(blastReads) using cached blast results (1186516 lines): megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI (blastReads) using cached parsed blast results (40961 lines): megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI (blastReads) cat megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed | megablastFilter.sh 98 200 > megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200 (blastReads) Looking for cached gi file megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200.gi ... (blastReads) Extracting gi numbers from megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200 (blastReads) 1581 unique gi numbers in megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200.gi (eukaryotaFilter) filtering gi numbers from megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200.gi by taxa (eukaryotaFilter) 3 unique eukaryotic gi numbers in megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200.gi (eukaryotaFilter) identifying eukaryotic reads from megablast.3634492_fasta.screen.v.nt.FmLD2a10p98e1e30JFfTI.parsed.P98L200 (eukaryotaFilter) 10 eukaryotic reads (contamFilter) Blast 3634492_fasta.screen against JGIContaminants (contamFilter) parsing megablast.3634492_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfTI (contamFilter) Parsing megablast.3634492_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfTI (contamFilter) 43 probable JGI contaminant reads (qualFilter) identifying low quality reads (<100 Q20 bases)... (qualFilter) 6918 low quality reads (smallContigFilter) identifying reads from 2-read contigs... (smallContigFilter) 38 reads from 2-read contigs found (cleanFasta) backing up 3634492_fasta.screen (cp 3634492_fasta.screen 3634492_fasta.screen.orig) (cleanFasta) creating master list of reads to remove... (cleanFasta) 6978 reads to remove (cleanFasta) /home/copeland/scripts/fasta_coll.pl -output fasta_good -exclude reads.toRemove -fasta 3634492_fasta.screen (cleanFasta) verifying read removal.../home/copeland/local/SPARC/bin/agrep-XL -c -f reads.toRemove fasta_good (cleanFasta) mv fasta_good 3634492_fasta.screen (cleanFasta) mv fasta_good.qual 3634492_fasta.screen.qual (cleanFasta) mv reads.toRemove reads_removed ####################################################################### WARNING. WARNING. WARNING. 22Jul04 This project has been automatically analyzed by the 'draftQD.sh' script, a crude zeroth order, project clean up script, designed to identify and remove low quality and contaminant reads from a project. The heuristics used by the script may both remove valid project data and fail to remove bona fide contaminants. The following sets of reads have been removed from the project fasta in this edit_dir only. The trace data of possible contaminants has not been removed from the project. Therefore, if you are using automated assembly procedures which recreate a project fasta from data in the partitions, then reads removed in this edit_dir will be present in new file. Removed reads lists: reads.lowQual.q20lt100 -- less than 100 contiguous q20 bases not X reads.2RdContigs -- all reads from 2 read contigs reads.possible.eukaryota -- 98%id, 200bp+ blast hits to eukaryotic entries in 'nt' After removing suspect reads from the project fasta, a new assembly was created in this directory using the cleaned fasta file. ####################################################################### reads removed from fasta: 10 reads.possible.eukaryota 43 reads.JGIContaminants 38 reads.2RdContigs 6917 reads.lowQual.q20lt100 6977 total unique reads removed 76909 reads prior to clean up ----------------------------------- Current assembly location: /psf/project/microbe3/3634492/edit_dir.22Jul04.QD ----------------------------------- assembly prior to QD: readsTotal: 83886 readsInAllContigs: 77766 readsInMajorContigs: 77684 contigsTotal: 71 contigsMajor: 45 contigsSingletons: 6120 basesInConsensusUntrimmed: 5023655 basesInConsensusTrimmed: 5008849 basesInConsensusMajContigsTrimmed: 5001264 basesInConsensusMajContigsUnrimmed: 5009511 depthMajorContigsTrimmed: 15 ----------------------------------- assembly after QD: readsTotal: 76909 readsInAllContigs: 76867 readsInMajorContigs: 76860 contigsTotal: 47 contigsMajor: 44 contigsSingletons: 42 basesInConsensusUntrimmed: 5011599 basesInConsensusTrimmed: 5001639 basesInConsensusMajContigsTrimmed: 5000356 basesInConsensusMajContigsUnrimmed: 5009007 depthMajorContigsTrimmed: 15