Commit c4347ffc authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

working. fixed some bugs. added 454

parent 11dc0b2e
......@@ -160,21 +160,21 @@ def main():
with open(CSV_OUT, 'w') as ofh:
outlines = []
for gname in sorted( data ):
ostr = gname
ostr = gname+"\t"+"illumina"
datal = data[gname]
for field in ['gtype', 'gsize', 'gmin', 'gmax', 'file_names']:
opart = ""
fieldl = datal[ field ]
if isinstance(fieldl, list):
opart += "," + ";".join( fieldl )
opart += "\t" + ";".join( fieldl )
else:
opart += "," + str(fieldl)
opart += "\t" + str(fieldl)
ostr += opart
print ostr
outlines.append( ostr + "\n" )
ofh.write("#group name,library name,library size,library size min,library size max,file names\n")
ofh.write("#group name\tplatform\tlibrary name\tlibrary size\tlibrary size min\tlibrary size max\tfile names\n")
ofh.writelines( outlines )
if __name__ == '__main__':
......
......@@ -5,7 +5,7 @@ import tempfile
import shutil
dry_run = False
#dry_run = True
dry_run = True
do_merge = True
#do_merge = False
......@@ -79,7 +79,7 @@ def run_cmd( CMD , name ):
def main():
data = {}
datas = {}
with open(CSV_GROUP, 'r') as fhd:
line_count = 0
......@@ -98,28 +98,29 @@ def main():
#120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz
cels = line.split(',')
cels = line.split('\t')
print "parsing line '%s'" % str(cels)
if len(cels) != 7:
print "wrong number of columns"
sys.exit(1)
cpref = cels[ 0 ]
gplat = cels[ 1 ]
datal = {
'gtype' : cels[ 1 ] ,
'gsize' : int( cels[ 2 ] ),
'gmin' : int( cels[ 3 ] ),
'gmax' : int( cels[ 4 ] ),
'file_names': cels[ 5 ].split(";"),
'gplat' : gplat,
'gtype' : cels[ 2 ] ,
'gsize' : int( cels[ 3 ] ),
'gmin' : int( cels[ 4 ] ),
'gmax' : int( cels[ 5 ] ),
'file_names': cels[ 6 ].split(";"),
'genomesize': GENOME_SIZE,
}
datal[ 'max2' ] = ( ( datal['gmax' ] - datal['gsize'] ) * 3 ) + datal['gsize']
num_files = len(datal['file_names'])
if num_files % 2 != 0:
print "oops. failed to glob"
sys.exit(1)
elif num_files == 2:
if num_files == 2:
for ffname in datal['file_names']:
print ffname
......@@ -127,13 +128,93 @@ def main():
print "file '%s' does not exists" % ffname
sys.exit(1)
elif num_files == 1:
ffname = datal['file_names'][0]
if not os.path.exists(ffname) or not os.path.isfile(ffname):
print "file '%s' does not exists" % ffname
sys.exit(1)
else:
print "oops2. globed more than 2 files"
sys.exit(1)
data[cpref] = datal
if gplat not in datas: datas[gplat] = {}
datas[gplat][cpref] = datal
for plat in sorted(datas):
data = datas[plat]
if plat == 'illumina':
datas[plat] = processIllumina(data)
elif plat == '454' :
datas[plat] = process454(data)
if len( datas ) == 0:
print "no valid files found. quitting"
sys.exit(1)
if len(datas['illumina']) == 0:
print "no valid illumina files found. quitting"
sys.exit(1)
#process454(datas['454'])
dataf = {}
for plat in datas:
for name in datas[plat]:
if name in dataf:
print "duplicated name %s. error" % name
sys.exit(1)
dataf[name] = datas[plat][name]
run_bwa(dataf)
def process454(data):
for comm_name in sorted(data):
infile = data['file_names'][0]
if not infile.endswith('.sff'):
print 'infile %s is not sff' % infile
sys.exit(1)
out_prefix = os.path.join( MAP_FOLDER , infile )
out_fastq = out_prefix + '.fastq'
out_fastq_f = out_fastq.replace('.fastq', '_1.fastq')
out_fastq_r = out_fastq.replace('.fastq', '_2.fastq')
out_fastq_n = out_fastq.replace('.fastq', '_n.fastq')
out_fastq_0 = out_fastq.replace('.fastq', '_0.fastq')
data['file_names' ] = [out_fastq_f, out_fastq_r]
data['file_names_454' ] = infile
