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moonwatcher/fastq2cram.py

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Example of generating configuration files for pheniqs 2.0 for packing fastq to CRAM
Raw
fastq2cram.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import io
import os
import re
import sys
import json
import logging
from datetime import date
inode_type = lambda path: ( os.path.isfile(path) and 'file' ) or 'directory'
def to_json(node):
return json.dumps(node, sort_keys=True, ensure_ascii=False, indent=4)
class Scanner(object):
def __init__(self, ontology):
self.log = logging.getLogger('Scanner')
self.ontology = ontology
self.inode = []
@property
def expression(self):
return self.ontology['expression']
def search(self):
def collect(path, recursive, depth=1):
result = []
# The path might actually not exist, for instance a dangling symlink
if os.path.exists(path):
decoded = {
'path': path,
'inode type': inode_type(path),
'dirname': os.path.dirname(path),
'basename': os.path.basename(path),
}
if decoded['inode type'] == 'directory':
if (recursive or depth > 0):
# recursively scan decedent paths
for next in os.listdir(decoded['path']):
next = os.path.abspath(os.path.join(decoded['path'],next))
result.extend(collect(next, recursive, depth - 1))
self.log.debug('considering %d inodes in %s', len(result), decoded['path'])
else:
match = self.expression.search(decoded['basename'])
if match:
for k,v in match.groupdict().items():
if k in [
'day',
'month',
'year',
'lane_number',
'segment_number'
]:
decoded[k] = int(v)
else:
decoded[k] = v
if 'year' in decoded:
decoded['year'] += 2000
if all(i in decoded for i in ('day', 'month', 'year')):
decoded['iso date'] = date(**dict([(i,decoded[i]) for i in ('day', 'month', 'year')])).isoformat()
result.append(decoded)
else:
self.log.debug('ignoring non exiting path %s', path)
return result
self.inode = []
if self.ontology['scan path']:
for path in self.ontology['scan path']:
if os.path.exists(path):
path = os.path.abspath(os.path.expanduser(os.path.expandvars(path)))
self.inode.extend(collect(path, self.ontology['recursive']))
else:
self.log.error('path %s does not exist', path)
self.log.info('%d locations resolved in %s', len(self.inode), ' '.join(self.ontology['scan path']))
def sort_by_library(inode_array):
inode_by_library = {}
for inode in inode_array:
if 'library' in inode:
if inode['library'] not in inode_by_library:
inode_by_library[inode['library']] = []
inode_by_library[inode['library']].append(inode)
for library in inode_by_library.keys():
inode_by_library[library] = sorted(inode_by_library[library], key=lambda o: o['segment_number'])
return inode_by_library
def sort_by_trimmed_library(inode_array):
inode_by_trimmed_library = {}
for inode in inode_array:
if 'library' in inode:
if inode['library'] not in inode_by_trimmed_library:
inode_by_trimmed_library[inode['library']] = {
'PE': [],
'1SE': [],
'2SE': []
}
if inode['trimmed_group'] == 'PE':
inode_by_trimmed_library[inode['library']]['PE'].append(inode)
elif inode['trimmed_group'] == 'SE':
if inode['segment_number'] == 1:
inode_by_trimmed_library[inode['library']]['1SE'].append(inode)
elif inode['segment_number'] == 2:
inode_by_trimmed_library[inode['library']]['2SE'].append(inode)
for library in inode_by_trimmed_library.keys():
for group in ['PE', '1SE', '2SE']:
inode_by_trimmed_library[library][group] = sorted(inode_by_trimmed_library[library][group], key=lambda o: o['segment_number'])
return inode_by_trimmed_library
def main():
logging.basicConfig()
logging.getLogger().setLevel(logging.DEBUG)
