1. Get working directories:

    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    mkdir raw ;
    cd raw ;

2. Get raw reads:

    ssh erichs@meyer32.mcb.berkeley.edu ;

    # Check out existence of 55 files:
    cd /what3/Illumina_backup/120323_HS1A_Caitlin_Ed ;

    ls CS004_NoIndex_L002_R1_* ;
    ls CS004_NoIndex_L002_R1_* | wc -l ;

    ls CS004_NoIndex_L002_R2_* ;
    ls CS004_NoIndex_L002_R2_* | wc -l ;

It looks to me like all 2*55 files are needed, so download them all on redivivus:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/raw ;
    scp -rp erichs@meyer32.mcb.berkeley.edu:/what3/Illumina_backup/120323_HS1A_Caitlin_Ed/*.fastq.gz . ;

Get them unpacked so that I can do something with them:

df -h | grep '/sternlab/redivivus/data02'
/dev/sda1              22T   20T  2.1T  91% /sternlab/redivivus/data02

Make and run script:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/raw ;
    pico 
    ls *.fastq.gz | ./make_job_10apr2012a.pl > job_10apr2012a.sh ;
    chmod +x job_10apr2012a.sh ;

    nohup ./job_10apr2012a.sh 1>job_10apr2012a.nohup.out.txt 2>job_10apr2012a.nohup.err.txt &

Contents of job_10apr2012a.sh: ---------------------------------------

    gunzip CS004_NoIndex_L002_R1_001.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_001.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_001.fastq CS004_NoIndex_L002_R2_001.fastq CS004_NoIndex_L002_R12_001.fastq ;

    gunzip CS004_NoIndex_L002_R1_002.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_002.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_002.fastq CS004_NoIndex_L002_R2_002.fastq CS004_NoIndex_L002_R12_002.fastq ;

    gunzip CS004_NoIndex_L002_R1_003.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_003.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_003.fastq CS004_NoIndex_L002_R2_003.fastq CS004_NoIndex_L002_R12_003.fastq ;

    gunzip CS004_NoIndex_L002_R1_004.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_004.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_004.fastq CS004_NoIndex_L002_R2_004.fastq CS004_NoIndex_L002_R12_004.fastq ;

    gunzip CS004_NoIndex_L002_R1_005.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_005.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_005.fastq CS004_NoIndex_L002_R2_005.fastq CS004_NoIndex_L002_R12_005.fastq ;

    gunzip CS004_NoIndex_L002_R1_006.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_006.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_006.fastq CS004_NoIndex_L002_R2_006.fastq CS004_NoIndex_L002_R12_006.fastq ;

    gunzip CS004_NoIndex_L002_R1_007.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_007.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_007.fastq CS004_NoIndex_L002_R2_007.fastq CS004_NoIndex_L002_R12_007.fastq ;

    gunzip CS004_NoIndex_L002_R1_008.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_008.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_008.fastq CS004_NoIndex_L002_R2_008.fastq CS004_NoIndex_L002_R12_008.fastq ;

    gunzip CS004_NoIndex_L002_R1_009.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_009.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_009.fastq CS004_NoIndex_L002_R2_009.fastq CS004_NoIndex_L002_R12_009.fastq ;

    gunzip CS004_NoIndex_L002_R1_010.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_010.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_010.fastq CS004_NoIndex_L002_R2_010.fastq CS004_NoIndex_L002_R12_010.fastq ;

    gunzip CS004_NoIndex_L002_R1_011.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_011.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_011.fastq CS004_NoIndex_L002_R2_011.fastq CS004_NoIndex_L002_R12_011.fastq ;

    gunzip CS004_NoIndex_L002_R1_012.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_012.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_012.fastq CS004_NoIndex_L002_R2_012.fastq CS004_NoIndex_L002_R12_012.fastq ;

    gunzip CS004_NoIndex_L002_R1_013.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_013.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_013.fastq CS004_NoIndex_L002_R2_013.fastq CS004_NoIndex_L002_R12_013.fastq ;

    gunzip CS004_NoIndex_L002_R1_014.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_014.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_014.fastq CS004_NoIndex_L002_R2_014.fastq CS004_NoIndex_L002_R12_014.fastq ;

    gunzip CS004_NoIndex_L002_R1_015.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_015.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_015.fastq CS004_NoIndex_L002_R2_015.fastq CS004_NoIndex_L002_R12_015.fastq ;

    gunzip CS004_NoIndex_L002_R1_016.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_016.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_016.fastq CS004_NoIndex_L002_R2_016.fastq CS004_NoIndex_L002_R12_016.fastq ;

    gunzip CS004_NoIndex_L002_R1_017.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_017.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_017.fastq CS004_NoIndex_L002_R2_017.fastq CS004_NoIndex_L002_R12_017.fastq ;

    gunzip CS004_NoIndex_L002_R1_018.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_018.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_018.fastq CS004_NoIndex_L002_R2_018.fastq CS004_NoIndex_L002_R12_018.fastq ;

    gunzip CS004_NoIndex_L002_R1_019.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_019.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_019.fastq CS004_NoIndex_L002_R2_019.fastq CS004_NoIndex_L002_R12_019.fastq ;

    gunzip CS004_NoIndex_L002_R1_020.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_020.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_020.fastq CS004_NoIndex_L002_R2_020.fastq CS004_NoIndex_L002_R12_020.fastq ;

    gunzip CS004_NoIndex_L002_R1_021.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_021.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_021.fastq CS004_NoIndex_L002_R2_021.fastq CS004_NoIndex_L002_R12_021.fastq ;

    gunzip CS004_NoIndex_L002_R1_022.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_022.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_022.fastq CS004_NoIndex_L002_R2_022.fastq CS004_NoIndex_L002_R12_022.fastq ;

    gunzip CS004_NoIndex_L002_R1_023.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_023.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_023.fastq CS004_NoIndex_L002_R2_023.fastq CS004_NoIndex_L002_R12_023.fastq ;

    gunzip CS004_NoIndex_L002_R1_024.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_024.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_024.fastq CS004_NoIndex_L002_R2_024.fastq CS004_NoIndex_L002_R12_024.fastq ;

    gunzip CS004_NoIndex_L002_R1_025.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_025.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_025.fastq CS004_NoIndex_L002_R2_025.fastq CS004_NoIndex_L002_R12_025.fastq ;

    gunzip CS004_NoIndex_L002_R1_026.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_026.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_026.fastq CS004_NoIndex_L002_R2_026.fastq CS004_NoIndex_L002_R12_026.fastq ;

    gunzip CS004_NoIndex_L002_R1_027.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_027.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_027.fastq CS004_NoIndex_L002_R2_027.fastq CS004_NoIndex_L002_R12_027.fastq ;

    gunzip CS004_NoIndex_L002_R1_028.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_028.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_028.fastq CS004_NoIndex_L002_R2_028.fastq CS004_NoIndex_L002_R12_028.fastq ;

    gunzip CS004_NoIndex_L002_R1_029.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_029.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_029.fastq CS004_NoIndex_L002_R2_029.fastq CS004_NoIndex_L002_R12_029.fastq ;

    gunzip CS004_NoIndex_L002_R1_030.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_030.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_030.fastq CS004_NoIndex_L002_R2_030.fastq CS004_NoIndex_L002_R12_030.fastq ;

    gunzip CS004_NoIndex_L002_R1_031.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_031.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_031.fastq CS004_NoIndex_L002_R2_031.fastq CS004_NoIndex_L002_R12_031.fastq ;

    gunzip CS004_NoIndex_L002_R1_032.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_032.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_032.fastq CS004_NoIndex_L002_R2_032.fastq CS004_NoIndex_L002_R12_032.fastq ;

    gunzip CS004_NoIndex_L002_R1_033.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_033.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_033.fastq CS004_NoIndex_L002_R2_033.fastq CS004_NoIndex_L002_R12_033.fastq ;