data['file_names_454_p'] = out_prefix
data['file_names_454_q'] = out_fastq
data['file_names_454_f'] = out_fastq_f
data['file_names_454_r'] = out_fastq_r
data['file_names_454_n'] = out_fastq_n
data['file_names_454_0'] = out_fastq_0
data['454_linker' ] = LINKER
CMD_EXTRACT = 'sff_extract -c -l %(454_linker)s -Q %(file_names_454)s -o %(file_names_454_p)s'
CMD_SPLIT = 'fastqSplitPe.pl %(file_names_454_q)s'
data['cmds'] = [
[CMD_EXTRACT % data, 'extracting sff'],
[CMD_SPLIT % data, 'splitting sff' ]
]
data = processIllumina(data)
return data
def processIllumina(data):
for comm_name in sorted(data):
RND_FILE1 = tempfile.mkstemp(dir=TMP_FOLDER, prefix='bwa_', suffix='.bam')
RND_NAME1 = RND_FILE1[1]
......@@ -187,20 +268,24 @@ def main():
if 'gtype' in data[ comm_name ] and data[ comm_name ]['gtype'] == 'mp':
#<(gunzip -c | fastqreversecomp.py )
data[comm_name]['fastq1' ] = "<(pigz -d -p3 -c %s | fastx_reverse_complement )" % data[comm_name]['fastq1']
if 'fastq2' in data[comm_name]:
data[comm_name]['fastq2' ] = "<(pigz -d -p3 -c %s | fastx_reverse_complement )" % data[comm_name]['fastq2']
fn = data[comm_name]['fastq1']
opener = 'cat'
if fn.endswith('.gz'):
opener = 'pigz -d -p3 -c'
data[comm_name]['fastq1' ] = "<(%(opener)s %(fn)s | fastx_reverse_complement )" % { 'opener': opener, 'fn': fn }
if len( data ) == 0:
print "no valid files found. quitting"
sys.exit(1)
if 'fastq2' in data[comm_name]:
fn = data[comm_name]['fastq2']
opener = 'cat'
run_bwa(data)
if fn.endswith('.gz'):
opener = 'pigz -d -p3 -c'
data[comm_name]['fastq2' ] = "<(%(opener)s %(fn)s | fastx_reverse_complement )" % { 'opener': opener, 'fn': fn }
return data
def run_bwa(data):
db_name = os.path.join(DB_FOLDER , CONTIG.replace('/', '_'))
......@@ -249,6 +334,9 @@ def run_bwa(data):
print " SKIPPING ALIGNING %(fastq1)s to %(sai1)s\n" % info
if 'cmds' in info:
for cmd in info['cmds']:
cmds.append(cmd)
if len(file_names) == 2:
......
......@@ -239,7 +239,7 @@ def move(*args, **kwargs):
print " MOVING: SOURCE and TARGET LENGHTS DIFFER %d vs %d" % (len(sources), len(targets))
return 1
for pos in len(sources):
for pos in range(len(sources)):
source = sources[pos]
target = targets[pos]
......@@ -442,7 +442,7 @@ def run_cmd( CMD , name ):
def main():
data = {}
datas = {}
##########################
## READ CSV
......@@ -464,27 +464,34 @@ def main():
#120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz
cels = line.split(',')
cels = line.split('\t')
print "parsing line '%s'" % str(cels)
if len(cels) != 7:
print "wrong number of columns"
sys.exit(1)
cpref = cels[ 0 ]
gplat = cels[ 1 ]
datal = {
'gtype' : cels[ 1 ] ,
'gsize' : int( cels[ 2 ] ),
'gmin' : int( cels[ 3 ] ),
'gmax' : int( cels[ 4 ] ),
'file_names': cels[ 5 ].split(";"),
'gplat' : gplat ,
'gtype' : cels[ 2 ] ,
'gsize' : int( cels[ 3 ] ),
'gmin' : int( cels[ 4 ] ),
'gmax' : int( cels[ 5 ] ),
'file_names': cels[ 6 ].split(";"),
'genomesize': GENOME_SIZE,
'threads' : num_threads
}
datal[ 'max2' ] = ( ( datal['gmax' ] - datal['gsize'] ) * 3 ) + datal['gsize']
num_files = len(datal['file_names'])
if num_files % 2 != 0:
print "oops. failed to glob"
sys.exit(1)
if num_files == 1:
ffname = datal['file_names'][0]
if not os.path.exists(ffname) or not os.path.isfile(ffname):
print "file '%s' does not exists" % ffname
sys.exit(1)
elif num_files == 2:
for ffname in datal['file_names']:
......@@ -498,10 +505,87 @@ def main():
print "oops2. globed more than 2 files"
sys.exit(1)
data[cpref] = datal
if gplat not in datas: datas[gplat] = {}
datas[gplat][cpref] = datal
for plat in sorted(datas):
