*** EDGE_UI: This project is queued. *** /opt/apps/edge/edge_ui/cgi-bin/../../runPipeline -c /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/config.txt -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x -cpu 8 -noColorLog -p /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.1.fastq /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.2.fastq > /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/process_current.log & *** EDGE_UI: Project unstarted *** Project Start: 2014 Oct 22 17:56:49 COMMAND perl /opt/apps/edge/edge_ui/cgi-bin/../../runPipeline -c /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/config.txt -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x -cpu 8 -noColorLog -p /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.1.fastq /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.2.fastq Version: 1.0 [system] ##edge_ui environmental vars edgeui_wwwroot=/opt/apps/edge/edge_ui edgeui_input=/opt/apps/edge/edge_ui/EDGE_input edgeui_output=/opt/apps/edge/edge_ui/EDGE_output edgeui_archive= edgeui_tol_cpu=12 edgeui_auto_queue=1 edgeui_auto_run=1 debug=0 ##number of cpu cpu=8 ##store output to [outpath]/[projname] outpath= projname=Ecoli_10x projdesc= [Count Fastq] DoCountFastq=auto [Quality Trim and Filter] ## boolean, 1=yes, 0=no DoQC=1 ##Targets quality level for trimming q=5 ##Trimmed sequence length will have at least minimum length min_L=50 ##Average quality cutoff avg_q=0 ##"N" base cutoff. Trimmed read has more than this number of continuous base "N" will be discarded. n=0 ##Low complexity filter ratio, Maximum fraction of mono-/di-nucleotide sequence lc=0.85 ## Trim reads with adapters or contamination sequences adapter= ## phiX filter, boolean, 1=yes, 0=no ## phiX=0 ## Cut # bp from 5 end before quality trimming/filtering 5end=0 ## Cut # bp from 3 end before quality trimming/filtering 3end=0 [Host Removal] ## boolean, 1=yes, 0=no DoHostRemoval=1 ## Use more Host= to remove multiple host reads Host=/opt/apps/edge/edge_ui/EDGE_input/Host/Human_ref_GRCh38_all/human_ref_GRCh38_all.fa,/opt/apps/edge/edge_ui/EDGE_input/Host/Inverterbrate_Vectors_of_Human_Pathogens/all_vector.fa bwaMemOptions="-T 90" similarity=90 [IDBA Assembly] ## boolean, 1=yes, 0=no DoAssembly=1 idbaOptions="--pre_correction --mink 31 --maxk 124 --step 20 --min_contig 200" [Reads Mapping To Contigs] # Reads mapping to contigs DoReadsMappingContigs=auto [Reads Mapping To Reference] # Reads mapping to reference DoReadsMappingReference=1 bowtieOptions= window_size=1000 step_size=200 reference=/opt/apps/edge/edge_ui/EDGE_input/Reference/Escherichia_coli_str._K-12_substr._MG1655/NC_000913.gbk [Reads Taxonomy Classification] ## boolean, 1=yes, 0=no DoTaxonomy=1 ## If reference genome exists, only use unmapped reads to do Taxonomy Classification. Turn on AllReads=1 will use all reads instead. AllReads=0 enabledTools=gottcha-genDB-b,gottcha-speDB-b,gottcha-strDB-b,gottcha-genDB-v,gottcha-speDB-v,gottcha-strDB-v,bwa,,metaphlan,kraken_mini,metaphyler-srv [Contigs Mapping To Reference] # Contig mapping to reference DoContigMapping=auto ## identity cutoff identity=85 [Variant Analysis] DoVariantAnalysis=auto [Contigs Annotation] ## boolean, 1=yes, 0=no DoAnnotation=1 ## kingdom: Archaea Bacteria Mitochondria Viruses kingdom=Bacteria [ProPhage Detection] DoProPhageDetection=1 [SNP Phylogeny] DoSNPtree=1 ## Availabe choices are Ecoli, Yersinia, Francisella, Brucella, Bacillus SNPdbName=Ecoli [Primer Validation] DoPrimerValidation=1 maxMismatch=1 primer=/opt/apps/edge/edge_ui/EDGE_input/testData/primers.fa [Primer Adjudication] ## boolean, 1=yes, 0=no DoPrimerDesign=1 ## desired primer tm tm=59 ## reject primer having Tm < tm_diff difference with background Tm tm_diff=5 ## display # top results for each target top=5 [Contig Blast] DoBlast=0 BLAST_nr_DB=0 BLAST_nt_DB=0 [Generate JBrowse Tracks] DoJBrowse=1 [HTML Report] DoHTMLReport=1 The Output Directory path exists If you use different input, it may mess up the result with existing files. [Quality Trim and Filter] Running perl /opt/apps/edge/scripts/illumina_fastq_QC.pl -p /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.1.fastq /opt/apps/edge/edge_ui/EDGE_input/testData/Ecoli_10x.2.fastq -q 5 -min_L 50 -avg_q 0 -n 2 -lc 0.85 -5end 0 -3end 0 -split_size 100000 -d /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/QcReads -t 8 Running time: 00:02:46 [Host Removal] human_ref_GRCh38_all Running perl /opt/apps/edge/scripts/host_reads_removal_by_mapping.pl -p /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/QcReads/QC.1.trimmed.fastq /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/QcReads/QC.2.trimmed.fastq -u /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/QcReads/QC.unpaired.trimmed.fastq -ref /opt/apps/edge/edge_ui/EDGE_input/Host/Human_ref_GRCh38_all/human_ref_GRCh38_all.fa -bwaMemOptions "-T 90" -s 90 -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/human_ref_GRCh38_all -cpu 8 -host -prefix human_ref_GRCh38_all.clean Running time: 00:01:03 [Host Removal] all_vector Running perl /opt/apps/edge/scripts/host_reads_removal_by_mapping.pl -p /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/human_ref_GRCh38_all/human_ref_GRCh38_all.clean.1.fastq /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/human_ref_GRCh38_all/human_ref_GRCh38_all.clean.2.fastq -u /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/human_ref_GRCh38_all/human_ref_GRCh38_all.clean.unpaired.fastq -ref /opt/apps/edge/edge_ui/EDGE_input/Host/Inverterbrate_Vectors_of_Human_Pathogens/all_vector.fa -bwaMemOptions "-T 90" -s 90 -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/all_vector -cpu 8 -host -prefix all_vector.clean Running time: 00:05:58 Host Removal Stat and plot [IDBA Assembly] Running ulimit -v 65438988;idba_ud -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/idba --pre_correction --mink 31 --maxk 124 --step 20 --min_contig 200 --num_threads 8 -r /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/short_single.fa --read_level_2 /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/short_paired.fa 2>/dev/null Running time: 00:02:15 [Reads Mapping To Contigs] Running perl /opt/apps/edge/scripts/runReadsToContig.pl -p '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.1.fastq /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.2.fastq' -u /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.unpaired.fastq -bowtie_options '-p 8 ' -d /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/readsMappingToContig -pre readsToContigs -aligner bowtie -ref /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa Running time: 00:00:46 Checking Reference genome Converting NC_000913 Genbank to Fasta and GFF [Reads Mapping To Reference] Running perl /opt/apps/edge/scripts/runReadsToGenome.pl -p '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.1.fastq /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.2.fastq' -u /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.unpaired.fastq -bowtie_options '-p 8 ' -d /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/ReadsBasedAnalysis -pre readsToRef -aligner bowtie -ref /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.fasta Running time: 00:04:20 Retrieveing unmapped reads Unmapped reads: Paired End: 1186 Single End: 1670 [Reads Taxonomy Classification] Running /opt/apps/edge/scripts/microbial_profiling/microbial_profiling.pl -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/ReadsBasedAnalysis/UnmappedReads/Taxonomy -s /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/ReadsBasedAnalysis/UnmappedReads/Taxonomy/microbial_profiling.settings.ini -c 8 /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/ReadsBasedAnalysis/UnmappedReads/Taxonomy/UnmappedReads.fastq 2>/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/ReadsBasedAnalysis/UnmappedReads/Taxonomy/error.log Running time: 00:22:15 [Contigs Mapping To Reference] Running perl /opt/apps/edge/scripts/nucmer_genome_coverage.pl -e 1 -i 85 -p /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigMappingToRef/contigsToRef /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.fasta /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa Running time: 00:00:36 [Variant Analysis] Running /opt/apps/edge/scripts/SNP_analysis.pl -genbank /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.gbk -SNP /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigMappingToRef/contigsToRef.snps -format nucmer -output /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Indels Running /opt/apps/edge/scripts/gap_analysis.pl -genbank /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.gbk -gap /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigMappingToRef/contigsToRef_ref_zero_cov_coord.txt > /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Indels/GapVSReference.report.txt Running time: 00:01:11 [Contigs Annotation] Running prokka --quiet --force --prefix Ecoli_10x --cpus 