Mercurial > repos > jdv > albacore

changeset 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
parents ce1fa05ffb6c
children 710ccd01ae81
files albacore_1D.py albacore_1D.xml bar.farb baz.farb foo.farb out_dir/configuration.cfg out_dir/pipeline.log out_dir/sequencing_summary.txt out_dir/workspace/fail/fastq_runid_d28f9f1c34b8f7416c367df1e0c4a864ba830c9c_0.fastq out_dir/workspace/pass/fastq_runid_d28f9f1c34b8f7416c367df1e0c4a864ba830c9c_0.fastq test-data/test_data_nofilt.fastq
diffstat 11 files changed, 220 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/albacore_1D.py	Sat Mar 10 15:43:07 2018 -0500
+++ b/albacore_1D.py	Mon Jun 18 12:20:28 2018 -0400
@@ -11,11 +11,12 @@
 from tempfile import mkdtemp
 
 def main():
-    tar_file = sys.argv[1]
-    out_file = sys.argv[2]
-    out_fmt  = sys.argv[3]
-    demux    = strtobool( sys.argv[4] )
-    threads  = sys.argv[5]
+    tar_file     = sys.argv[1]
+    out_file     = sys.argv[2]
+    out_fmt      = sys.argv[3]
+    demux        = strtobool( sys.argv[4] )
+    disable_filt = strtobool( sys.argv[5] )
+    threads      = sys.argv[6]
 
     tempdir = mkdtemp()
 
@@ -32,7 +33,8 @@
         "--files_per_batch_folder", "0",
         "--output_format", out_fmt,
         "--reads_per_fastq_batch", "999999999" ] +
-        ["--barcoding"] * demux )
+        ["--barcoding"] * demux +
+        ["--disable_filtering"] * disable_filt )
 
     out_path = "out_dir/workspace"
     pass_path = os.path.join( out_path, "pass" )
--- a/albacore_1D.xml	Sat Mar 10 15:43:07 2018 -0500
+++ b/albacore_1D.xml	Mon Jun 18 12:20:28 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="albacore_1D" name="Albacore 1D" version="2.0.2">
+<tool id="albacore_1D" name="Albacore 1D" version="2.0.2b">
 
     <description>ONT production basecaller</description>
 
@@ -6,7 +6,7 @@
    
     <!--
     <requirements>
-        <requirement type="package" version="1.2.6">albacore</requirement>
+        <requirement type="package" version="2.0.2">albacore</requirement>
     </requirements>
     -->
 
@@ -19,7 +19,7 @@
     <command detect_errors="aggressive">
     <![CDATA[
 
-    python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux \${GALAXY_SLOTS:-1}
+    python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux $disable_filt \${GALAXY_SLOTS:-1}
 
     ]]>
     </command>
@@ -34,6 +34,7 @@
             <option value="fast5">fast5</option>
         </param>
         <param name="demux" type="boolean" checked="false" label="Demultiplex" />
+        <param name="disable_filt" type="boolean" checked="false" label="Disable quality filtering" />
         <param name="output_table" type="boolean" checked="false" label="Include table in output" />
 
     </inputs>
@@ -56,7 +57,6 @@
             <filter>demux is True and out_format == 'fast5'</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
         </collection>
-
         <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
             <filter>output_table is True</filter>
         </data>
@@ -70,6 +70,11 @@
             <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
             <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
         </test>
+        <test>