data = datas[plat]
if plat == 'illumina':
datas[plat] = processIllumina(data)
elif plat == '454' :
datas[plat] = process454(data)
if len( datas ) == 0:
print "no valid files found. quitting"
sys.exit(1)
if len(datas['illumina']) == 0:
print "no valid illumina files found. quitting"
sys.exit(1)
dataf = {}
for plat in datas:
for name in datas[plat]:
if name in dataf:
print "duplicated name %s. error" % name
sys.exit(1)
dataf[name] = datas[plat][name]
run_bwa(dataf)
def process454(data):
for comm_name in sorted(data):
print "parsing 454 :: %s" % comm_name
infile = data[comm_name]['file_names'][0]
print "parsing 454 :: %s :: %s" % ( comm_name, infile )
if not infile.endswith('.sff'):
print 'infile %s is not sff' % infile
sys.exit(1)
out_prefix = os.path.join( MAP_FOLDER , comm_name )
print "parsing 454 :: %s :: %s :: out prefix %s" % ( comm_name, infile, out_prefix )
out_fastq = out_prefix + '.fastq'
out_fastq_f = out_fastq.replace('.fastq', '_1.fastq')
out_fastq_r = out_fastq.replace('.fastq', '_2.fastq')
out_fastq_n = out_fastq.replace('.fastq', '_n.fastq')
out_fastq_0 = out_fastq.replace('.fastq', '_0.fastq')
data[comm_name]['file_names' ] = [out_fastq_f, out_fastq_r]
data[comm_name]['file_names_454' ] = infile
data[comm_name]['file_names_454_p'] = out_prefix
data[comm_name]['file_names_454_q'] = out_fastq
data[comm_name]['file_names_454_f'] = out_fastq_f
data[comm_name]['file_names_454_r'] = out_fastq_r
data[comm_name]['file_names_454_n'] = out_fastq_n
data[comm_name]['file_names_454_0'] = out_fastq_0
data[comm_name]['454_linker' ] = LINKER
CMD_EXTRACT = 'sff_extract -c -l %(454_linker)s -Q %(file_names_454)s -o %(file_names_454_p)s'
CMD_SPLIT = 'fastqSplitPe.pl %(file_names_454_q)s'
addCommand('extracting sff', CMD_EXTRACT, TARGET = data[comm_name]['file_names_454_q'], SOURCE = data[comm_name]['file_names_454' ], DATA = data[comm_name], REQS = [ ])
addCommand('splitting sff' , CMD_SPLIT , TARGET = data[comm_name]['file_names' ], SOURCE = data[comm_name]['file_names_454_q'], DATA = data[comm_name], REQS = [ ])
data = processIllumina(data)
return data
def processIllumina(data):
##########################
## GENERATE FILE NAMES
##########################
......@@ -531,6 +615,7 @@ def main():
data[comm_name]['bwa_exe' ] = BWA_EXE
data[comm_name]['samtools_exe' ] = SAMTOOLS_EXE
data[comm_name]['frc_exe' ] = FRC_EXE
data[comm_name]['threads' ] = num_threads
data[comm_name]['sam' ] = out_sam
data[comm_name]['bam_tmp' ] = out_bam_tmp
......@@ -559,20 +644,26 @@ def main():
if 'gtype' in data[ comm_name ] and data[ comm_name ]['gtype'] == 'mp':
#<(gunzip -c | fastqreversecomp.py )
data[comm_name]['fastq1cmd' ] = "<(pigz -d -p3 -c %s | fastx_reverse_complement )" % data[comm_name]['fastq1']
if 'fastq2' in data[comm_name]:
data[comm_name]['fastq2cmd' ] = "<(pigz -d -p3 -c %s | fastx_reverse_complement )" % data[comm_name]['fastq2']
if data[ comm_name ]['gplat'] == 'illumina':
#<(gunzip -c | fastqreversecomp.py )
fn = data[comm_name]['fastq1']
opener = 'cat'
if fn.endswith('.gz'):
opener = 'pigz -d -p3 -c'
data[comm_name]['fastq1cmd' ] = "<(%(opener)s %(fn)s | fastx_reverse_complement )" % { 'opener': opener, 'fn': fn }
if len( data ) == 0:
print "no valid files found. quitting"
sys.exit(1)
if 'fastq2' in data[comm_name]:
fn = data[comm_name]['fastq2']
opener = 'cat'
if fn.endswith('.gz'):
opener = 'pigz -d -p3 -c'
data[comm_name]['fastq2cmd' ] = "<(%(opener)s %(fn)s | fastx_reverse_complement )" % { 'opener': opener, 'fn': fn }
run_bwa(data)
return data
##########################
......
