastq read library 2 (gzipped) inputfastq_2.fq.gz perl $specify_librarynumber > 1 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 2 inputfastq_2.fq.gz" Please select the second paired end read library perl $specify_librarynumber > 1 && $specify_readtype ne "-s" && !defined $inputfastq22 5 inputfastq23 Select fastq read library 3 (gzipped) inputfastq_3.fq.gz perl $specify_librarynumber > 2 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 3 inputfastq_3.fq.gz" Please select the third paired end library perl $specify_librarynumber > 2 && $specify_readtype ne "-s" && !defined $inputfastq23 6 inputfastq24 Select fastq read library 4 (gzipped) inputfastq_4.fq.gz perl $specify_librarynumber > 3 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 4 inputfastq_4.fq.gz" Please select the fourth paired end read library perl $specify_librarynumber > 3 && $specify_readtype ne "-s" && !defined $inputfastq24 7 inputfastq25 Select fastq read library5 (gzipped) inputfastq_5.fq.gz perl $specify_librarynumber > 4 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 5 inputfastq_5.fq.gz" Please select the fifth paired end read library perl $specify_librarynumber > 4 && $specify_readtype ne "-s" && !defined $inputfastq25 8 inputfastq26 Select fastq read library 6 (gzipped) inputfastq_6.fq.gz perl $specify_librarynumber > 5 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 6 inputfastq_6.fq.gz" Please select the sixth paired end read library perl $specify_librarynumber > 5 && $specify_readtype ne "-s" && !defined $inputfastq26 9 inputfastq27 Select fastq read library7 (gzipped) inputfastq_7.fq.gz perl $specify_librarynumber > 6 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 7 inputfastq_7.fq.gz" Please select the seventh paired end read library perl $specify_librarynumber > 6 && $specify_readtype ne "-s" && !defined $inputfastq27 10 inputfastq28 Select fastq read library 8 (gzipped) inputfastq_8.fq.gz perl $specify_librarynumber > 7 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 8 inputfastq_8.fq.gz" Please select the eighth paired end read library perl $specify_librarynumber > 7 && $specify_readtype ne "-s" && !defined $inputfastq28 11 inputfastq29 Select fastq read library 9 (gzipped) inputfastq_9.fq.gz perl $specify_librarynumber > 8 && $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 9 inputfastq_9.fq.gz" Please select the ninth paired end library perl $specify_librarynumber > 8 && $specify_readtype ne "-s" && !defined $inputfastq29 12 select_singleperlibs Unpaired Reads from Libraries inputfastq1s Input unpaired fastq reads for library 1 (gzipped) inputfastq_S1.fq.gz perl $specify_readtype eq "--pe" perl "$specify_readtype-s 1 inputfastq_S1.fq.gz" 13 inputfastq2s Input fastq unpaired reads from paired-end library 2 (gzipped) inputfastq_S2.fq.gz perl $specify_librarynumber > 1 && $specify_inputtype < 20 perl "$specify_readtype-s 2 inputfastq_S2.fq.gz" 13 inputfastq3s Input fastq unpaired reads from paired-end library 3 (gzipped) inputfastq_S3.fq.gz perl $specify_librarynumber > 2 && $specify_inputtype < 20 perl "$specify_readtype-s 3 inputfastq_S3.fq.gz" 13 inputfastq4s Input fastq unpaired reads from paired-end library 4 (gzipped) inputfastq_S4.fq.gz perl $specify_librarynumber > 3 && $specify_inputtype < 20 perl "$specify_readtype-s 4 inputfastq_S4.fq.gz" 16 inputfastq25s Input fastq unpaired reads from paired-end library 