+            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="disable_filt" value="true" />
+            <output name="output" file="test_data_nofilt.fastq" compare="sim_size" delta="0"/>
+        </test>
     </tests>
 
     <!-- ***************************************************************** -->
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bar.farb	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,32 @@
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+ACTCATTTAGCCGCTAATTCGTGTGTGCTAATCCTAATGGCTTTTGAAAGTGAGTAAGCAAGTATTTTCTAATAAATAATGAAGCGAAAGTTATATCTCTCAACTCTACTCGGCGTAATTGCTGCTCAAGCATATTGGCTGTTATACTGTACTTGTACGTCGTTGTACTTCCTTTATAGAAGCACATGAAGTATTTACCAAGAACACCATTTGCTTTGAGTACTCACTCAAATTATCGGCGTCTAGAACAAGTAATGATATCGTAAATTCGCGAAGTACTCGTCGAAAGAGCTGTGCATTTCTGACATCTCTGTGTAATCTCGAAGATAACGTGAATGCTCGCAGTAACTCTCTAGTAATGTCAGAATTTCTGGCCAAATCGAAAATGCATAAAGTAAACAATATGATATTGCCAGCCATTAATATGAATGCATTATTAAATAACAGAAACTCGCCTGATATGATATTATCATTATTCGTCATATCGATTAAACCATAATCGAGCAGAAGCGTAGTCGGCCTGAAATTATATCGGGCCTTACTGGTATAAATAACTCATATTTTAAAACCGGCTGTTTAAATGGCCGACGTGCTTGCTCTTACTCGCGGCCATCAATCAGGCATCTTCATTATCAATCTGCAAATCATTGCTGAGCATGCGAAAACGTCTACTCGAAACCCGGCGACCAGTGAATCCGTATTTGTCGCGCAACTTTTCGACTCATAAATGATA
++
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+ACGCGGGTGTGGATCGATCCATGATGTCGAAACCTCATTCATGAGATCGTCAGAAATAGAATGTCAGACAGTATCAGATAATGACCGATGGCGTTAATGATGCGTCATCGAAGGAATCGAACCGTCGTCAATGAAGGCCAGGTCATCAGGAAATCTCAATCCAATAGTATGTTTTAGAATCACGAGTCCCGGTCCCGGGTCGATAAAGTCTTCGAACAATGAGCATTTATCGTCAGTGAAAGGCCCCTCGAGATGCTTGCTCAGGCCAATCAGGCCAATAATCAAAATTCTGCGATAGGCCTTCTCCGCTCCAGGCCATGTTCCCGATATTTTCAGTCATGCTCTCTTCGACAGGAATTAAAACTCAATCTTCTCAGTGAGAATGAGAATGCAGCTCCTGTCGAGAAAAATGTTGGGCTCCATCAAACATCGTTCTCCATGGCCATCAATAATAACAATA
++
+$&%%%*&'%&'(&,()'((%%$'%-+-.'&''*&&'&'%$&%&))'**&)(&((+*0+',&'$'&&&21&,../,)).,('&&&)&''(.('&'%&&)'%&&'()%''&''',+()))''&&#%&&%)')'%%((&+-0'+&&''&&&'(%%%)),,)++,(,(),%(*,'171&)'+,(*''(&&)/+))),-.))($)(%((&('%+')('&(&*--&)%)*+-4&$%&&-,'&'&))(**:51,'('&%'$$')&$$&%%'%%$)&'&&'$('*&'()'%+'')&(&&$('(*)'&)&&*&)&(%&'-&&$$&+()%'*)+('&''%&%%%%$&'&(%'),.*+'&&&,),))*)*))(&+)*(,,%**''''&+((*'(&&'&'&&%*(%%&('(%(%%'$''(-('&+**'&''(%)(&*)%&$&%%.+('%%%%$%%$%%%$%&%&&%%&$%%%
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+GCATTATATACATTCGTGCATGTCCTTAAAAGCGCTAATGAGAAATGAAATATTCAAATGAAGCAGAAGTATATGCTCTTCACTAATTGTGAGCTCATAAATGTAATGACTCAAACTATACTATGATCTTGATCATAACTTTGCTCTTTAATCGGCTATTTCTGAAACTTATGACTCGAACATTTATCAACCGTATTTCATTTGAAGTGAAATTATACGTAAGTGGCGCTGCTCAGGCGAAATATATAGCAAAATTCTAGAACTCGAGCACATTACATCGGCATTTGAGGCCGGAATGGCTGGGAAAACGTGCGTGGCATCTCCATCGGTATAATATGAAATGCGGCCGTGCTTCAGCCTGAAATGAAACACTGATGTCAGCCTTCCGCGTGATGAAATCACTTCGAGAATTTCAGCGATATTGAAGGCCTGCTATGAAACAAGCGTGCTCGACCATAAGTATAAATGGCATGAAGAGAAGAAATGAAGGTAATGGTACTCATCAATTATATCAAATGCTTCTATTCCGGCGCGATGGCCTCGATATGCATTGAAATAACTCTTCATCTCGAGGCTTTCGATCTCGGCGCGGAAGCTTGCATCGAAATCAATTATGCAAAATCGTCAGGCATACCGTCTTCGAAGCGCGTCAGAATCATCATTTTGCCTCACTTTTAATAAATGAAGGCTGTCGAGGGTAATATGACATCAACAACTAACAATGCTCTGCCGAATGGAGCCAAACGTAATGGCGTAATCTTCAGTATCGCGAGAAGGCGTCTTCGGCGAAGGCTGAGATAATAATCGAGGCATCACCAAGTAACTAATATTTTGAAATCAATGCTGAGTACAAATGCGCTGGAAATAAAGAAAACTTCTCAGCTAAATGAAAGTATAATTGGCGAATATAGGCTAATCTCATATGCATCATCATATAAATGTTTCTCAGCTCGCATAGGCGCTCGCAGTAACATCTCGCTTGGCAAAGTAATTCTGAATCTCTCATGTCAATATACAACCATACAAATGACGTCATCCTCTTGAAATCAATCATCTTGCAAAAGTCTTCATTATAATCCGAGTATCAAGAGTAACTCTCCAACAAGCCATCCCAG