    gunzip CS004_NoIndex_L002_R1_034.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_034.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_034.fastq CS004_NoIndex_L002_R2_034.fastq CS004_NoIndex_L002_R12_034.fastq ;

    gunzip CS004_NoIndex_L002_R1_035.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_035.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_035.fastq CS004_NoIndex_L002_R2_035.fastq CS004_NoIndex_L002_R12_035.fastq ;

    gunzip CS004_NoIndex_L002_R1_036.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_036.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_036.fastq CS004_NoIndex_L002_R2_036.fastq CS004_NoIndex_L002_R12_036.fastq ;

    gunzip CS004_NoIndex_L002_R1_037.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_037.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_037.fastq CS004_NoIndex_L002_R2_037.fastq CS004_NoIndex_L002_R12_037.fastq ;

    gunzip CS004_NoIndex_L002_R1_038.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_038.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_038.fastq CS004_NoIndex_L002_R2_038.fastq CS004_NoIndex_L002_R12_038.fastq ;

    gunzip CS004_NoIndex_L002_R1_039.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_039.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_039.fastq CS004_NoIndex_L002_R2_039.fastq CS004_NoIndex_L002_R12_039.fastq ;

    gunzip CS004_NoIndex_L002_R1_040.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_040.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_040.fastq CS004_NoIndex_L002_R2_040.fastq CS004_NoIndex_L002_R12_040.fastq ;

    gunzip CS004_NoIndex_L002_R1_041.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_041.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_041.fastq CS004_NoIndex_L002_R2_041.fastq CS004_NoIndex_L002_R12_041.fastq ;

    gunzip CS004_NoIndex_L002_R1_042.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_042.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_042.fastq CS004_NoIndex_L002_R2_042.fastq CS004_NoIndex_L002_R12_042.fastq ;

    gunzip CS004_NoIndex_L002_R1_043.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_043.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_043.fastq CS004_NoIndex_L002_R2_043.fastq CS004_NoIndex_L002_R12_043.fastq ;

    gunzip CS004_NoIndex_L002_R1_044.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_044.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_044.fastq CS004_NoIndex_L002_R2_044.fastq CS004_NoIndex_L002_R12_044.fastq ;

    gunzip CS004_NoIndex_L002_R1_045.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_045.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_045.fastq CS004_NoIndex_L002_R2_045.fastq CS004_NoIndex_L002_R12_045.fastq ;

    gunzip CS004_NoIndex_L002_R1_046.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_046.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_046.fastq CS004_NoIndex_L002_R2_046.fastq CS004_NoIndex_L002_R12_046.fastq ;

    gunzip CS004_NoIndex_L002_R1_047.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_047.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_047.fastq CS004_NoIndex_L002_R2_047.fastq CS004_NoIndex_L002_R12_047.fastq ;

    gunzip CS004_NoIndex_L002_R1_048.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_048.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_048.fastq CS004_NoIndex_L002_R2_048.fastq CS004_NoIndex_L002_R12_048.fastq ;

    gunzip CS004_NoIndex_L002_R1_049.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_049.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_049.fastq CS004_NoIndex_L002_R2_049.fastq CS004_NoIndex_L002_R12_049.fastq ;

    gunzip CS004_NoIndex_L002_R1_050.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_050.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_050.fastq CS004_NoIndex_L002_R2_050.fastq CS004_NoIndex_L002_R12_050.fastq ;

    gunzip CS004_NoIndex_L002_R1_051.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_051.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_051.fastq CS004_NoIndex_L002_R2_051.fastq CS004_NoIndex_L002_R12_051.fastq ;

    gunzip CS004_NoIndex_L002_R1_052.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_052.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_052.fastq CS004_NoIndex_L002_R2_052.fastq CS004_NoIndex_L002_R12_052.fastq ;

    gunzip CS004_NoIndex_L002_R1_053.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_053.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_053.fastq CS004_NoIndex_L002_R2_053.fastq CS004_NoIndex_L002_R12_053.fastq ;

    gunzip CS004_NoIndex_L002_R1_054.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_054.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_054.fastq CS004_NoIndex_L002_R2_054.fastq CS004_NoIndex_L002_R12_054.fastq ;

    gunzip CS004_NoIndex_L002_R1_055.fastq.gz ;
    gunzip CS004_NoIndex_L002_R2_055.fastq.gz ;
    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_055.fastq CS004_NoIndex_L002_R2_055.fastq CS004_NoIndex_L002_R12_055.fastq ;

    # Get rid of now-unneeded single-end FASTQ files:
    rm CS004_NoIndex_L002_R1_*.fastq ;
    rm CS004_NoIndex_L002_R2_*.fastq ;

A bit less size now:

df -h | grep '/sternlab/redivivus/data02'
/dev/sda1              22T   20T  2.0T  92% /sternlab/redivivus/data02

3. Clean up:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/raw ;
    mkdir ../scripts ;
    mv -i *.pl *.sh ../scripts ;
    rm job_10apr2012a.nohup.*.txt ;

4. Get reads renamed and filtered.

    Correct the naming format so that bowtie will work.
    Filter out poor reads and nucleotides.
    Map against MtDNA, E. coli, and Illumina primers.
    Sort out results into paired and unpaired.

Set up working directories and PATH:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    PATH="$PATH:/home/schwarz/perl.svn/trunk/illumina" ; PATH="$PATH:/home/schwarz/perl.svn/trunk/fasta" ;
    mkdir jumbled paired unpaired ;

# Ideally I would make a contaminant database with both C. elegans MtDNA and E. coli OP50, but I foolishly discarded the E. coli OP50
#    sequence file which had taken overnight to build.  So do the next best thing, and put two contaminant databases together.

    nohup cp -rip /woldlab/loxcyc/data00/schwarz/ce6splices/contams . &

    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_elegans/c_elegans.WS230.genomic.fa.gz ;
    gunzip c_elegans.WS230.genomic.fa.gz ;
    extract_fasta_subset.pl -l CHROMOSOME_MtDNA -f c_elegans.WS230.genomic.fa > Cel_MtDNA.fa ;
    rm c_elegans.WS230.genomic.fa ;

    nohup bowtie-build --seed 2832 -f Cel_MtDNA.fa contams/CelMt &

# Given this, work through filtering and sorting out of each readset in turn.

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/XXX.fq -o jumbled/XXX.jumb.filt1.neo_n.fq ;   # I can accept quite low minimum reads -- most will be higher!

    retroname_fastq_reads.pl jumbled/XXX.jumb.filt1.neo_n.fq > jumbled/XXX.jumb.filt1.paleo_n.fq ;

    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/XXX.jumb.filt2.paleo_n.fq jumbled/XXX.jumb.filt1.paleo_n.fq /dev/null ;

    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/XXX.jumb.filt3.paleo_n.fq jumbled/XXX.jumb.filt2.paleo_n.fq /dev/null ;

    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0\/1" --r2 "#0\/2" \
        -i jumbled/XXX.jumb.filt3.paleo_n.fq \
        -p paired/XXX.pe.filt3.paleo_n.fq    \
        -u unpaired/XXX.se.filt3.paleo_n.fq  ;

    # After all readsets are done:
    program_done_e-ping.pl -p Csp9_read_filt_sort_10apr2012 ;

# To get the actual script running:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    ls raw/*.fastq | ./make_job_10apr2012b.pl > job_10apr2012b.sh ;
    chmod +x job_10apr2012b.sh ;

    nohup ./job_10apr2012b.sh 1>job_10apr2012b.nohup.out.txt 2>job_10apr2012b.nohup.err.txt &

# Note that I had to run everything over again because everything after quality_trim_fastq.pl failed.

Remove all the failed files:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    rm unpaired/* paired/* ;
    rm jumbled/*paleo_n* ;
    rm job_10apr2012b.nohup.err.txt job_10apr2012b.nohup.out.txt ;
    mv -i job_10apr2012b.sh scripts ;

