(blastReads) using cached blast results: megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT ... (blastReads) using cached filtered blast results: megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 ... extracting gi numbers from megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 extracting gi numbers failed (blastReads) using cached blast results: megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT ... (blastReads) using cached filtered blast results: megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 ... extracting gi numbers from megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 extracting gi numbers failed (blastReads) using cached blast results: megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT ... cat megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsed | megablastFilter.sh 98 200 > megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 extracting gi numbers from megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (blastReads) 1150 unique gi numbers in megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (eukaryotaFilter) filtering gi numbers from megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi by taxa (eukaryotaFilter) 121 unique eukaryotic gi numbers in megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi (eukaryotaFilter) identifying eukaryotic reads from megablast.2351493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (eukaryotaFilter) 120 eukaryotic reads (contamFilter) run_megablast 2351493_fasta.screen JGIContaminants (contamFilter) parsing megablast.2351493_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT (contamFilter) /home/copeland/scripts/blastParser_P.pl megablast.2351493_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT (contamFilter) 633 probable JGI contaminant reads (qualFilter) identifying low quality reads... (qualFilter) using cached copy of low quality reads file: reads.lowQual.q20lt100 (qualFilter) 27097 low quality reads (smallContigFilter) using cached copy of 2 read contigs file: reads.2RdContigs (smallContigFilter) 261 reads from 2 reads contigs found (cleanFasta) creating master list of reads to remove... (cleanFasta) 27964 reads to remove (cleanFasta) /home/copeland/scripts/extractReads.pl -o fasta_good -X reads.toRemove 2351493_fasta.screen (cleanFasta) verifying read removal... (cleanFasta) backing up 2351493_fasta.screen (cleanFasta) mv fasta_good 2351493_fasta.screen (cleanFasta) mv fasta_good.qual 2351493_fasta.screen.qual (cleanFasta) mv reads.toRemove reads_removed ####################################################################### WARNING. WARNING. WARNING. 14Apr04 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: 120 reads.possible.eukaryota 633 reads.JGIContaminants 261 reads.2RdContigs 27096 reads.lowQual.q20lt100 27963 total unique reads removed 105004 reads prior to clean up