++
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+ACAAATCATCTCGATCGATCTTTATCTGAATCAAACCAGCAATCGAATCGGAAACAGAATGATGTCGAAGATCGAATAATCAAATATCTATCATCTATCAGGCCAAAATGGCATCCTTATAAATGAGAATGTCGGCTGAATCGAAATATCGGAAATAATGAACAAAATAATCGCGCAATAAAGAGAATAAATTAATCAGCAAGAAACCAGCCCTTCAGCTCCGCTCGCCATAAAACCGCTTTCTTCAAAACAATAAAACAAAGCAAGCAATAAACAAAGCTCTTTACTCAAATCCCAAACAAATTACCTTTCTCCCCAGCCGAATAAAACGGCCAACCAGCTAATGCCGCAAATACCCCGGCATCGAAACAAGCAAAGCAGCCAATACTCACGGCCAAAGCCATATAAACAATAAGGCCAAACCATCACCGTCGGCAAATAACAATCAGGCTGCAGATAAACAATGCAAATACTGCCAATCAAGCAACATGTCACATAATACTGTCCGCTATGAGAGAGGCATACCCAGAAATGCTAAAATAAATATTT
++
+((')'*&'(('''&)-&)++-.(&'%&&*('&*('*')$%',*(()*)()''(*&''+0/)**&()**+)*''(&((')'.-.)('*)(')().,+++,&&&.)+--*&(&%',,%&$%&'*'$%'''(%$%&'&'%%&(('&(*'&'(',(./.*.('%)''('&+)+))&$&$&(')*0,')'+)((,&(%&%&'+%*)+&,,'(+''2*'&'((%&%(&&)*+$''&$&'+(-'&'&&'&''&+,2.-1&%&&'()02*%%'(%'&'%'.,*-1-&%&&,,'&(()')&+(&&)'&()*)'&&*((&&&%&120+-/8'&%%)22++',-(-$&&&%)((%&$(%$%&3/,&,.-(+',&&(%&*$&&%$%)*&$&%&2.3+'$')('*%&()(+0*64+&&(//*++(&&%&$%%')'%%+&%&(%$&'&&'%'&$''%*''%%*$&$$&('&'&('&&&$%('**)*((+--.'&&&&(**)**&%&%&'&%&&%&(%$$&''&&%&%+')((((('(%))**(())$$$$%&&'&',))')($
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+GCAGTAATATGAGCCAGTCATGTCCAACATAGGCGGCGTGAGTGAGCGAGATGGTACCTAAATTGAAGCATGATATTGGCGTAAATTGCCTGATGTATTCTGGCTGTCGTCAATGTGCTGATAAATTTAAAATTTAATGCCCGGCGCTATTATGCATAACATCGGCGCAATATTTTATATGCATAGCGAGAATATTTGATGAATGATATCGTGAGATGGCATGCTGTCTCTGGCGCTGAGAATGAAGCCTCTCATCATCATGTCATTTCAATGATAAATTTTAAATGGCGATAATTATTTAATTTGCCGGTAGAATTGTATATGCATACAGCCAGCTAGCGATAACTATATTGGCGGCGCTGATGCGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGATATATCGGTAACTGTATATCATGGCCCGTGTATTTATTTTGCTTTTGGCGCCGCGCCGTGTTTAACCAGGTGGTAGTATGA
++
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+ACGATAGCCTTAGATCGATCACGTATCATGCGGCATCGGCACTGGCGTGATAACGAAAACGTAATGAATTGACATATCGAAGCTCGGTGGGCCTAACTATGACATCGCAGGCATTAACGACCGAAATGTCACATTATCGATAAGCAAGAATCTCATCCCTAAAGAGAAGAGGCGGCGCTCGTGGGCGTCGGGGCGACGCTGAAGCGTGTCAGGCGGGAATTGCCAGAGAGAAATCCCATCGAAGCATCAAAATGATATAACATACTCGCCTAACTGGCGGACTCGAGAATATCGAGAACTGGTCATGTCATGCCCGAAAACCCGAAAATGTGAGCTCATCAAAGAATGGGCCGACGTCTTGAATATGAGCATCATGAAAAGCAAACTCGGTATGTTTCGGTAAGCTTCGGCCGTCAATATATCGGAAGCATCGCCGAAAAGAGAGCATA
++
+()*%)*&'&%&&'%-*+,,'#&)*..'()&(+,+)23'$(%')8*)+&'%%(*.(*.('&%&.'&*&&.)++)&'$',*)'%%&'''(&())+)'%%')&(%,),),9..86)4*.&-,+-2'()(&&&'&(&,()(''&$-.&*)'&)2*+$$%%%*-(,/)*,--)((-,5460())'&&)&'.-1/)-.-,($%%%$()(('&&%''(/-**-+'&,&('+(+*,-,.14/)5-$%*()'))'*)(,/*&%(()''&%')&))+*+(&&%'&)''('%&'&&)'+)+*+.++)''*((+-.*.)+*.0)()('*9;3-2''+.*-+-,*(''()%&'(')-'+*+*+2+.*0143.2*&+,'%'&*2240%'%+.01(*69.312,2.1.)%(&%'*)*)&')(&'&..11016(('%&)()'&&(%+,/30-156,&)&(&&&&%
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+CTGATGGTCGATCAAGCCAAATAGTCGATGAATCATATCATCGAATCAGGCTCAAACAATCTCGAATAAAACAATCATCCATCTTTCTCGAATCAGCAACAATCTTATCAAAACAATCAAGCAATCAAAGCCACACAAAATAATAACAACTCTTTACTCGCCCAAACAAAATAACAAAGCAAGCAATAATAAACAAGCTCTGCTCCAGCCCTCAAGCTTTCAATAAAACCATGTAGAATGCCTCTTCCCTAGTCAAAGCCAGCAACAGACTATATTCAG
++