Edit retroname_fastq_reads.pl, which seems to be the culprit, so that it copes with Berkeley headers and not just Caltech headers.
Make a new version of retroname_fastq_reads.pl:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    PATH="$PATH:/home/schwarz/perl.svn/trunk/illumina" ; PATH="$PATH:/home/schwarz/perl.svn/trunk/fasta" ;
    pico retroname_fastq_reads.pl ;  # Revised version, tested on snippet of Berkeley filtered reads.
    rm /home/schwarz/perl.svn/trunk/illumina/retroname_fastq_reads.pl ;
    mv -i retroname_fastq_reads.pl /home/schwarz/perl.svn/trunk/illumina ;
    cd /home/schwarz/perl.svn/trunk/illumina ;
    svn commit retroname_fastq_reads.pl -m 'Alter to cope with Berkeley vs. Caltech style of new read header lines.' ;
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;

Make a new version of the job script job_10apr2012b.sh, which has everything but the quality_trim_fastq.pl line:

    cp -ip make_job_10apr2012b.pl make_job_11apr2012a.pl ;
    pico make_job_11apr2012a.pl ;
    ls raw/*.fastq | ./make_job_11apr2012a.pl > job_11apr2012a.sh ;
    chmod +x job_11apr2012a.sh ;

    nohup ./job_11apr2012a.sh 1>job_11apr2012a.nohup.out.txt 2>job_11apr2012a.nohup.err.txt &

# Start contents of original job_10apr2012b.sh:

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_001.fastq -o jumbled/CS004_NoIndex_L002_R12_001.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_001.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_001.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_001.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_001.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_001.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_001.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_001.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_001.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_001.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_002.fastq -o jumbled/CS004_NoIndex_L002_R12_002.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_002.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_002.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_002.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_002.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_002.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_002.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_002.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_002.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_002.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_003.fastq -o jumbled/CS004_NoIndex_L002_R12_003.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_003.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_003.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_003.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_003.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_003.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_003.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_003.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_003.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_003.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_004.fastq -o jumbled/CS004_NoIndex_L002_R12_004.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_004.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_004.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_004.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_004.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_004.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_004.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_004.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_004.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_004.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_005.fastq -o jumbled/CS004_NoIndex_L002_R12_005.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_005.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_005.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_005.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_005.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_005.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_005.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_005.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_005.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_005.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_006.fastq -o jumbled/CS004_NoIndex_L002_R12_006.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_006.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_006.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_006.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_006.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_006.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_006.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_006.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_006.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_006.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_007.fastq -o jumbled/CS004_NoIndex_L002_R12_007.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_007.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_007.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_007.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_007.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_007.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_007.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_007.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_007.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_007.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_008.fastq -o jumbled/CS004_NoIndex_L002_R12_008.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_008.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_008.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_008.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_008.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_008.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_008.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_008.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_008.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_008.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_009.fastq -o jumbled/CS004_NoIndex_L002_R12_009.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_009.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_009.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_009.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_009.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_009.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_009.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_009.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_009.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_009.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_010.fastq -o jumbled/CS004_NoIndex_L002_R12_010.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_010.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_010.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_010.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_010.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_010.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_010.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_010.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_010.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_010.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_011.fastq -o jumbled/CS004_NoIndex_L002_R12_011.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_011.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_011.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_011.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_011.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_011.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_011.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_011.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_011.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_011.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_012.fastq -o jumbled/CS004_NoIndex_L002_R12_012.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_012.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_012.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_012.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_012.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_012.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_012.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_012.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_012.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_012.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_013.fastq -o jumbled/CS004_NoIndex_L002_R12_013.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_013.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_013.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_013.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_013.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_013.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_013.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_013.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_013.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_013.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_014.fastq -o jumbled/CS004_NoIndex_L002_R12_014.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_014.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_014.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_014.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_014.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_014.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_014.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_014.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_014.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_014.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_015.fastq -o jumbled/CS004_NoIndex_L002_R12_015.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_015.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_015.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_015.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_015.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_015.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_015.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_015.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_015.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_015.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_016.fastq -o jumbled/CS004_NoIndex_L002_R12_016.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_016.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_016.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_016.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_016.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_016.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_016.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_016.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_016.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_016.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_017.fastq -o jumbled/CS004_NoIndex_L002_R12_017.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_017.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_017.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_017.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_017.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_017.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_017.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_017.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_017.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_017.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_018.fastq -o jumbled/CS004_NoIndex_L002_R12_018.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_018.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_018.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_018.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_018.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_018.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_018.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_018.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_018.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_018.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_019.fastq -o jumbled/CS004_NoIndex_L002_R12_019.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_019.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_019.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_019.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_019.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_019.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_019.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_019.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_019.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_019.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_020.fastq -o jumbled/CS004_NoIndex_L002_R12_020.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_020.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_020.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_020.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_020.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_020.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_020.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_020.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_020.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_020.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_021.fastq -o jumbled/CS004_NoIndex_L002_R12_021.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_021.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_021.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_021.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_021.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_021.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_021.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_021.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_021.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_021.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_022.fastq -o jumbled/CS004_NoIndex_L002_R12_022.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_022.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_022.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_022.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_022.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_022.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_022.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_022.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_022.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_022.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_023.fastq -o jumbled/CS004_NoIndex_L002_R12_023.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_023.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_023.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_023.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_023.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_023.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_023.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_023.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_023.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_023.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_024.fastq -o jumbled/CS004_NoIndex_L002_R12_024.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_024.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_024.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_024.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_024.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_024.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_024.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_024.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_024.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_024.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_025.fastq -o jumbled/CS004_NoIndex_L002_R12_025.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_025.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_025.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_025.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_025.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_025.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_025.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_025.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_025.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_025.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_026.fastq -o jumbled/CS004_NoIndex_L002_R12_026.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_026.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_026.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_026.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_026.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_026.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_026.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_026.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_026.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_026.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_027.fastq -o jumbled/CS004_NoIndex_L002_R12_027.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_027.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_027.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_027.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_027.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_027.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_027.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_027.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_027.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_027.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_028.fastq -o jumbled/CS004_NoIndex_L002_R12_028.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_028.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_028.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_028.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_028.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_028.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_028.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_028.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_028.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_028.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_029.fastq -o jumbled/CS004_NoIndex_L002_R12_029.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_029.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_029.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_029.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_029.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_029.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_029.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_029.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_029.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_029.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_030.fastq -o jumbled/CS004_NoIndex_L002_R12_030.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_030.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_030.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_030.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_030.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_030.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_030.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_030.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_030.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_030.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_031.fastq -o jumbled/CS004_NoIndex_L002_R12_031.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_031.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_031.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_031.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_031.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_031.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_031.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_031.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_031.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_031.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_032.fastq -o jumbled/CS004_NoIndex_L002_R12_032.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_032.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_032.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_032.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_032.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_032.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_032.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_032.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_032.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_032.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_033.fastq -o jumbled/CS004_NoIndex_L002_R12_033.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_033.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_033.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_033.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_033.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_033.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_033.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_033.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_033.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_033.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_034.fastq -o jumbled/CS004_NoIndex_L002_R12_034.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_034.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_034.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_034.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_034.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_034.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_034.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_034.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_034.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_034.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_035.fastq -o jumbled/CS004_NoIndex_L002_R12_035.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_035.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_035.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_035.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_035.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_035.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_035.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_035.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_035.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_035.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_036.fastq -o jumbled/CS004_NoIndex_L002_R12_036.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_036.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_036.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_036.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_036.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_036.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_036.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_036.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_036.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_036.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_037.fastq -o jumbled/CS004_NoIndex_L002_R12_037.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_037.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_037.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_037.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_037.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_037.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_037.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_037.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_037.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_037.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_038.fastq -o jumbled/CS004_NoIndex_L002_R12_038.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_038.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_038.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_038.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_038.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_038.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_038.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_038.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_038.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_038.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_039.fastq -o jumbled/CS004_NoIndex_L002_R12_039.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_039.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_039.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_039.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_039.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_039.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_039.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_039.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_039.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_039.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_040.fastq -o jumbled/CS004_NoIndex_L002_R12_040.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_040.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_040.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_040.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_040.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_040.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_040.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_040.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_040.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_040.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_041.fastq -o jumbled/CS004_NoIndex_L002_R12_041.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_041.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_041.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_041.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_041.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_041.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_041.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_041.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_041.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_041.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_042.fastq -o jumbled/CS004_NoIndex_L002_R12_042.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_042.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_042.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_042.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_042.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_042.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_042.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_042.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_042.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_042.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_043.fastq -o jumbled/CS004_NoIndex_L002_R12_043.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_043.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_043.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_043.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_043.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_043.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_043.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_043.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_043.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_043.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_044.fastq -o jumbled/CS004_NoIndex_L002_R12_044.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_044.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_044.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_044.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_044.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_044.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_044.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_044.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_044.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_044.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_045.fastq -o jumbled/CS004_NoIndex_L002_R12_045.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_045.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_045.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_045.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_045.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_045.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_045.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_045.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_045.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_045.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_046.fastq -o jumbled/CS004_NoIndex_L002_R12_046.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_046.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_046.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_046.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_046.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_046.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_046.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_046.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_046.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_046.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_047.fastq -o jumbled/CS004_NoIndex_L002_R12_047.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_047.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_047.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_047.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_047.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_047.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_047.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_047.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_047.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_047.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_048.fastq -o jumbled/CS004_NoIndex_L002_R12_048.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_048.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_048.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_048.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_048.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_048.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_048.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_048.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_048.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_048.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_049.fastq -o jumbled/CS004_NoIndex_L002_R12_049.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_049.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_049.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_049.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_049.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_049.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_049.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_049.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_049.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_049.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_050.fastq -o jumbled/CS004_NoIndex_L002_R12_050.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_050.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_050.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_050.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_050.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_050.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_050.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_050.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_050.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_050.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_051.fastq -o jumbled/CS004_NoIndex_L002_R12_051.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_051.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_051.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_051.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_051.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_051.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_051.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_051.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_051.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_051.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_052.fastq -o jumbled/CS004_NoIndex_L002_R12_052.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_052.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_052.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_052.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_052.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_052.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_052.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_052.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_052.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_052.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_053.fastq -o jumbled/CS004_NoIndex_L002_R12_053.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_053.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_053.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_053.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_053.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_053.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_053.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_053.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_053.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_053.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_054.fastq -o jumbled/CS004_NoIndex_L002_R12_054.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_054.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_054.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_054.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_054.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_054.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_054.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_054.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_054.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_054.se.filt3.paleo_n.fq ;

