(blastReads) using cached blast results: megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT ... (blastReads) using cached filtered blast results: megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 ... (blastReads) extracting gi numbers from megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (blastReads) 1359 unique gi numbers in megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (eukaryotaFilter) filtering gi numbers from megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi by taxa (eukaryotaFilter) 44 unique eukaryotic gi numbers in megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi (eukaryotaFilter) identifying eukaryotic reads from megablast.2662201_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200 (eukaryotaFilter) 140 eukaryotic reads (contamFilter) run_megablast 2662201_fasta.screen JGIContaminants (contamFilter) parsing megablast.2662201_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT (contamFilter) /home/copeland/scripts/blastParser_P.pl megablast.2662201_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT (contamFilter) 746 probable JGI contaminant reads (qualFilter) identifying low quality reads (<100 Q20 bases)... (qualFilter) 9870 low quality reads (smallContigFilter) identifying reads from 2-read contigs... (smallContigFilter) 113 reads from 2-read contigs found (cleanFasta) backing up 2662201_fasta.screen (cp 2662201_fasta.screen 2662201_fasta.screen.orig) (cleanFasta) creating master list of reads to remove... (cleanFasta) 10425 reads to remove (cleanFasta) /home/copeland/scripts/fasta_coll.pl -output fasta_good -exclude reads.toRemove -fasta 2662201_fasta.screen (cleanFasta) verifying read removal... (cleanFasta) mv fasta_good 2662201_fasta.screen (cleanFasta) mv fasta_good.qual 2662201_fasta.screen.qual (cleanFasta) mv reads.toRemove reads_removed ####################################################################### WARNING. WARNING. WARNING. 14Jun04 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: 140 reads.possible.eukaryota 746 reads.JGIContaminants 113 reads.2RdContigs 9869 reads.lowQual.q20lt100 10424 total unique reads removed 35797 reads prior to clean up ----------------------------------- Assembly prior to QD readsTotal: 46221 readsInAllContigs: 37854 readsInMajorContigs: 36062 contigsTotal: 330 contigsMajor: 176 contigsSingletons: 8367 basesInConsensusUntrimmed: 2173646 basesInConsensusTrimmed: 2126571 basesInConsensusMajContigsTrimmed: 1982626 basesInConsensusMajContigsUnrimmed: 2007176 depthMajorContigsTrimmed: 16 ----------------------------------- Assembly after QD: readsTotal: 35797 readsInAllContigs: 35701 readsInMajorContigs: 35112 contigsTotal: 269 contigsMajor: 177 basesInConsensusUntrimmed: 2125955 basesInConsensusTrimmed: 2087146 basesInConsensusMajContigsTrimmed: 1978218 basesInConsensusMajContigsUnrimmed: 2002539 depthMajorContigsTrimmed: 16