+%%&%&%'(*+%&%%%''*)+&&'&%$&&$$&&((&&('&%%&%(''%'$#&%%()'&0512-+((('*-''%(((&&&)(&)(*+*((,&,/$%'%&%$&('&&%%)'')24+%&&%%-)&)++*&&'($,+%%$$*/5,)($($$&%%%%%'(&'$$$$'())&$'()*(''$%&&&%&)(&'0+*)&&')&(),)*+)$$%%%(&'*)((&'')&&$$%%%%%&'*((&&$%'&&&%$%%&&..,-($(#&&&'+$%%&$$%&%&#&$%()'(,&&%
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+AACATTGTGCTTAGGTAGAGCGTAACTAATCTGAAAGCAGCGCGAGTGGTAAGCAGTATTTATCGCTAAATAATTCAGCGAGATTTACTCGCTCTCCGGCTCTGCTCGGCGTAATTGAAACAATAAGCGTCTCTGTTGAAGCTATTCTCTGTGTTGCTAATGTGGCAGCGATCGGCCGCTCAATTTCGCCAAAACTTGCGCTCAGTATTGCTGCCAGCACAAAACTGGGAGGCGAGAATGCCATGCTGGCGGCGTGTAATTTCGCTCGACTGTGATACGTAAATTGCATTAAAATGCTCATCGAGGGGCTTTGATATTTCAGGCATCTCGTCAATGTAATATGAAGAGAAGCCAGCGTGTTGCTCACCATTAACCATAACTTCTGTAAAGTACAATGACCGTAGATTTCTGGCGTCATCGCTGAAAGTAAACACCGACCATATGATATTTGCCAATGGTATTAACAATGCGTGCAATGCGAGGCGCAGCTTCTGTTGGTATGACGCATCAGGCAATCATCGGCCATCGTCATATCGGTCGTATGGTAGCGTAGAGCAGAAGCGGCTAGTAAATGCAAGTGCTCAAATTATACTCTAAATCGCTCATATCTATTTTACGCGCGATATTTCTTTAAATGTCCGGAGCCCGAAATGCCTGTGCTCTTGCGCCAGAACCTGATGCGGCGGCCATCGAGGCGGTGCTCGATGCTGCCAATCGTGCGAGCATGCTTGAAAACGTCTACTCGAAAGCTCTGACGCGTGTCAAAAGCTAAAGTATGTTTTTGTCGCATATTTCTCCGCGCCAG
++
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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baz.farb	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,16 @@
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+ACTCATTTAGCCGCTAATTCGTGTGTGCTAATCCTAATGGCTTTTGAAAGTGAGTAAGCAAGTATTTTCTAATAAATAATGAAGCGAAAGTTATATCTCTCAACTCTACTCGGCGTAATTGCTGCTCAAGCATATTGGCTGTTATACTGTACTTGTACGTCGTTGTACTTCCTTTATAGAAGCACATGAAGTATTTACCAAGAACACCATTTGCTTTGAGTACTCACTCAAATTATCGGCGTCTAGAACAAGTAATGATATCGTAAATTCGCGAAGTACTCGTCGAAAGAGCTGTGCATTTCTGACATCTCTGTGTAATCTCGAAGATAACGTGAATGCTCGCAGTAACTCTCTAGTAATGTCAGAATTTCTGGCCAAATCGAAAATGCATAAAGTAAACAATATGATATTGCCAGCCATTAATATGAATGCATTATTAAATAACAGAAACTCGCCTGATATGATATTATCATTATTCGTCATATCGATTAAACCATAATCGAGCAGAAGCGTAGTCGGCCTGAAATTATATCGGGCCTTACTGGTATAAATAACTCATATTTTAAAACCGGCTGTTTAAATGGCCGACGTGCTTGCTCTTACTCGCGGCCATCAATCAGGCATCTTCATTATCAATCTGCAAATCATTGCTGAGCATGCGAAAACGTCTACTCGAAACCCGGCGACCAGTGAATCCGTATTTGTCGCGCAACTTTTCGACTCATAAATGATA
++
+%%'%$).&&+2+()+**3+''+%&%+%%'&*,()',((),&%''%&%)*&%&(').7,-*/..-/4.+%+'('-20,1*+)+/*))+-,'*'(/..,+)*')3...-+)-+)*((++),&('&()&',*()%&%$$&(((*-*''&&&'&%%&%%(%&&('&+'(($)''+'.2(%)&*'(%&%&#%%%%%*&)'&%&%'(&(&'&(*&*0*&%%%$&'%)'(&%'$''''$%%%%&'&$$%#'*%1(+()%%)**'+0.01&)(,*)+*)()+1%+*,-.*''&.0(((,,0/--0-42)'(*)0+100-*()&+)'(*/+&.)&(+)%,)*&((*%%(,).,(.)(%&%&%),$&'''%()*0&1(49,(%))+&)''(&()*-)''%((02,14(&&('('&&'*')*'*)('1201.1,(('')()*.-22,.2*/-)*&()%*(&(*/*-+'&%&&&&*(*81--)))(%%&%,02-,++.+$+((,-)'*'*(*''('+(&(&&'%&(%)',)1*,(+)&''((&&&'()+(('%''%&%((+,*%(&$''%(&058*)(('(()*''%)*(+2//(,0.*%$'%%&)''*)+5/+)('&&-(4**((*(&&'*3/0/,*)%().-/0-,+''%&(+*'%&1''&%&'$'(&%&(-40'.-)*)'%&'()-+*.''%'&'*&(%+&(*)'&%&$*./*-/((%)*'*047-*(,/70&(((&'%$'&
+@2dd21811-c9af-4c4a-aaa0-4fd1f605abf8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12153 ch=399 start_time=2017-08-09T20:02:16Z
+GCAGTAATATGAGCCAGTCATGTCCAACATAGGCGGCGTGAGTGAGCGAGATGGTACCTAAATTGAAGCATGATATTGGCGTAAATTGCCTGATGTATTCTGGCTGTCGTCAATGTGCTGATAAATTTAAAATTTAATGCCCGGCGCTATTATGCATAACATCGGCGCAATATTTTATATGCATAGCGAGAATATTTGATGAATGATATCGTGAGATGGCATGCTGTCTCTGGCGCTGAGAATGAAGCCTCTCATCATCATGTCATTTCAATGATAAATTTTAAATGGCGATAATTATTTAATTTGCCGGTAGAATTGTATATGCATACAGCCAGCTAGCGATAACTATATTGGCGGCGCTGATGCGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGATATATCGGTAACTGTATATCATGGCCCGTGTATTTATTTTGCTTTTGGCGCCGCGCCGTGTTTAACCAGGTGGTAGTATGA