5 (gzipped) inputfastq_S5.fq.gz perl $specify_librarynumber > 4 && $specify_inputtype < 20 perl "$specify_readtype-s 5 inputfastq_S5.fq.gz" 17 inputfastq26s Input fastq unpaired reads from paired-end library 6 (gzipped) inputfastq_S6.fq.gz perl $specify_librarynumber > 5 && $specify_inputtype < 20 perl "$specify_readtype-s 6 inputfastq_S6.fq.gz" 18 inputfastq27s Input fastq unpaired reads from paired-end library 7 (gzipped) inputfastq_S7.fq.gz perl $specify_librarynumber > 6 && $specify_inputtype < 20 perl "$specify_readtype-s 7 inputfastq_S7.fq.gz" 19 inputfastq28s Input fastq unpaired reads from paired-end library 8 (gzipped) inputfastq_S8.fq.gz perl $specify_librarynumber > 7 && $specify_inputtype < "20" perl "$specify_readtype-s 8 inputfastq_S8.fq.gz" 20 inputfastq29s Input fastq unpaired reads from paired-end library 9 (gzipped) inputfastq_S9.fq.gz perl $specify_librarynumber > 8 && $specify_inputtype < 20 perl "$specify_readtype-s 9 inputfastq_S9.fq.gz" 21 select_revperlibs Reverse Read Libraries inputfastq2r Select reverse read library 1 (gzipped) inputfastq_R1.fq.gz perl $specify_inputtype eq "-1" perl "$specify_readtype-2 1 inputfastq_R1.fq.gz" Please select the reverse read library 1 perl $specify_inputtype eq "-1" && !defined $inputfastq2r 13 inputfastq22r Select fastq paired end reverse read library 2 (gzipped) inputfastq_R2.fq.gz perl $specify_librarynumber > 1 && $specify_inputtype eq "-1" perl "$specify_readtype-2 2 inputfastq_R2.fq.gz" Please select the reverse read library 2 perl $specify_librarynumber > 1 && $specify_inputtype eq "-1" && !defined $inputfastq22r 14 inputfastq23r Select fastq paired end reverse read library 3 (gzipped) inputfastq_R3.fq.gz perl $specify_librarynumber > 2 && $specify_inputtype eq "-1" perl "$specify_readtype-2 3 inputfastq_R3.fq.gz" Please select the reverse read library 3 perl $specify_librarynumber > 2 && $specify_inputtype eq "-1" && !defined $inputfastq23r 15 inputfastq24r Select fastq paired end reverse read library 4 (gzipped) inputfastq_R4.fq.gz perl $specify_librarynumber > 3 && $specify_inputtype eq "-1" perl "$specify_readtype-2 4 inputfastq_R4.fq.gz" Please select the reverse read library 3 perl $specify_librarynumber > 3 && $specify_inputtype eq "-1" && !defined $inputfastq24r 16 inputfastq25r Select fastq paired end reverse read library 5 (gzipped) inputfastq_R5.fq.gz perl $specify_librarynumber > 4 && $specify_inputtype eq "-1" perl "$specify_readtype-2 5 inputfastq_R5.fq.gz" Please select the reverse read library 5 perl $specify_librarynumber > 4 && $specify_inputtype eq "-1" && !defined $inputfastq25r 17 inputfastq26r Select fastq paired end reverse read library 6 (gzipped) inputfastq_R6.fq.gz perl $specify_librarynumber > 5 && $specify_inputtype eq "-1" perl "$specify_readtype-2 6 inputfastq_R6.fq.gz" Please select the reverse read library 6 perl $specify_librarynumber > 5 && $specify_inputtype eq "-1" && !defined $inputfastq26r 18 inputfastq27r Select fastq paired end reverse read library 7 (gzipped) inputfastq_R7.fq.gz perl $specify_librarynumber > 6 && $specify_inputtype eq "-1" perl "$specify_readtype-2 7 inputfastq_R7.fq.gz" Please select the reverse read library 7 perl $specify_librarynumber > 6 && $specify_inputtype eq "-1" && !defined $inputfastq27r 19 inputfastq28r Select fastq paired end reverse read library 8 (gzipped) inputfastq_R8.fq.gz perl $specify_librarynumber > 7 && $specify_inputtype eq "-1" perl "$specify_readtype-2 8 inputfastq_R8.fq.gz" Please select the reverse read library 8 perl $specify_librarynumber > 7 && $specify_inputtype eq "-1" && !defined $inputfastq28r 21 inputfastq29r Select fastq paired end reverse read library 9 (gzipped) inputfastq_R9.fq.gz perl $specify_librarynumber > 8 && $specify_inputtype eq "-1" perl "$specify_readtype-2 9 inputfastq_R9.fq.gz" Please select the reverse read library 9 perl $specify_librarynumber > 8 && $specify_inputtype eq "-1" && !defined $inputfastq29r 22 select_singlelibs Select Additional Single Read Libraries inputfastq22sr Select single paired end read library 2 (gzipped) inputfastq_sr2.fq.gz perl $specify_librarynumber > 1 && $specify_readtype eq "-s" perl "--s 2 inputfastq_sr2.fq.gz" Please select single read library 2 (gzipped) perl $specify_librarynumber > 1 && $specify_readtype eq "-s" && !defined $inputfastq22sr 5 inputfastq23sr Select single paired end read library 3 (gzipped) inputfastq_sr3.fq.gz perl $specify_readtype eq "-s" perl "--s 3 inputfastq_sr3.fq.gz" Please select single read library 3 (gzipped) perl $specify_librarynumber > 2 && $specify_readtype eq "-s" && !defined $inputfastq23sr 6 inputfastq24sr Select fastq single read library 4 (gzipped) inputfastq_4sr.fq.gz perl $specify_librarynumber > 3 && $specify_inputtype eq "80" perl "--s 4 inputfastq_4sr.fq.gz" Please select the fourth single read library perl $specify_librarynumber > 3 && $specify_inputtype eq "80" && !defined $inputfastq24sr 8 inputfastq25sr Select fastq single read library 5 (gzipped) inputfastq_5sr.fq.gz perl $specify_librarynumber > 4 && $specify_inputtype eq "80" perl "--s 5 inputfastq_5sr.fq.gz" Please select the fifth single read library perl $specify_librarynumber > 4 && $specify_inputtype eq "80" && !defined $inputfastq25sr 9 inputfastq26sr Select fastq single read library 6 (gzipped) inputfastq_6sr.fq.gz perl $specify_librarynumber > 5 && $specify_inputtype eq "80" perl "--s 6 inputfastq_6sr.fq.gz" Please select the sixth single read library perl $specify_librarynumber > 5 && $specify_inputtype eq "80" && !defined $inputfastq26sr 9 inputfastq27sr Select fastq single read library 7 (gzipped) inputfastq_7sr.fq.gz perl $specify_librarynumber > 6 && $specify_inputtype eq "80" perl "--s 7 inputfastq_7sr.fq.gz" Please select the seventh single read library perl $specify_librarynumber > 6 && $specify_inputtype eq "80" && !defined $inputfastq27sr 10 inputfastq28sr Select fastq single read library 8 (gzipped) inputfastq_8sr.fq.gz perl $specify_librarynumber > 7 && $specify_inputtype eq "80" perl "--s 8 inputfastq_8sr.fq.gz" Please select the eighth single read library perl $specify_librarynumber > 7 && $specify_inputtype eq "80" && !defined $inputfastq28sr 11 inputfastq29sr Select fastq single read library 9 (gzipped) inputfastq_8sr.fq.gz perl $specify_librarynumber > 8 && $specify_inputtype eq "80" perl "--s 9 inputfastq_9sr.fq.gz" Please select the ninth single read library perl $specify_librarynumber > 8 && $specify_inputtype eq "80" && !defined $inputfastq29sr 12 name_spadesoutputdir Name for the spades output directory perl "-o spades_$name_spadesoutputdir" output 30 more_memory I need more memory specify_datatype Specify if your data type perl $specify_pipelineopt ne "--only-error-correction" --isolate High coverage isolate/multicell --sc Single cell (MDA) --meta Metagenomic perl defined $specify_datatype ? "$value":"" Please specify the kind of data you are using (High coverage/single cell/metagenomic) perl !defined $specify_datatype && $specify_pipelineopt ne "--only-error-correction" 31 specify_spadesmode Specify a specialized SPAdes mode --bio biosyntheticSPAdes mode --corona coronaSPAdes mode --rna RNA-Seq data perl defined $specify_spadesmode ? "$value":"" 32 hybrid_options Hybrid Assembly Options specify_pacbio Specify a PacBio readfile perl defined $specify_pacbio ? "--pacbio pacbio.fq.gz":"" pacbio.fq.gz 37 specify_nanopore Specify a Nanopore readfile perl defined $specify_nanopore ? "--nanopore nanopore.fq.gz":"" nanopore.fq.gz 37 specify_sanger Specify a Sanger readfile perl defined $specify_sanger ? "--sanger sanger.fq.gz":"" sanger.fq.gz 37 specify_trusted Specify a Trusted Contig file perl defined $specify_trusted ? "--trusted trusted.fq.gz":"" trusted.fq.gz 37 specify_untrusted Specify an Untrusted Contig file perl defined $specify_untrusted ? "--untrusted-contigs trusted.fq.gz":"" untrusted.fq.gz 37 specify_spadespipeline Specify a specialized SPAdes pipeline --plasmid plasmid SPAdes pipeline --metaviral metaviral SPAdes pipeline --metaplasmid metaPlasmid SPAdes pipeline perl defined $specify_spadespipeline ? "$value":"" Sorry, --plasmid cannot be used with single cell mode (--sc) perl $specify_spadespipeline eq "--plasmid" && $specify_datatype eq "--sc" Sorry, --metaplasmid cannot be used with single cell mode (--sc) perl $specify_spadespipeline eq "--metaplasmid" && $specify_datatype eq "--sc" 35 specify_datasource Specify a specialized data source --rnaviral RNA-Seq Viral assembly module --iontorrent Ion Torrent data perl defined $specify_datasource ? "$value":"" The --rnaviral option cannot be used with the --careful option perl $specify_datasource eq "--rnaviral" && $specify_pipelineopt2 The --rnaviral option cannot be used with the - -only-error-correction option perl $specify_datasource eq "--rnaviral" && $specify_pipelineopt eq "--only-error-correction" 36 pipeline_options Pipeline Options specify_pipelineopt Specify the Pipeline to run --only-error-correction Error correction without assembling --only-assembler Assembling without Error Correction perl defined $specify_pipelineopt ? "$value":"" 37 specify_pipelineopt2 Minimize number of mismatches and short indels perl $specify_datatype eq "--sc" perl $specify_pipelineopt2 ? "--careful":"" 38 specify_pipelineopt3 Save all check-points (default=last) perl $specify_pipelineopt3 ? "--checkpoint all":"" 39 specify_pipelineopt5 Do not compress the corrected reads perl $specify_pipelineopt ne "--only-assembler" perl $specify_pipelineopt5 ? "--disable-gzip-output":"" 40 specify_pipelineopt6 Disable repeat resolution stage of assembling perl $specify_pipelineopt6 ? "--disable-rr":"" 41 advanced_options Advanced Options specify_yaml File with dataset description in YAML format perl "--dataset $value" data_description.yaml 42 specify_kmer Specify the kmer values perl defined $specify_kmer ? "-k $specify_kmer":"" 21,33,55,77,99,127 43 specify_covcutoff Specify the coverage cutoff value perl $specify_datatype ne "--meta" perl defined $specify_covcutoff ? "--cov-cutoff $value":"" 44 specify_phredoffset Specify the Phrad quality offset 33 33 64 64 perl defined $specify_phredoffset ? "--phred-offset $value":"" 45 all_outputfiles *