    quality_trim_fastq.pl -q 33 -u 100 -n -t 3 -m 21 -i raw/CS004_NoIndex_L002_R12_055.fastq -o jumbled/CS004_NoIndex_L002_R12_055.jumb.filt1.neo_n.fq ;
    retroname_fastq_reads.pl jumbled/CS004_NoIndex_L002_R12_055.jumb.filt1.neo_n.fq > jumbled/CS004_NoIndex_L002_R12_055.jumb.filt1.paleo_n.fq ;
    bowtie contams/Ecoli_OP50 -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_055.jumb.filt2.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_055.jumb.filt1.paleo_n.fq /dev/null ;
    bowtie contams/CelMt      -p 8 -k 11 -v 2 --best -m 10 -t --strata --un jumbled/CS004_NoIndex_L002_R12_055.jumb.filt3.paleo_n.fq jumbled/CS004_NoIndex_L002_R12_055.jumb.filt2.paleo_n.fq /dev/null ;
    paired_vs_unp_fastq.or.a.pl --fastq --r1 "#0/1" --r2 "#0/2" -i jumbled/CS004_NoIndex_L002_R12_055.jumb.filt3.paleo_n.fq -p paired/CS004_NoIndex_L002_R12_055.pe.filt3.paleo_n.fq -u unpaired/CS004_NoIndex_L002_R12_055.se.filt3.paleo_n.fq ;

    program_done_e-ping.pl -p Csp9_read_filt_sort_10apr2012 ;

# End contents of original job_10apr2012b.sh.

Given successful filtering and sorting out, run a series of assemblies to see what the rough location of an optimal k might be.

Current version of velvet is:  1.2.03

Current insert size of library, based on Bioanalyzer data from Berkeley, is:  335 nt

So, set up a series of assemblies to run like this:

# Set up environment:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    PATH="$PATH:/home/schwarz/perl.svn/trunk/illumina" ; PATH="$PATH:/home/schwarz/perl.svn/trunk/fasta" ;

# Clean up:

    mv -i make_job_10apr2012b.pl make_job_11apr2012a.pl job_11apr2012a.sh scripts ;
    mkdir docs ;
    mv -i job_11apr2012a.nohup.out.txt job_11apr2012a.nohup.err.txt docs ;

# Get an actual coverage estimate (which will take a while); then get the reads into compressed form, duh.
# Run like so --  nohup ./job_12apr2012a.sh 1>job_12apr2012a.nohup.out.txt 2>job_12apr2012a.nohup.err.txt &

    count_simple_fastq_residues.pl unpaired/*.fq > Csp9_Berkeley_11apr2012_unpaired_readcount.txt ;
    count_simple_fastq_residues.pl paired/*.fq > Csp9_Berkeley_11apr2012_paired_readcount.txt ;
    program_done_e-ping.pl -p Csp9_Berkeley_11apr2012_readcount ;

    gzip -9 paired/*.fq unpaired/*.fq ;
    program_done_e-ping.pl -p Csp9_Berkeley_11apr2012_readzip ;

# While that's going on, realize that I am hogging lots of disc space with intermediate files (we're down to 1.6T free space!) and decide to remove them:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    nohup rm -rf jumbled &

# ... which immediately boosts us back up to 2.0T free space on /sternlab/redivivus/data02.

# Examine Csp9_Berkeley_11apr2012_*paired_readcount.txt to get the expected coverage:

Csp9_Berkeley_11apr2012_paired_readcount.txt:

Total:  35,558,555,061 nt in 372,122,310 reads.
Mean:   95.56; std. dev. 14.05; min. 21; max. 100
Median: 100.00
N50:    100.00

Csp9_Berkeley_11apr2012_unpaired_readcount.txt:

Total:  305,957,178 nt in 3,610,559 reads.
Mean:   84.74; std. dev. 21.79; min. 21; max. 100
Median: 96.00
N50:    100.00

Making a conservative estimate of 200 MB for the C. sp. 9 genome, the coverage is --

    paired-end:     178x, 372 M reads, 35.6 Gb
    unpaired-end:   1.5x, 3.6 M reads, 306 Mb
    total:          179x, 376 M reads, 35.9 Gb

I compute the theoretical ideal:

[k=85]

    velveth Csp9_Berkeley_12apr2012_k85 85 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ;
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_12apr2012_k85 ;

    velvetg Csp9_Berkeley_12apr2012_k85 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ;
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_12apr2012_k85 ;

[I try several other k values, but find that the optimum really is k=85:]

Try:  /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl Csp9_Berkeley_17apr2012_k85/stats.txt

    to see what the empirical coverage distribution looks like.

I also try various other parameters for -cov_cutoff and -exp_cutoff.
To sum up:

    Lowering the -cov_cutoff from 17-18 to 4 increases the assembly size from ~145 Mb to ~182 Mb, and lowers contig N50 from ~21 to ~16 kb,
        while leaving the scaffold N50 and max. scaffold size largely unchanged.

    Raising the -exp_cov from 35 to 178 increases the scaffold N50 from 44 to ~70 kb, and max. scaffold size from ~880 kb to ~2 Mb, 
        while leaving the assembly size and contig N50 largely unchanged!