#group name,library name,library size,library size min,library size max,file names
120524_I238_FCD1174ACXX_L2_SZAXPI009264-133,pe,170,153,187,/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_1.fq.gz
120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133,pe,170,153,187,/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_1.fq.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz
120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_1.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_2.fq.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133,pe,170,153,187,/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_1.fq.gz
120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46,pe,500,450,550,/home/assembly/tomato150/reseq/raw/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_1.fq.gz;/home/assembly/tomato150/reseq/raw/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_2.fq.gz
120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz
120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93,mp,2000,1800,2200,/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz;/home/assembly/tomato150/denovo/arcanum/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz
#group name platform library name library size library size min library size max file names
120524_I238_FCD1174ACXX_L2_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46 illumina pe 500 450 550 /home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_2.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/arcanum/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/arcanum/filtered/454/8000/8000.dedup.sff
#group name platform library name library size library size min library size max file names
120524_I238_FCD1174ACXX_L2_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133 illumina pe 170 153 187 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46 illumina pe 500 450 550 /home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_2.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/arcanum/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/arcanum/filtered/454/8000/8000.dedup.sff
#group name,library name,library size,library size min,library size max,file names
120512_I238_FCD115HACXX_L1_SZAXPI008752-75,pe,500,450,550,/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_2.fq.gz;/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_1.fq.gz
120524_I238_FCD1174ACXX_L3_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_2.fq.gz
120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_2.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_1.fq.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_2.fq.gz
120530_I235_FCD117YACXX_L7_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_2.fq.gz
120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75,pe,500,450,550,/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_2.fq.gz;/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_1.fq.gz
#group name,library name,library size,library size min,library size max,file names
120512_I238_FCD115HACXX_L1_SZAXPI008752-75,pe,500,450,550,/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_2.fq.gz;/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_1.fq.gz
120524_I238_FCD1174ACXX_L3_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_2.fq.gz
120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90,mp,2000,1800,2200,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_2.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_1.fq.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_2.fq.gz
120530_I235_FCD117YACXX_L7_SZAXPI009265-136,pe,170,153,187,/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_1.fq.gz;/home/assembly/tomato150/denovo/habrochaites/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_2.fq.gz
120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75,pe,500,450,550,/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_2.fq.gz;/home/assembly/tomato150/reseq/raw/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_1.fq.gz
#group name platform library name library size library size min library size max file names
120524_I238_FCD1174ACXX_L3_SZAXPI009265-136 illumina pe 170 153 187 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136 illumina pe 170 153 187 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L7_SZAXPI009265-136 illumina pe 170 153 187 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
120512_I238_FCD115HACXX_L1_SZAXPI008752-75 illumina pe 500 450 550 /home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz
120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75 illumina pe 500 450 550 /home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/habrochaites/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/habrochaites/filtered/454/8000/8000.dedup.sff
../../allpaths_lg_habrochaites_raw/in_groups.csv
\ No newline at end of file
../sh1/sh.csv
\ No newline at end of file
../../allpaths_lg_habrochaites_raw/in_groups.csv
\ No newline at end of file
#group name,library name,library size,library size min,library size max,file names
3018DAAXX_1,mp,1640,1440,1840,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/3018DAAXX_1_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/3018DAAXX_1_f.fastq
3018DAAXX_2,mp,2430,2180,2680,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/3018DAAXX_2_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/3018DAAXX_2_r.fastq
3018DAAXX_3,mp,2850,2550,3150,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/3018DAAXX_3_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/3018DAAXX_3_f.fastq
3018DAAXX_4,mp,3000,2500,3500,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/3018DAAXX_4_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/3018DAAXX_4_f.fastq
30507AAXX_1,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_1_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_1_f.fastq
30507AAXX_2,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_2_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_2_f.fastq
30507AAXX_3,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_3_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_3_f.fastq
30507AAXX_4,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_4_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_4_f.fastq
30507AAXX_6,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_6_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_6_f.fastq
30507AAXX_7,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_7_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_7_f.fastq
30507AAXX_8,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_8_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_8_f.fastq
30THBAAXX_1,mp,1640,1440,1840,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/30THBAAXX_1_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/30THBAAXX_1_r.fastq
30THBAAXX_2,mp,2430,2180,2680,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/30THBAAXX_2_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/30THBAAXX_2_f.fastq
