Failed to cd to /psf/project/microbe3/3634480/edit_dir
(blastReads) Didn't find blast results file. blast 3634480_fasta.screen against nt ...
cat megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsed | megablastFilter.sh 98 200 > megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(blastReads) extracting gi numbers from megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(blastReads) 1871 unique gi numbers in megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(eukaryotaFilter) filtering gi numbers from megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi by taxa
(eukaryotaFilter) 1063 unique eukaryotic gi numbers in megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200.gi
(eukaryotaFilter) identifying eukaryotic reads from megablast.3634480_fasta.screen.v.nt.FmLD2a10p98e1e30JFfT.parsedL200
(eukaryotaFilter) 3934 eukaryotic reads
(contamFilter) run_megablast 3634480_fasta.screen JGIContaminants
(contamFilter) parsing megablast.3634480_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT
(contamFilter) /home/copeland/scripts/blastParser_P.pl megablast.3634480_fasta.screen.v.JGIContaminants.FmLD2a10p98e1e30JFfT
(contamFilter) 4042 probable JGI contaminant reads
(qualFilter) identifying low quality reads (<100 Q20 bases)...
(qualFilter) 40693 low quality reads
(smallContigFilter) identifying reads from 2-read contigs...
(smallContigFilter) 452 reads from 2-read contigs found
(cleanFasta) backing up 3634480_fasta.screen (cp 3634480_fasta.screen 3634480_fasta.screen.orig)
(cleanFasta) creating master list of reads to remove...
(cleanFasta) 47722 reads to remove
(cleanFasta) /home/copeland/scripts/fasta_coll.pl -output fasta_good -exclude reads.toRemove -fasta 3634480_fasta.screen
(cleanFasta) verifying read removal...
(cleanFasta) mv fasta_good 3634480_fasta.screen
(cleanFasta) mv fasta_good.qual 3634480_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:


3934 reads.possible.eukaryota
4042 reads.JGIContaminants
452 reads.2RdContigs
40692 reads.lowQual.q20lt100
47721 total unique reads removed

228818 reads prior to clean up