# example file name HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz
# Bellow is my educated guess for the metadata encoded in the file name, i might be wrong about some
# I am going to assume a single _ is used as separator
# HJWKJCCXX : flowcell id
# 2 : lane number
# 151215 : run date in < day >< month >< year > format
# FR05811676 : Library, I will assume this is the unique key we to aggregate segments for
# Homo-sapiens : species
# _R : Not sure what this is
# 151215 : The run date again
# YOUIDA : Not sure about this, is this part of the library name?
# M001 : part of the illumina flowcell geometry naming scheme, probably redundant
# R1 : segment number prefixed by the letter R
# .fastq.gz : compressed fastq text file
raw = Scanner({
'recursive': False,
'scan path': [ 'example' ],
'expression': re.compile (
r'^{}\.fastq\.gz$'.format (
r'_'.join (
[
r'(?P<flowcell_id>[^_]+)',
r'(?P<lane_number>[0-9])',
r'(?P<day>[0-9]{2})(?P<month>[0-9]{2})(?P<year>[0-9]{2})',
r'(?P<library>[^_]+)',
r'(?P<species>[^_]+)',
r'(?:_R)',
r'(?:[0-9]{6})',
r'(?:[^_]+)',
r'(?:M[0-9]{3})',
r'R(?P<segment_number>[0-9]+)',
]
)
)
)
})
raw.search()
inode_by_library = sort_by_library(raw.inode)
instruction_array =[]
for k, v in inode_by_library.items():
lead = v[0]
instruction = {
'PL': 'ILLUMINA',
'DT': lead['iso date'],
'flowcell id': lead['flowcell_id'],
'flowcell lane number': lead['lane_number'],
'multiplex': {
'undetermined': {
'LB': lead['library'],
'output': [
'{}_l0{}_{}.cram'.format(lead['flowcell_id'], str(lead['lane_number']), lead['library'])
]
}
}
}
base_input = os.path.commonpath([i['dirname'] for i in v])
if base_input:
instruction['base input url'] = base_input
instruction['input'] = [os.path.relpath(i['path'], base_input) for i in v]
else:
instruction['input'] = [i['path'] for i in v]
instruction_array.append(instruction)
# print(to_json(inode_by_library))
# 151215_FR05811634_read1_trimmomatic_1PE.fastq.gz;
# 151215_FR05811634_read2_trimmomatic_2PE.fastq.gz;
# 151215_FR05811634_read1_trimmomatic_1SE.fastq.gz;
# 151215_FR05811634_read2_trimmomatic_2SE.fastq.gz;
#
# 151215 : run date in < day >< month >< year > format
# FR05811634 : Library, I will assume this is the unique key we to aggregate segments for
# read1 : segment 1 of the read
# trimmomatic : not really informative
# (1|2)(PE|SE) : the first integer is actually redundant since we already encoded the segment number and second is a trim group
# .fastq.gz : compressed fastq text file
raw = Scanner({
'recursive': True,
'scan path': [ 'example/TRIMMED' ],
'expression': re.compile (
r'^{}\.fastq\.gz$'.format (
r'_'.join (
[
r'(?P<day>[0-9]{2})(?P<month>[0-9]{2})(?P<year>[0-9]{2})',
r'(?P<library>[^_]+)',
r'read(?P<segment_number>[0-9]+)',
r'(?:trimmomatic)',
r'[0-9]+(?P<trimmed_group>PE|SE)',
]
)
)
)
})
raw.search()
inode_by_trimmed_library = sort_by_trimmed_library(raw.inode)
for library in inode_by_trimmed_library.values():
for group in library.values():
lead = group[0]
instruction = {
'PL': 'ILLUMINA',
'DT': lead['iso date'],
'multiplex': {
'undetermined': {
'LB': lead['library'],
'output': []
}
}
}
if 'flowcell_id' in lead:
instruction['flowcell id'] = lead['flowcell_id']
if 'lane_number' in lead:
instruction['flowcell lane number'] = lead['lane_number']
base_input = os.path.commonpath([i['dirname'] for i in group])
if base_input:
instruction['base input url'] = base_input
instruction['input'] = [os.path.relpath(i['path'], base_input) for i in group]
else:
instruction['input'] = [i['path'] for i in group]
if lead['trimmed_group'] == 'SE':
instruction['multiplex']['undetermined']['output'].append (
'{}_trimmed_SE{}.cram'.format(lead['library'], str(lead['segment_number']))
)
else:
instruction['multiplex']['undetermined']['output'].append (
'{}_trimmed_PE.cram'.format(lead['library'])
)
instruction_array.append(instruction)
# print(to_json(inode_by_trimmed_library))
print(to_json(instruction_array))
sys.exit(0)
if __name__ == '__main__':
main()
Raw
instruction.json
[
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJWVCCXX",
"flowcell lane number": 8,
"input": [
"HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811644",
"output": [
"HKJWVCCXX_l08_FR05811644.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 3,
"input": [
"HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811658",
"output": [
"HKJHJCCXX_l03_FR05811658.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 6,
"input": [
"HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811666",
"output": [
"HKJHJCCXX_l06_FR05811666.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HJWKJCCXX",
"flowcell lane number": 2,
"input": [
"HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811676",
"output": [
"HJWKJCCXX_l02_FR05811676.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HK7YCCCXX",
"flowcell lane number": 4,
"input": [
"HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811634",
"output": [
"HK7YCCCXX_l04_FR05811634.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 2,
"input": [
"HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811652",
"output": [
"HKJHJCCXX_l02_FR05811652.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 4,
"input": [
"HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811659",
"output": [
"HKJHJCCXX_l04_FR05811659.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJWVCCXX",
"flowcell lane number": 5,
"input": [
"HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811636",
"output": [
"HKJWVCCXX_l05_FR05811636.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 1,
"input": [
"HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811674",
"output": [
"HKJHJCCXX_l01_FR05811674.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 7,
"input": [
"HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811667",
"output": [
"HKJHJCCXX_l07_FR05811667.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HJWKJCCXX",
"flowcell lane number": 4,
"input": [
"HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811683",
"output": [
"HJWKJCCXX_l04_FR05811683.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJWVCCXX",
"flowcell lane number": 4,
"input": [
"HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811651",
"output": [
"HKJWVCCXX_l04_FR05811651.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HK7YCCCXX",
"flowcell lane number": 5,
"input": [
"HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811650",
"output": [
"HK7YCCCXX_l05_FR05811650.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 5,
"input": [
"HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811660",
"output": [
"HKJHJCCXX_l05_FR05811660.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJWVCCXX",
"flowcell lane number": 7,
"input": [
"HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811643",
"output": [
"HKJWVCCXX_l07_FR05811643.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKK7VCCXX",
"flowcell lane number": 5,
"input": [
"HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811635",
"output": [
"HKK7VCCXX_l05_FR05811635.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJHJCCXX",
"flowcell lane number": 8,
"input": [
"HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811668",
"output": [
"HKJHJCCXX_l08_FR05811668.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HJWKJCCXX",