Decide to systematically explore likely k optima for '-cov_cutoff auto -exp_cov auto'.  The *theoretical* optimum is 85...

To compute the k optimum that I should use:
    
    if     C^k = ( ( C * ( L - k + 1) ) / L )
    then   k   = L + 1 - ( (L * C^k) /C )
    
For my existing filtered paired-end data -- ignoring the relatively small residue of single-read data:
    
Total:  35,558,555,061 nt in 372,122,310 reads.
Mean:   95.56; std. dev. 14.05; min. 21; max. 100
Median: 100.00
N50:    100.00

assuming a genome size of 200 Mb, then C   = 177.8
                                       L   = 95.6
                                       C^k = 20 [the goal]
    
                   k = 95.6 + 1 - 10.75 = 85
    
So try k = 75, 77, 79, 81, 83, 85, 87, 89.

Reference: pmid20836074.pdf -> /home/schwarz/src/velvet_1.2.03/contrib/VelvetOptimiser-2.2.0/README 

Look at it, but get frustrated and decide that it's not really doing what I want.  So clean up older stuff:

    rm -rf Csp9_Berkeley_13apr2012_k79 Csp9_Berkeley_17apr2012_k79 ;

Make my own line-command script ("perl make_velvet_job_19apr2012b.pl > velvet_job_19apr2012b.sh"):

    velveth Csp9_Berkeley_19apr2012_k75 75 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k75 ; 

    velvetg Csp9_Berkeley_19apr2012_k75 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k75 ; 

    velveth Csp9_Berkeley_19apr2012_k77 77 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k77 ; 

    velvetg Csp9_Berkeley_19apr2012_k77 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k77 ; 

    velveth Csp9_Berkeley_19apr2012_k79 79 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k79 ; 

    velvetg Csp9_Berkeley_19apr2012_k79 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k79 ; 

    velveth Csp9_Berkeley_19apr2012_k81 81 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k81 ; 

    velvetg Csp9_Berkeley_19apr2012_k81 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k81 ; 

    velveth Csp9_Berkeley_19apr2012_k83 83 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k83 ; 

    velvetg Csp9_Berkeley_19apr2012_k83 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k83 ; 

    velveth Csp9_Berkeley_19apr2012_k85 85 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k85 ; 

    velvetg Csp9_Berkeley_19apr2012_k85 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k85 ; 

    velveth Csp9_Berkeley_19apr2012_k87 87 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k87 ; 

    velvetg Csp9_Berkeley_19apr2012_k87 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k87 ; 

    velveth Csp9_Berkeley_19apr2012_k89 89 -create_binary -fastq.gz -short unpaired/*.fq.gz -shortPaired paired/*.fq.gz ; 
    program_done_e-ping.pl -p velveth_Csp9_Berkeley_17apr2012_k89 ; 

    velvetg Csp9_Berkeley_19apr2012_k89 -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; 
    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_17apr2012_k89 ; 

Run like so --  nohup ./velvet_job_19apr2012b.sh 1>velvet_job_19apr2012b.nohup.out.txt 2>velvet_job_19apr2012b.nohup.err.txt &

Stats. on assemblies:

count_fasta_residues.pl -i */contigs.fa ;

Sequence: Csp9_Berkeley_19apr2012_k75/contigs.fa

Total nt:           144,430,790
Scaffolds:          17,127
Contigs:            25,324

ACGT nt:            143,329,823
N-res. nt:          1,100,967
% non-N:            99.2

Scaffold N50 nt:    42,315.0
Scaf. max. nt:      880,625
Scaf. min. nt:      200

Contig N50:         20,665.0
Contig max. nt:     826,653
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k77/contigs.fa

Total nt:           144,871,000
Scaffolds:          17,232
Contigs:            25,424

ACGT nt:            143,761,701
N-res. nt:          1,109,299
% non-N:            99.2

Scaffold N50 nt:    43,380.0
Scaf. max. nt:      880,631
Scaf. min. nt:      200

Contig N50:         20,367.0
Contig max. nt:     730,552
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k79/contigs.fa

Total nt:           144,564,215
Scaffolds:          17,193
Contigs:            25,220

ACGT nt:            143,430,674
N-res. nt:          1,133,541
% non-N:            99.2

Scaffold N50 nt:    43,559.0
Scaf. max. nt:      880,639
Scaf. min. nt:      200

Contig N50:         20,864.0
Contig max. nt:     663,182
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k81/contigs.fa

Total nt:           144,833,537
Scaffolds:          17,374
Contigs:            25,225

ACGT nt:            143,709,307
N-res. nt:          1,124,230
% non-N:            99.2

Scaffold N50 nt:    43,891.0
Scaf. max. nt:      880,671
Scaf. min. nt:      200

Contig N50:         21,364.0
Contig max. nt:     663,230
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k83/contigs.fa

Total nt:           145,016,259
Scaffolds:          17,408
Contigs:            25,188

ACGT nt:            143,873,293
N-res. nt:          1,142,966
% non-N:            99.2

Scaffold N50 nt:    43,703.0
Scaf. max. nt:      880,916
Scaf. min. nt:      200

Contig N50:         21,321.0
Contig max. nt:     556,855
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k85/contigs.fa

Total nt:           145,186,623
Scaffolds:          17,659
Contigs:            25,612

ACGT nt:            143,986,676
N-res. nt:          1,199,947
% non-N:            99.2

Scaffold N50 nt:    44,488.0    # highest value in series! and it was the theoretical optimum...
Scaf. max. nt:      880,874
Scaf. min. nt:      200

Contig N50:         21,150.0
Contig max. nt:     560,950
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k87/contigs.fa

Total nt:           145,728,912
Scaffolds:          18,036
Contigs:            26,547

ACGT nt:            144,406,842
N-res. nt:          1,322,070
% non-N:            99.1

Scaffold N50 nt:    43,893.0
Scaf. max. nt:      881,593
Scaf. min. nt:      200

Contig N50:         20,408.0
Contig max. nt:     534,878
Contig min. nt:     51

Sequence: Csp9_Berkeley_19apr2012_k89/contigs.fa

Total nt:           145,574,212
Scaffolds:          18,067
Contigs:            27,333

ACGT nt:            144,135,687
N-res. nt:          1,438,525
% non-N:            99.0

Scaffold N50 nt:    43,253.0
Scaf. max. nt:      813,393
Scaf. min. nt:      200

Contig N50:         18,484.0
Contig max. nt:     447,633
Contig min. nt:     51

Look at results of 'auto'.  Decide that k=85 has best scaffold N50 ... emprically, not just theoretically.

After archiving the results:

    cp -ip Csp9_Berkeley_19apr2012_k75/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k75_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k75/Log docs/Csp9_Berkeley_19apr2012_k75_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k75/stats.txt docs/Csp9_Berkeley_19apr2012_k75_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k75_stats.txt > docs/Csp9_Berkeley_19apr2012_k75_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k77/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k77_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k77/Log docs/Csp9_Berkeley_19apr2012_k77_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k77/stats.txt docs/Csp9_Berkeley_19apr2012_k77_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k77_stats.txt > docs/Csp9_Berkeley_19apr2012_k77_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k79/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k79_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k79/Log docs/Csp9_Berkeley_19apr2012_k79_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k79/stats.txt docs/Csp9_Berkeley_19apr2012_k79_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k79_stats.txt > docs/Csp9_Berkeley_19apr2012_k79_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k81/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k81_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k81/Log docs/Csp9_Berkeley_19apr2012_k81_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k81/stats.txt docs/Csp9_Berkeley_19apr2012_k81_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k81_stats.txt > docs/Csp9_Berkeley_19apr2012_k81_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k83/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k83_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k83/Log docs/Csp9_Berkeley_19apr2012_k83_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k83/stats.txt docs/Csp9_Berkeley_19apr2012_k83_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k83_stats.txt > docs/Csp9_Berkeley_19apr2012_k83_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k85/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k85/Log docs/Csp9_Berkeley_19apr2012_k85_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k85/stats.txt docs/Csp9_Berkeley_19apr2012_k85_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k85_stats.txt > docs/Csp9_Berkeley_19apr2012_k85_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k87/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k87_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k87/Log docs/Csp9_Berkeley_19apr2012_k87_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k87/stats.txt docs/Csp9_Berkeley_19apr2012_k87_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k87_stats.txt > docs/Csp9_Berkeley_19apr2012_k87_stats_graph.txt ;