++
+$$&&'*.+,,**--(&'(&')&)0)*&**,*,0(*)&'&(%)**)&%(')-,,*,%)''()()*'*((*((&%+***.()(*+-,--(*'&''((%'*2.+3***:80).&)&)&('%%)%**.)25-(')&+--.41-25-.*+'&('*+,,+++-*('''./--('(&'&,'(&()+-&(+../1.-,../2278//1+*')&&&&&()0)&()/(++*.-03----+*,.,))))))*)**2-*+,*-/4+-('*.&(&+)*-.'&(+))+-*('*,-**-(*,5-,))(%*%&+01,*30.).(1))*%)'8*,0/0/1%&%'')))4,.'((*%('$&((')-.+.*&)'.)()('+%)&(+*-78+::/*:7+6.*--0220%'*+-*)&&&+)+*&,(*+0011,()&%'%)*+*'*%)%%(),,0('*''%'&'(%(()*,(,//,'(,1-&*''$,&').,12748<21-/*(*),(&&&),*(&&
+@3030a28d-1f16-4086-9ba1-ff31a97f434d runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12068 ch=399 start_time=2017-08-09T20:01:48Z
+ACGATAGCCTTAGATCGATCACGTATCATGCGGCATCGGCACTGGCGTGATAACGAAAACGTAATGAATTGACATATCGAAGCTCGGTGGGCCTAACTATGACATCGCAGGCATTAACGACCGAAATGTCACATTATCGATAAGCAAGAATCTCATCCCTAAAGAGAAGAGGCGGCGCTCGTGGGCGTCGGGGCGACGCTGAAGCGTGTCAGGCGGGAATTGCCAGAGAGAAATCCCATCGAAGCATCAAAATGATATAACATACTCGCCTAACTGGCGGACTCGAGAATATCGAGAACTGGTCATGTCATGCCCGAAAACCCGAAAATGTGAGCTCATCAAAGAATGGGCCGACGTCTTGAATATGAGCATCATGAAAAGCAAACTCGGTATGTTTCGGTAAGCTTCGGCCGTCAATATATCGGAAGCATCGCCGAAAAGAGAGCATA
++
+()*%)*&'&%&&'%-*+,,'#&)*..'()&(+,+)23'$(%')8*)+&'%%(*.(*.('&%&.'&*&&.)++)&'$',*)'%%&'''(&())+)'%%')&(%,),),9..86)4*.&-,+-2'()(&&&'&(&,()(''&$-.&*)'&)2*+$$%%%*-(,/)*,--)((-,5460())'&&)&'.-1/)-.-,($%%%$()(('&&%''(/-**-+'&,&('+(+*,-,.14/)5-$%*()'))'*)(,/*&%(()''&%')&))+*+(&&%'&)''('%&'&&)'+)+*+.++)''*((+-.*.)+*.0)()('*9;3-2''+.*-+-,*(''()%&'(')-'+*+*+2+.*0143.2*&+,'%'&*2240%'%+.01(*69.312,2.1.)%(&%'*)*)&')(&'&..11016(('%&)()'&&(%+,/30-156,&)&(&&&&%
+@310f7b48-a3e0-4cdc-b396-09f4b86081dd runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12113 ch=399 start_time=2017-08-09T20:02:08Z
+AACATTGTGCTTAGGTAGAGCGTAACTAATCTGAAAGCAGCGCGAGTGGTAAGCAGTATTTATCGCTAAATAATTCAGCGAGATTTACTCGCTCTCCGGCTCTGCTCGGCGTAATTGAAACAATAAGCGTCTCTGTTGAAGCTATTCTCTGTGTTGCTAATGTGGCAGCGATCGGCCGCTCAATTTCGCCAAAACTTGCGCTCAGTATTGCTGCCAGCACAAAACTGGGAGGCGAGAATGCCATGCTGGCGGCGTGTAATTTCGCTCGACTGTGATACGTAAATTGCATTAAAATGCTCATCGAGGGGCTTTGATATTTCAGGCATCTCGTCAATGTAATATGAAGAGAAGCCAGCGTGTTGCTCACCATTAACCATAACTTCTGTAAAGTACAATGACCGTAGATTTCTGGCGTCATCGCTGAAAGTAAACACCGACCATATGATATTTGCCAATGGTATTAACAATGCGTGCAATGCGAGGCGCAGCTTCTGTTGGTATGACGCATCAGGCAATCATCGGCCATCGTCATATCGGTCGTATGGTAGCGTAGAGCAGAAGCGGCTAGTAAATGCAAGTGCTCAAATTATACTCTAAATCGCTCATATCTATTTTACGCGCGATATTTCTTTAAATGTCCGGAGCCCGAAATGCCTGTGCTCTTGCGCCAGAACCTGATGCGGCGGCCATCGAGGCGGTGCTCGATGCTGCCAATCGTGCGAGCATGCTTGAAAACGTCTACTCGAAAGCTCTGACGCGTGTCAAAAGCTAAAGTATGTTTTTGTCGCATATTTCTCCGCGCCAG
++
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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/foo.farb	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,16 @@
+@aabaf035-7aa8-439b-8773-523c69a350ca runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12103 ch=399 start_time=2017-08-09T20:02:04Z