30THBAAXX_3,mp,2850,2550,3150,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/30THBAAXX_3_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/30THBAAXX_3_r.fastq
30THBAAXX_4,mp,3000,2500,3500,/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/30THBAAXX_4_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/30THBAAXX_4_r.fastq
314TYAAXX_1,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_1_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_1_r.fastq
314TYAAXX_2,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_2_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_2_r.fastq
314TYAAXX_3,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_3_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_3_r.fastq
314TYAAXX_4,pe,160,144,176,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_4_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_4_r.fastq
314TYAAXX_6,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_6_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_6_r.fastq
314TYAAXX_7,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_7_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_7_r.fastq
314TYAAXX_8,pe,215,193,237,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_8_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_8_r.fastq
sample_R,pe,500,450,550,/home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R1_001.64.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R2_001.64.fastq
#group name platform library name library size library size min library size max file names
30507AAXX_6 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_6_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_6_f.fastq
30507AAXX_7 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_7_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_7_f.fastq
30507AAXX_8 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_8_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/30507AAXX_8_f.fastq
314TYAAXX_1 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_1_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_1_r.fastq
314TYAAXX_2 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_2_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_2_r.fastq
314TYAAXX_3 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_3_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_3_r.fastq
314TYAAXX_4 illumina pe 160 144 176 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_4_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_250/314TYAAXX_4_r.fastq
30507AAXX_1 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_1_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_1_f.fastq
30507AAXX_2 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_2_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_2_f.fastq
30507AAXX_3 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_3_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_3_f.fastq
30507AAXX_4 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_4_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/30507AAXX_4_f.fastq
314TYAAXX_6 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_6_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_6_r.fastq
314TYAAXX_7 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_7_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_7_r.fastq
314TYAAXX_8 illumina pe 215 193 237 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_8_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_300/314TYAAXX_8_r.fastq
sample_R illumina pe 500 450 550 /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R1_001.64.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R2_001.64.fastq
3018DAAXX_1 illumina mp 1640 1440 1840 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/3018DAAXX_1_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/3018DAAXX_1_f.fastq
3018DAAXX_2 illumina mp 2430 2180 2680 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/3018DAAXX_2_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/3018DAAXX_2_r.fastq
3018DAAXX_3 illumina mp 2850 2550 3150 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/3018DAAXX_3_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/3018DAAXX_3_f.fastq
3018DAAXX_4 illumina mp 3000 2500 3500 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/3018DAAXX_4_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/3018DAAXX_4_f.fastq
30THBAAXX_1 illumina mp 1640 1440 1840 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/30THBAAXX_1_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_2000/30THBAAXX_1_r.fastq
30THBAAXX_2 illumina mp 2430 2180 2680 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/30THBAAXX_2_r.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_3000/30THBAAXX_2_f.fastq
30THBAAXX_3 illumina mp 2850 2550 3150 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/30THBAAXX_3_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_4000/30THBAAXX_3_r.fastq
30THBAAXX_4 illumina mp 3000 2500 3500 /home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/30THBAAXX_4_f.fastq;/home/assembly/dev_150/sample_heinz/raw/illumina/MP_5000/30THBAAXX_4_r.fastq
#group name,library name,library size,library size min,library size max,file names
120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79,pe,500,450,550,/home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_1.fq.gz;/home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_2.fq.gz
120524_I238_FCD1174ACXX_L4_SZAXPI009266-140,pe,170,153,187,/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_2.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_1.fq.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89,mp,2000,1800,2200,/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89,mp,2000,1800,2200,/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz
120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140,pe,170,153,187,/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_1.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_2.fq.gz
120530_I235_FCD117YACXX_L1_SZAXPI009266-140,pe,170,153,187,/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_2.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_1.fq.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89,mp,2000,1800,2200,/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89,mp,2000,1800,2200,/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89,mp,2000,1800,2200,/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz
#group name platform library name library size library size min library size max file names
120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79 illumina pe 500 450 550 /home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L1_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
3000.dedup 454 mp 3000 2700 3300 /home/assembly/tomato150/denovo/pennellii/filtered/454/3000/3000.dedup.sff
../../allpaths_lg_pennellii_raw/in_groups2.csv
\ No newline at end of file
../sp1/sp.csv
\ No newline at end of file
../../allpaths_lg_pennellii_raw/in_groups2.csv
\ No newline at end of file
../../allpaths_lg_pennellii_raw/in_libs2.csv
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment