(blastReads) using cached blast results: megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT ...
cat megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsed | megablastFilter.sh 98 200 > megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
extracting gi numbers from megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(blastReads) 367 unique gi numbers in megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(eukaryotaFilter) filtering gi numbers from megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi by taxa
(eukaryotaFilter) 17 unique eukaryotic gi numbers in megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi
(eukaryotaFilter) identifying eukaryotic reads from megablast.3634493_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(eukaryotaFilter) 80 eukaryotic reads
(contamFilter) run_megablast 3634493_fasta.screen JGIContaminants
(contamFilter) parsing megablast.3634493_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT
(contamFilter) /home/copeland/scripts/blastParser_P.pl megablast.3634493_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT
(contamFilter) 437 probable JGI contaminant reads
(qualFilter) identifying low quality reads...
(qualFilter) 4159 low quality reads
(smallContigFilter) identifying reads from 2 reads contigs...
(smallContigFilter) 80 reads from 2 reads contigs found
(cleanFasta) creating master list of reads to remove...
(cleanFasta) 4479 reads to remove
(cleanFasta) /home/copeland/scripts/extractReads.pl -o fasta_good -X reads.toRemove 3634493_fasta.screen
(cleanFasta) verifying read removal...
(cleanFasta) backing up 3634493_fasta.screen
(cleanFasta) mv fasta_good 3634493_fasta.screen
(cleanFasta) mv fasta_good.qual 3634493_fasta.screen.qual
(cleanFasta) mv reads.toRemove reads_removed

#######################################################################

WARNING. WARNING. WARNING.

26Apr04

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:


80 reads.possible.eukaryota
437 reads.JGIContaminants
80 reads.2RdContigs
4158 reads.lowQual.q20lt100
4478 total unique reads removed

45759 reads prior to clean up