+ACTCATTTAGCCGCTAATTCGTGTGTGCTAATCCTAATGGCTTTTGAAAGTGAGTAAGCAAGTATTTTCTAATAAATAATGAAGCGAAAGTTATATCTCTCAACTCTACTCGGCGTAATTGCTGCTCAAGCATATTGGCTGTTATACTGTACTTGTACGTCGTTGTACTTCCTTTATAGAAGCACATGAAGTATTTACCAAGAACACCATTTGCTTTGAGTACTCACTCAAATTATCGGCGTCTAGAACAAGTAATGATATCGTAAATTCGCGAAGTACTCGTCGAAAGAGCTGTGCATTTCTGACATCTCTGTGTAATCTCGAAGATAACGTGAATGCTCGCAGTAACTCTCTAGTAATGTCAGAATTTCTGGCCAAATCGAAAATGCATAAAGTAAACAATATGATATTGCCAGCCATTAATATGAATGCATTATTAAATAACAGAAACTCGCCTGATATGATATTATCATTATTCGTCATATCGATTAAACCATAATCGAGCAGAAGCGTAGTCGGCCTGAAATTATATCGGGCCTTACTGGTATAAATAACTCATATTTTAAAACCGGCTGTTTAAATGGCCGACGTGCTTGCTCTTACTCGCGGCCATCAATCAGGCATCTTCATTATCAATCTGCAAATCATTGCTGAGCATGCGAAAACGTCTACTCGAAACCCGGCGACCAGTGAATCCGTATTTGTCGCGCAACTTTTCGACTCATAAATGATA
++
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
+@2dd21811-c9af-4c4a-aaa0-4fd1f605abf8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12153 ch=399 start_time=2017-08-09T20:02:16Z
+GCAGTAATATGAGCCAGTCATGTCCAACATAGGCGGCGTGAGTGAGCGAGATGGTACCTAAATTGAAGCATGATATTGGCGTAAATTGCCTGATGTATTCTGGCTGTCGTCAATGTGCTGATAAATTTAAAATTTAATGCCCGGCGCTATTATGCATAACATCGGCGCAATATTTTATATGCATAGCGAGAATATTTGATGAATGATATCGTGAGATGGCATGCTGTCTCTGGCGCTGAGAATGAAGCCTCTCATCATCATGTCATTTCAATGATAAATTTTAAATGGCGATAATTATTTAATTTGCCGGTAGAATTGTATATGCATACAGCCAGCTAGCGATAACTATATTGGCGGCGCTGATGCGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGATATATCGGTAACTGTATATCATGGCCCGTGTATTTATTTTGCTTTTGGCGCCGCGCCGTGTTTAACCAGGTGGTAGTATGA
++
+$$&&'*.+,,**--(&'(&')&)0)*&**,*,0(*)&'&(%)**)&%(')-,,*,%)''()()*'*((*((&%+***.()(*+-,--(*'&''((%'*2.+3***:80).&)&)&('%%)%**.)25-(')&+--.41-25-.*+'&('*+,,+++-*('''./--('(&'&,'(&()+-&(+../1.-,../2278//1+*')&&&&&()0)&()/(++*.-03----+*,.,))))))*)**2-*+,*-/4+-('*.&(&+)*-.'&(+))+-*('*,-**-(*,5-,))(%*%&+01,*30.).(1))*%)'8*,0/0/1%&%'')))4,.'((*%('$&((')-.+.*&)'.)()('+%)&(+*-78+::/*:7+6.*--0220%'*+-*)&&&+)+*&,(*+0011,()&%'%)*+*'*%)%%(),,0('*''%'&'(%(()*,(,//,'(,1-&*''$,&').,12748<21-/*(*),(&&&),*(&&
+@3030a28d-1f16-4086-9ba1-ff31a97f434d runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12068 ch=399 start_time=2017-08-09T20:01:48Z
+ACGATAGCCTTAGATCGATCACGTATCATGCGGCATCGGCACTGGCGTGATAACGAAAACGTAATGAATTGACATATCGAAGCTCGGTGGGCCTAACTATGACATCGCAGGCATTAACGACCGAAATGTCACATTATCGATAAGCAAGAATCTCATCCCTAAAGAGAAGAGGCGGCGCTCGTGGGCGTCGGGGCGACGCTGAAGCGTGTCAGGCGGGAATTGCCAGAGAGAAATCCCATCGAAGCATCAAAATGATATAACATACTCGCCTAACTGGCGGACTCGAGAATATCGAGAACTGGTCATGTCATGCCCGAAAACCCGAAAATGTGAGCTCATCAAAGAATGGGCCGACGTCTTGAATATGAGCATCATGAAAAGCAAACTCGGTATGTTTCGGTAAGCTTCGGCCGTCAATATATCGGAAGCATCGCCGAAAAGAGAGCATA
++
+()*%)*&'&%&&'%-*+,,'#&)*..'()&(+,+)23'$(%')8*)+&'%%(*.(*.('&%&.'&*&&.)++)&'$',*)'%%&'''(&())+)'%%')&(%,),),9..86)4*.&-,+-2'()(&&&'&(&,()(''&$-.&*)'&)2*+$$%%%*-(,/)*,--)((-,5460())'&&)&'.-1/)-.-,($%%%$()(('&&%''(/-**-+'&,&('+(+*,-,.14/)5-$%*()'))'*)(,/*&%(()''&%')&))+*+(&&%'&)''('%&'&&)'+)+*+.++)''*((+-.*.)+*.0)()('*9;3-2''+.*-+-,*(''()%&'(')-'+*+*+2+.*0143.2*&+,'%'&*2240%'%+.01(*69.312,2.1.)%(&%'*)*)&')(&'&..11016(('%&)()'&&(%+,/30-156,&)&(&&&&%
+@310f7b48-a3e0-4cdc-b396-09f4b86081dd runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12113 ch=399 start_time=2017-08-09T20:02:08Z