8 --outdir /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Annotation --kingdom Bacteria /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa Running time: 00:03:25 [ProPhage Detection] Running /opt/apps/edge/scripts/phageFinder_prepare.pl -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/ProphageTmp /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Annotation/Ecoli_10x.gff Running /opt/apps/edge/thirdParty/phage_finder_v2.1/bin/phage_finder_v2.1.sh Assembly 8 1>/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Prophage/log.txt 2>&1 Numaber of prophage hit found: 0 Running time: 00:01:53 [SNP Phylogeny] Prepare SNPdb Running /opt/apps/edge/scripts/prepare_SNP_phylogeny.pl -o /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/SNP_Phylogeny/Ecoli -map /opt/apps/edge/database/SNPdb/reference.txt -db Ecoli -n Ecoli_10x -cpu 8 -p /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.1.fastq /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.2.fastq -c /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa -s /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HostRemoval/hostclean.unpaired.fastq >> /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/SNP_Phylogeny/Ecoli/log.txt Compute SNP tree Running /opt/apps/edge/scripts/SNPphy/runSNPphylogeny.pl /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/SNP_Phylogeny/Ecoli/SNPphy.ctrl >> /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/SNP_Phylogeny/Ecoli/log.txt Running time: 01:06:13 [Primer Validation] Running perl /opt/apps/edge/scripts/pcrValidation/validate_primers.pl -prefix pcrContigValidation -ref /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa -primer /opt/apps/edge/edge_ui/EDGE_input/testData/primers.fa -mismatch 1 -threads 8 -output /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck Validate primers binding to Contigs Primer Pair Forward and Reverse PCR success! Primer Forward Alignment to (Ecoli_10x_221) r TGAGGGACCTGCGAAGCCCGGAT |||||||||||||| |||||||| p TGAGGGACCTGCGAGGCCCGGAT Primer Reverse Alignment to (Ecoli_10x_221) r TTCATCGTGAATCCATTAGACTT ||||||||||||||||||||||| p TTCATCGTGAATCCATTAGACTT The primers amplify Ecoli_10x_221 from 4336 to 4958, with size 623 ---------- Running perl /opt/apps/edge/scripts/pcrValidation/validate_primers.pl -prefix pcrRefValidation -ref /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.fasta -primer /opt/apps/edge/edge_ui/EDGE_input/testData/primers.fa -mismatch 1 -threads 8 -output /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck Validate primers binding to Reference Primer Pair Forward and Reverse PCR success! Primer Forward Alignment to (NC_000913) r ATCCGGGCCTCGCAGGTCCCTCA ||||||||||||||||||||||| p ATCCGGGCCTCGCAGGTCCCTCA Primer Reverse Alignment to (NC_000913) r AAGTCTAATGGATTCACGATGAA ||||||||||||||||||||||| p AAGTCTAATGGATTCACGATGAA The primers amplify NC_000913 from 3957949 to 3958571, with size 623 ---------- Running time: 00:00:08 [Primer Adjudication] Running perl /opt/apps/edge/scripts/pcrAdjudication/pcrUniquePrimer.pl --input /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/contigs.fa --tm 59 --tm_diff 5 --threads 8 --top 5 --gff3 /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck/PCR.Adjudication.primers.gff3 1>/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck/PCR.Adjudication.primers.txt 2>/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck/PCR.Adjudication.log See primer adjudication results at /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssayCheck/PCR.Adjudication.primers.txt and PCR.Adjudication.primers.gff3 Running time: 00:10:06 [Generate JBrowse Tracks] Running /opt/apps/edge/scripts/edge2jbrowse_converter.pl --in-ref-fa '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.fasta' --in-ctg-anno-gff3 '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/AssemblyBasedAnalysis/Annotation/Ecoli_10x.gff' --in-ref-gff3 '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/Reference//reference.gff' --proj_outdir '/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x' 2>&1 1>/opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/JBrowse/log.txt Running time: 00:01:44 Produce Final PDF Report Total Running time: 02:05:39 [HTML Report] Converting pdf to png ... Running /opt/apps/edge/scripts/munger/outputMunger_w_temp.pl /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x > /opt/apps/edge/edge_ui/EDGE_output/Ecoli_10x/HTML_Report/log.txt Running time: 00:00:14 All Done.