    cp -ip Csp9_Berkeley_19apr2012_k89/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k89_contigs.fa.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k89/Log docs/Csp9_Berkeley_19apr2012_k89_Log.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k89/stats.txt docs/Csp9_Berkeley_19apr2012_k89_stats.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k89_stats.txt > docs/Csp9_Berkeley_19apr2012_k89_stats_graph.txt ;

remove all of the Csp9_Berkeley_19apr2012_k* directories except Csp9_Berkeley_19apr2012_k85:

    rm -rf Csp9_Berkeley_19apr2012_k75 Csp9_Berkeley_19apr2012_k77 Csp9_Berkeley_19apr2012_k79 Csp9_Berkeley_19apr2012_k81 \
        Csp9_Berkeley_19apr2012_k83 Csp9_Berkeley_19apr2012_k87 Csp9_Berkeley_19apr2012_k89 ;

which frees up disk space from 1.7 Tb to 2.1 Tb.

To explore alternative parameters for the k=85 assembly -- 

Look at docs/Csp9_Berkeley_19apr2012_k85_Log.txt: see "Median coverage depth = 25.099499".

Look at docs/velvet_job_19apr2012b.nohup.out.txt, and find:

[5568.160290] Writing into graph file Csp9_Berkeley_19apr2012_k85/Graph2...
[5837.269454] Measuring median coverage depth...
[5837.870404] Median coverage depth = 25.099499
[5837.876744] Removing contigs with coverage < 12.549749...

    So, the upshot is that 'auto' on k=85 gave me -cov_cutoff 12.549749, -exp_cov 25.099499.
    I can presumably get fast results on the options by setting up:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;

and then running like so --  nohup ./velvet_job_23apr2012b.sh 1>velvet_job_23apr2012b.nohup.out.txt 2>velvet_job_23apr2012b.nohup.err.txt &

    velvetg Csp9_Berkeley_19apr2012_k85 -cov_cutoff 6.3 -exp_cov 25.1 -min_contig_lgth 200 -ins_length 335 ;

    cp -ip Csp9_Berkeley_19apr2012_k85/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc6.3.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k85/Log docs/Csp9_Berkeley_19apr2012_k85_Log.cc6.3.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k85/stats.txt docs/Csp9_Berkeley_19apr2012_k85_stats.cc6.3.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k85_stats.cc6.3.txt > docs/Csp9_Berkeley_19apr2012_k85_stats_graph.cc6.3.txt ;

    program_done_e-ping.pl -p Csp9_Berkeley_19apr2012_k85.cc6.3 ;

    velvetg Csp9_Berkeley_19apr2012_k85 -cov_cutoff 4 -exp_cov 25.1 -min_contig_lgth 200 -ins_length 335 ;

    cp -ip Csp9_Berkeley_19apr2012_k85/contigs.fa assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc4.orig ;
    cp -ip Csp9_Berkeley_19apr2012_k85/Log docs/Csp9_Berkeley_19apr2012_k85_Log.cc4.txt ;
    cp -ip Csp9_Berkeley_19apr2012_k85/stats.txt docs/Csp9_Berkeley_19apr2012_k85_stats.cc4.txt ;
    /home/schwarz/src/velvet_1.2.03/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl docs/Csp9_Berkeley_19apr2012_k85_stats.cc4.txt > docs/Csp9_Berkeley_19apr2012_k85_stats_graph.cc4.txt ;

    program_done_e-ping.pl -p Csp9_Berkeley_19apr2012_k85.cc4 ;

Results?
count_fasta_residues.pl -i assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.orig ;
count_fasta_residues.pl -i assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc6.3.orig ;
count_fasta_residues.pl -i assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc4.orig ;

                    # cc4:         # Vs. cc6.3:    # Vs. auto:

Total nt:           176,894,567    # 161,171,392   # 145,186,623
Scaffolds:          28,087         # 21,058        # 17,659
Contigs:            59,063         # 33,084        # 25,612

ACGT nt:            172,467,849    # 159,443,047   # 143,986,676
N-res. nt:          4,426,718      # 1,728,345     # 1,199,947
% non-N:            97.5           # 98.9          # 99.2

Scaffold N50 nt:    41,327.0       # 45,669.0      # 44,488.0
Scaf. max. nt:      880,874        # 880,874       # 880,874
Scaf. min. nt:      200            # 200           # 200

Contig N50:         15,796.0       # 18,800.0      # 21,150.0
Contig max. nt:     573,679        # 560,950       # 560,950
Contig min. nt:     51             # 51            # 51

Now that I have these, I can test them with cDNA (and CEGMA, further below).
The best check on completeness I have is probably to map cDNAs from sp. 9 and count hit rates.  So, do that.  [See MAPPING cDNAs below.]
    
MAPPING cDNAs:
    
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;

Run these three scans in parallel, like so:
    
# nohup ./blat_job_23apr2012a.sh 1>blat_job_23apr2012a.nohup.out.txt 2>blat_job_23apr2012a.nohup.err.txt &

    blat -minIdentity=92 \
       assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.orig \
       rnaseq/Csp9_64JFEAAXX_7.khmer20-2.oases_k21.37.27Merged/transcripts.fa Csp9_k85_nokhmer_auto_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl ;
       
    program_done_e-ping.pl -p Csp9_k85_nokhmer_auto_gDNA_blat ;
    
    pslCDnaFilter -maxAligns=1 Csp9_k85_nokhmer_auto_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl Csp9_k85_nokhmer_auto_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl ;
    
    program_done_e-ping.pl -p Csp9_k85_nokhmer_auto_pslCDnaFilter ;

# nohup ./blat_job_23apr2012b.sh 1>blat_job_23apr2012b.nohup.out.txt 2>blat_job_23apr2012b.nohup.err.txt &

    blat -minIdentity=92 \
       assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc6.3.orig \
       rnaseq/Csp9_64JFEAAXX_7.khmer20-2.oases_k21.37.27Merged/transcripts.fa Csp9_k85_nokhmer_cc6.3_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl ;
       
    program_done_e-ping.pl -p Csp9_k85_nokhmer_cc6.3_gDNA_blat ;
    
    pslCDnaFilter -maxAligns=1 Csp9_k85_nokhmer_cc6.3_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl Csp9_k85_nokhmer_cc6.3_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl ;

    program_done_e-ping.pl -p Csp9_k85_nokhmer_cc6.3_pslCDnaFilter ;

# nohup ./blat_job_23apr2012c.sh 1>blat_job_23apr2012c.nohup.out.txt 2>blat_job_23apr2012c.nohup.err.txt &

    blat -minIdentity=92 \
       assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc4.orig \
       rnaseq/Csp9_64JFEAAXX_7.khmer20-2.oases_k21.37.27Merged/transcripts.fa Csp9_k85_nokhmer_cc4_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl ;
       
    program_done_e-ping.pl -p Csp9_k85_nokhmer_cc4_gDNA_blat ;
    
    pslCDnaFilter -maxAligns=1 Csp9_k85_nokhmer_cc4_gDNA_vs_rna_khmer20-2.oases_k21.37.27.psl Csp9_k85_nokhmer_cc4_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl ;

    program_done_e-ping.pl -p Csp9_k85_nokhmer_cc4_pslCDnaFilter ;

Examine results:

cat Csp9_k85_nokhmer_auto_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(\S+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
18144

cat Csp9_k85_nokhmer_auto_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(Locus_\d+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
2505

cat Csp9_k85_nokhmer_cc6.3_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(\S+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
18298

cat Csp9_k85_nokhmer_cc6.3_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(Locus_\d+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
2518

cat Csp9_k85_nokhmer_cc4_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(\S+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
18430

cat Csp9_k85_nokhmer_cc4_gDNA_vs_rna_khmer20-2.oases_k21.37.27.Kent_filt.psl | perl -ne '$input = $_; if ( $input =~ /\A(\S+\s+){9}(Locus_\d+)/ ) { print "$2\n"; } ' | sort | uniq | wc -l ;
2529

[These numbers are better than I got for khmer-filtered assemblies.]