"flowcell lane number": 5,
"input": [
"HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811684",
"output": [
"HJWKJCCXX_l05_FR05811684.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HKJWVCCXX",
"flowcell lane number": 6,
"input": [
"HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811642",
"output": [
"HKJWVCCXX_l06_FR05811642.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example",
"flowcell id": "HJWKJCCXX",
"flowcell lane number": 3,
"input": [
"HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz",
"HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811682",
"output": [
"HJWKJCCXX_l03_FR05811682.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811634_read1_trimmomatic_1PE.fastq.gz",
"151215_FR05811634_read2_trimmomatic_2PE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811634",
"output": [
"FR05811634_trimmed_PE.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811634_read1_trimmomatic_1SE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811634",
"output": [
"FR05811634_trimmed_SE1.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
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"LB": "FR05811644",
"output": [
"FR05811644_trimmed_SE1.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811644_read2_trimmomatic_2SE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811644",
"output": [
"FR05811644_trimmed_SE2.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811658_read1_trimmomatic_1PE.fastq.gz",
"151215_FR05811658_read2_trimmomatic_2PE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811658",
"output": [
"FR05811658_trimmed_PE.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811658_read1_trimmomatic_1SE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811658",
"output": [
"FR05811658_trimmed_SE1.cram"
]
}
}
},
{
"DT": "2015-12-15",
"PL": "ILLUMINA",
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED",
"input": [
"151215_FR05811658_read2_trimmomatic_2SE.fastq.gz"
],
"multiplex": {
"undetermined": {
"LB": "FR05811658",
"output": [
"FR05811658_trimmed_SE2.cram"
]
}
}
}
]
Raw
simulate.sh
#!/bin/sh
mkdir example;
( cd example;
touch HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz;
touch HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz;
touch md5sum_2.txt;
touch md5Sum.sh;
touch md5sum.txt;
touch nohup.out;
touch nohup.out.Download2;
touch nohup.out.old;
touch nohup.out.upload.old;
touch pwd.txt;
mkdir TRIMMED;
( cd TRIMMED;
touch 151215_FR05811634_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811634_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811634_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811634_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811635_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811635_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811635_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811635_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811636_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811636_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811636_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811636_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811642_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811642_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811642_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811642_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811643_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811643_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811643_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811643_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811644_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811644_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811644_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811644_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811650_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811650_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811650_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811650_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811651_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811651_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811651_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811651_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811652_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811652_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811652_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811652_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811658_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811658_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811658_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811658_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811659_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811659_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811659_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811659_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811660_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811660_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811660_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811660_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811666_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811666_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811666_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811666_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811667_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811667_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811667_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811667_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811668_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811668_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811668_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811668_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811674_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811674_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811674_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811674_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811676_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811676_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811676_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811676_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811682_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811682_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811682_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811682_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811683_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811683_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811683_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811683_read2_trimmomatic_2SE.fastq.gz
touch 151215_FR05811684_read1_trimmomatic_1PE.fastq.gz
touch 151215_FR05811684_read1_trimmomatic_1SE.fastq.gz
touch 151215_FR05811684_read2_trimmomatic_2PE.fastq.gz
touch 151215_FR05811684_read2_trimmomatic_2SE.fastq.gz
touch nohup.out;
);
);
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