+AACATTGTGCTTAGGTAGAGCGTAACTAATCTGAAAGCAGCGCGAGTGGTAAGCAGTATTTATCGCTAAATAATTCAGCGAGATTTACTCGCTCTCCGGCTCTGCTCGGCGTAATTGAAACAATAAGCGTCTCTGTTGAAGCTATTCTCTGTGTTGCTAATGTGGCAGCGATCGGCCGCTCAATTTCGCCAAAACTTGCGCTCAGTATTGCTGCCAGCACAAAACTGGGAGGCGAGAATGCCATGCTGGCGGCGTGTAATTTCGCTCGACTGTGATACGTAAATTGCATTAAAATGCTCATCGAGGGGCTTTGATATTTCAGGCATCTCGTCAATGTAATATGAAGAGAAGCCAGCGTGTTGCTCACCATTAACCATAACTTCTGTAAAGTACAATGACCGTAGATTTCTGGCGTCATCGCTGAAAGTAAACACCGACCATATGATATTTGCCAATGGTATTAACAATGCGTGCAATGCGAGGCGCAGCTTCTGTTGGTATGACGCATCAGGCAATCATCGGCCATCGTCATATCGGTCGTATGGTAGCGTAGAGCAGAAGCGGCTAGTAAATGCAAGTGCTCAAATTATACTCTAAATCGCTCATATCTATTTTACGCGCGATATTTCTTTAAATGTCCGGAGCCCGAAATGCCTGTGCTCTTGCGCCAGAACCTGATGCGGCGGCCATCGAGGCGGTGCTCGATGCTGCCAATCGTGCGAGCATGCTTGAAAACGTCTACTCGAAAGCTCTGACGCGTGTCAAAAGCTAAAGTATGTTTTTGTCGCATATTTCTCCGCGCCAG
++
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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/configuration.cfg	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,43 @@
+[pipeline]
+basecall_type = linear
+min_qscore_1d = 7.0
+desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_raw_basecall_1d.jsn
+log_intermodule_messages = False
+
+[data_trimmer]
+ev_window = 20
+ev_threshold = 5
+min_events = 3
+delta = 2
+chunk_size_out = 0      # Use a nonzero value to chunk output
+
+[basecaller]
+model = template_r9.5_450bps_5mer_raw.jsn
+implementation = auto
+min_events = 100
+max_events = 10000
+overlap = 50
+min_quality = -10.0
+min_prob = 1e-5
+simple_decoding = 1
+homopolymer_correct = 0
+model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
+
+[call_handler]
+record_base = read
+qscore_adjuster_intercept = 1.5
+qscore_adjuster_slope = 1.5
+
+[barcode_detector]
+
+[fastq]
+identifier = {read_id}
+header = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
+header_with_barcoding = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
+batch_file_name = fastq_runid_{run_id}_{batch_counter}.{extension}
+single_file_name = {read_id}.{extension}
+all_file_name = fastq_runid_{run_id}.fastq
+
+[fast5]
+basecall_columns = mean,start,stdv,length,model_state,move,p_model_state,weights
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/pipeline.log	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,23 @@
+2018-06-18 10:19:54,951 ONT Albacore Sequencing Pipeline Software (version 2.0.2)
+2018-06-18 10:19:54,951 Debug level is 0
+2018-06-18 10:19:54,959 Selected config file /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/r95_450bps_linear.cfg to match flowcell FLO-MIN107 and kit SQK-LSK108
+2018-06-18 10:19:54,959 Using config file: layout_raw_basecall_1d.jsn
+2018-06-18 10:19:55,006 No option 'pipeline > min_qscore_1dsq' in the config, so using the default of 0.0
+2018-06-18 10:19:55,008 No option 'pipeline > min_qscore_1dsq' in the config, so using the default of 0.0
+2018-06-18 10:19:57,745 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5".
+2018-06-18 10:19:57,918 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5".
+2018-06-18 10:19:57,984 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5".
+2018-06-18 10:19:58,068 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5".
+2018-06-18 10:19:58,125 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5".
+2018-06-18 10:19:58,229 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5".
+2018-06-18 10:19:58,283 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5".
+2018-06-18 10:19:58,335 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5".