... In other words, I am *definitely* seeing more of the genome with non-khmer-filtered reads than I am managing with filtered ones -- more cDNAs, and (more importantly) more loci!
Moreover, it looks like the completeness is quite high even with just 'auto' parameters; I only see 24 more loci with the most permissive assembly.
On one hand, that probably means that the larger one is catching slightly more genes, and is slightly more useful.
On the other hand, I can probably safely go with that assembly and not the larger ones, if I want to.

Clean up:

    mv -i *.psl PSLs ;


RUNNING CEGMA MYSELF:

    cd /home/schwarz/TGZ ;
    wget http://korflab.ucdavis.edu/Datasets/cegma/cegma_v2.4.010312.tar.gz ;
    cd /home/schwarz/src/unpack ;
    zcat /home/schwarz/TGZ/cegma_v2.4.010312.tar.gz | tar xf - ;
    mv -i cegma_v2.4.010312 .. ; 
    cd ../cegma_v2.4.010312 ;
    [For further details of CEGMA installation, see: /sternlab/redivivus/data02/schwarz/docs/NOTE_installing_CEGMA_22apr2012.txt ]

After CEGMA setup:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9 ;
    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_22apr2012 ;
    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_cc9.8_22apr2012 ;
    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_cc4.9_22apr2012 ;

Run as follows --   nohup ./cegma_job_22apr2012a.sh 1>cegma_job_22apr2012a.nohup.out.txt 2>cegma_job_22apr2012a.nohup.err.txt &   # first stanza
                    nohup ./cegma_job_22apr2012b.sh 1>cegma_job_22apr2012b.nohup.out.txt 2>cegma_job_22apr2012b.nohup.err.txt &   # 2cd-3rd stanzas, after fixing: "assemblies" -> "../assemblies"

    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_22apr2012 ;
    cegma --genome ../assemblies/Csp9_Berkeley_20apr2012_k73_contigs.fa.orig --output cegma_k73_22apr2012 --threads 8 ;
    program_done_e-ping.pl -p cegma_k73_22apr2012 ;
    
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_cc9.8_22apr2012 ;
    cegma --genome ../assemblies/Csp9_Berkeley_20apr2012_k73_contigs.fa.cc9.8.orig --output cegma_k73_cc9.8_22apr2012 --threads 8 ;
    program_done_e-ping.pl -p cegma_k73_cc9.8_22apr2012 ;
    
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/cegma_k73_cc4.9_22apr2012 ;
    cegma --genome ../assemblies/Csp9_Berkeley_20apr2012_k73_contigs.fa.cc4.9.orig --output cegma_k73_cc4.9_22apr2012 --threads 8 ;
    program_done_e-ping.pl -p cegma_k73_cc4.9_22apr2012 ;

Doing this makes me realize that I want to do it on all sorts of things, including controls (elegans and briggsae) 
to see what a verified success looks like, as well as on my two latest Hco assemblies.

So I've run CEGMA locally on my three sp. 9 assemblies.  Even the *smallest* one shows clear signs of heterozygosity.

One thing I'd like to do is test the same CEGMA program on genomes where I'm sure there's no heterozygosity, and also on genomes I've worked on elsewhere.

So, set up a working environment:

    cd /sternlab/redivivus/data02/schwarz/N_genomes/assemblies ;

# Run as --  nohup ./job_23apr2012a.sh 1>job_23apr2012a.nohup.out.txt 2>job_23apr2012a.nohup.err.txt &

    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_elegans/c_elegans.WS230.genomic.fa.gz ;
    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_briggsae/c_briggsae.WS230.genomic.fa.gz ;
    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_sp11/c_sp11.WS230.genomic.fa.gz ;

    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_remanei/c_remanei.WS230.genomic.fa.gz ;
    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_brenneri/c_brenneri.WS230.genomic.fa.gz ;
    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_sp5/c_sp5.WS230.genomic.fa.gz ;

    wget ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_japonica/c_japonica.WS230.genomic.fa.gz ;

    gunzip *.WS230.genomic.fa.gz ;

    program_done_e-ping.pl -p downloading_WS230_caeno_genomes ;

Test various genomes.  Set up working location:

    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma ;
    cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma ;

Then, run the following general job:

    mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/XXX ;
    cd /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/XXX ;
    cegma --genome [PATH]/XXX --output XXX --threads 8 ;
    program_done_e-ping.pl -p cegma_XXX_23apr2012 ;

on the following genomes:

## Set 1: ##

# khmer-filtered optimum:
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.orig
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.cc12.orig
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.cc6.orig 

# pre-khmer-filtered optimum:
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.orig
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc6.3.orig
/sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc4.orig

# known to be homozygous:
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_elegans.WS230.genomic.fa
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_briggsae.WS230.genomic.fa
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_sp11.WS230.genomic.fa

## Set 2: ##

/sternlab/redivivus/data02/schwarz/H_contortus_genome/assemblies/Hco_25dec2011_k41.nosheep.fa
/sternlab/redivivus/data02/schwarz/H_contortus_genome/assemblies/Hco_25dec2011_k21.nosheep.fa

/sternlab/redivivus/data02/schwarz/Acey_genomics/assemblies/Acey_2012.02.04_k69.genDNA.fa

/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_remanei.WS230.genomic.fa
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_brenneri.WS230.genomic.fa
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_japonica.WS230.genomic.fa
/sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_sp5.WS230.genomic.fa

## Not in a set, currently: ##

# Lower priority, since at this point it's irreproducible and deprecated:
/sternlab/redivivus/data02/schwarz/H_contortus_genome/assemblies/Hco_VelGen_02jun2011_k35.nosheep.fa

Generate and run the scripts.
In particular, produce script for Set 1 as follows: 

    cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma ;
    ./make_cegma_set1_job_23apr2012.pl > cegma_set1_job_23apr2012.sh ;
    chmod +x cegma_set1_job_23apr2012.sh ;

And run it as follows --  

    nohup ./cegma_set1_job_23apr2012.sh 1>cegma_set1_job_23apr2012.nohup.out.txt 2>cegma_set1_job_23apr2012.nohup.err.txt &

# Start contents of /sternlab/redivivus/data02/schwarz/N_genomes/cegma/cegma_set1_job_23apr2012.sh:

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.orig --output Csp9_Berkeley_20apr2012_k67 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_20apr2012_k67_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67.cc12 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67.cc12 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.cc12.orig --output Csp9_Berkeley_20apr2012_k67.cc12 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_20apr2012_k67.cc12_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67.cc6 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_20apr2012_k67.cc6 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_20apr2012_k67_contigs.fa.cc6.orig --output Csp9_Berkeley_20apr2012_k67.cc6 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_20apr2012_k67.cc6_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.orig --output Csp9_Berkeley_19apr2012_k85 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_19apr2012_k85_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85.cc6.3 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85.cc6.3 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc6.3.orig --output Csp9_Berkeley_19apr2012_k85.cc6.3 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_19apr2012_k85.cc6.3_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85.cc4 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/Csp9_Berkeley_19apr2012_k85.cc4 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/Csp9/assemblies/Csp9_Berkeley_19apr2012_k85_contigs.fa.cc4.orig --output Csp9_Berkeley_19apr2012_k85.cc4 --threads 8 ;
program_done_e-ping.pl -p cegma_Csp9_Berkeley_19apr2012_k85.cc4_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_elegans.WS230 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_elegans.WS230 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_elegans.WS230.genomic.fa --output c_elegans.WS230 --threads 8 ;
program_done_e-ping.pl -p cegma_c_elegans.WS230_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_briggsae.WS230 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_briggsae.WS230 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_briggsae.WS230.genomic.fa --output c_briggsae.WS230 --threads 8 ;
program_done_e-ping.pl -p cegma_c_briggsae.WS230_23apr2012 ;

mkdir /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_sp11.WS230 ;
cd /sternlab/redivivus/data02/schwarz/N_genomes/cegma/c_sp11.WS230 ;
cegma --genome /sternlab/redivivus/data02/schwarz/N_genomes/assemblies/c_sp11.WS230.genomic.fa --output c_sp11.WS230 --threads 8 ;
program_done_e-ping.pl -p cegma_c_sp11.WS230_23apr2012 ;

# End contents of cegma_set1_job_23apr2012.sh.

Results -- 

c_elegans.WS230/c_elegans.WS230.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      244       98.39      -   271     1.11     10.25

   Group 1       63       95.45      -    66     1.05      4.76
   Group 2       55       98.21      -    62     1.13     10.91
   Group 3       61      100.00      -    70     1.15     13.11
   Group 4       65      100.00      -    73     1.12     12.31

   Partial      248      100.00      -   298     1.20     17.74

   Group 1       66      100.00      -    75     1.14     13.64
   Group 2       56      100.00      -    69     1.23     17.86
   Group 3       61      100.00      -    73     1.20     18.03
   Group 4       65      100.00      -    81     1.25     21.54

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

c_briggsae.WS230/c_briggsae.WS230.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      246       99.19      -   274     1.11     11.38

   Group 1       66      100.00      -    71     1.08      7.58
   Group 2       56      100.00      -    61     1.09      8.93
   Group 3       60       98.36      -    69     1.15     15.00
   Group 4       64       98.46      -    73     1.14     14.06

   Partial      247       99.60      -   295     1.19     18.62

   Group 1       66      100.00      -    74     1.12     12.12
   Group 2       56      100.00      -    68     1.21     21.43
   Group 3       61      100.00      -    74     1.21     19.67
   Group 4       64       98.46      -    79     1.23     21.88

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_19apr2012_k85/Csp9_Berkeley_19apr2012_k85.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      246       99.19      -   473     1.92     39.43

   Group 1       65       98.48      -   109     1.68     32.31
   Group 2       55       98.21      -    98     1.78     34.55
   Group 3       61      100.00      -   143     2.34     57.38
   Group 4       65      100.00      -   123     1.89     33.85

   Partial      247       99.60      -   507     2.05     44.13

   Group 1       66      100.00      -   117     1.77     36.36
   Group 2       55       98.21      -   114     2.07     45.45
   Group 3       61      100.00      -   147     2.41     59.02
   Group 4       65      100.00      -   129     1.98     36.92

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_19apr2012_k85.cc6.3/Csp9_Berkeley_19apr2012_k85.cc6.3.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      246       99.19      -   486     1.98     39.02

   Group 1       65       98.48      -   109     1.68     29.23
   Group 2       55       98.21      -   105     1.91     36.36
   Group 3       61      100.00      -   147     2.41     54.10
   Group 4       65      100.00      -   125     1.92     36.92

   Partial      247       99.60      -   517     2.09     43.32

   Group 1       66      100.00      -   116     1.76     33.33
   Group 2       55       98.21      -   118     2.15     45.45
   Group 3       61      100.00      -   152     2.49     55.74
   Group 4       65      100.00      -   131     2.02     40.00

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_19apr2012_k85.cc4/Csp9_Berkeley_19apr2012_k85.cc4.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      246       99.19      -   482     1.96     37.40

   Group 1       65       98.48      -   109     1.68     27.69
   Group 2       55       98.21      -   105     1.91     36.36
   Group 3       61      100.00      -   146     2.39     50.82
   Group 4       65      100.00      -   122     1.88     35.38

   Partial      247       99.60      -   527     2.13     43.72

   Group 1       66      100.00      -   121     1.83     33.33
   Group 2       55       98.21      -   122     2.22     47.27
   Group 3       61      100.00      -   152     2.49     54.10
   Group 4       65      100.00      -   132     2.03     41.54

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_20apr2012_k67/Csp9_Berkeley_20apr2012_k67.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      244       98.39      -   478     1.96     39.34

   Group 1       64       96.97      -   109     1.70     34.38
   Group 2       54       96.43      -   104     1.93     38.89
   Group 3       61      100.00      -   140     2.30     49.18
   Group 4       65      100.00      -   125     1.92     35.38

   Partial      247       99.60      -   515     2.09     46.15

   Group 1       66      100.00      -   119     1.80     37.88
   Group 2       55       98.21      -   119     2.16     54.55
   Group 3       61      100.00      -   145     2.38     52.46
   Group 4       65      100.00      -   132     2.03     41.54

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_20apr2012_k67.cc12/Csp9_Berkeley_20apr2012_k67.cc12.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      246       99.19      -   498     2.02     41.46

   Group 1       65       98.48      -   116     1.78     38.46
   Group 2       55       98.21      -   109     1.98     36.36
   Group 3       61      100.00      -   143     2.34     45.90
   Group 4       65      100.00      -   130     2.00     44.62

   Partial      247       99.60      -   531     2.15     46.15

   Group 1       66      100.00      -   125     1.89     40.91
   Group 2       55       98.21      -   122     2.22     47.27
   Group 3       61      100.00      -   148     2.43     49.18
   Group 4       65      100.00      -   136     2.09     47.69

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #

Csp9_Berkeley_20apr2012_k67.cc6/Csp9_Berkeley_20apr2012_k67.cc6.completeness_report:

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho 

  Complete      247       99.60      -   507     2.05     42.91

   Group 1       66      100.00      -   120     1.82     37.88
   Group 2       55       98.21      -   111     2.02     41.82
   Group 3       61      100.00      -   145     2.38     49.18
   Group 4       65      100.00      -   131     2.02     43.08

   Partial      247       99.60      -   552     2.23     49.80

   Group 1       66      100.00      -   130     1.97     43.94
   Group 2       55       98.21      -   127     2.31     50.91
   Group 3       61      100.00      -   156     2.56     55.74
   Group 4       65      100.00      -   139     2.14     49.23

#    These results are based on the set of genes selected by Genis Parra   #

#    Key:                                                                  #
#    Prots = number of 248 ultra-conserved CEGs present in genome          #
#    %Completeness = percentage of 248 ultra-conserved CEGs present        #
#    Total = total number of CEGs present including putative orthologs     #
#    Average = average number of orthologs per CEG                         #
#    %Ortho = percentage of detected CEGS that have more than 1 ortholog   #


# 

After going through all this, make a final decision about which assembly to work up.
Decision -- k=85 'auto'!
So, clean up all the directories that I expect to no longer need:

    rm -rf Csp9_Berkeley_20apr2012_k73 Csp9_Berkeley_20apr2012_k67 Csp9_Berkeley_23apr2012_k25 ;
    mv -i cegma_k73_22apr2012 cegma_k73_cc9.8_22apr2012 cegma_k73_cc4.9_22apr2012 /sternlab/redivivus/data02/schwarz/N_genomes/cegma ;
    mv -i *.psl PSLs ;
    mv -i blat_job_* misc ;

    mv -i assemblies assemblies.prov ;
    mkdir assemblies ;
    mv -i *.pl scripts ;
    mv -i Csp9_17apr2012_k79_stats_graph.txt docs ;