+2018-06-18 10:19:58,391 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5".
+2018-06-18 10:19:58,423 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5".
+2018-06-18 10:19:58,482 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5".
+2018-06-18 10:19:58,535 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5".
+2018-06-18 10:19:58,590 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5".
+2018-06-18 10:19:58,632 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5".
+2018-06-18 10:19:58,689 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5".
+2018-06-18 10:19:58,797 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5".
+2018-06-18 10:19:58,798 Done.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/sequencing_summary.txt	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,9 @@
+filename	read_id	run_id	channel	start_time	duration	num_events	passes_filtering	template_start	num_events_template	template_duration	num_called_template	sequence_length_template	mean_qscore_template	strand_score_template
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5	aabaf035-7aa8-439b-8773-523c69a350ca	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5212.72327	1.70734	1469	True	0.0	1469	1.70734	1469	733	7.02	-0.0014
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5	921ea44a-1215-4f98-9f38-bf36b1bdf69c	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5206.51394	1.57155	1352	False	0.0	1352	1.57155	1352	460	6.093	-0.0016
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5	15bdfe23-0646-4c89-b523-185bc14c3a2a	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5202.95983	2.90405	2484	False	0.01726	2484	2.88679	2484	1115	6.771	-0.0004
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5	28daae22-d0dc-4fee-8453-3a2178b331c8	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5230.13961	2.28967	1870	False	0.11604	1870	2.17364	1870	549	6.326	-0.0012
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5	2dd21811-c9af-4c4a-aaa0-4fd1f605abf8	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5224.53552	1.14675	943	True	0.04997	943	1.09678	943	495	8.086	-0.0018
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5	3030a28d-1f16-4086-9ba1-ff31a97f434d	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5196.22842	1.10525	907	True	0.05129	907	1.05395	907	449	7.436	-0.0024
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5	86fd3e14-b5ee-4453-98fa-084d75821456	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5208.88562	1.84645	1508	False	0.09329	1508	1.75315	1508	279	5.511	-0.0014
+macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5	310f7b48-a3e0-4cdc-b396-09f4b86081dd	d28f9f1c34b8f7416c367df1e0c4a864ba830c9c	399	5216.31192	1.84894	1591	True	0.0	1591	1.84894	1591	805	7.87	-0.0005
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/workspace/fail/fastq_runid_d28f9f1c34b8f7416c367df1e0c4a864ba830c9c_0.fastq	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,16 @@
+@921ea44a-1215-4f98-9f38-bf36b1bdf69c runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12085 ch=399 start_time=2017-08-09T20:01:58Z
+ACGCGGGTGTGGATCGATCCATGATGTCGAAACCTCATTCATGAGATCGTCAGAAATAGAATGTCAGACAGTATCAGATAATGACCGATGGCGTTAATGATGCGTCATCGAAGGAATCGAACCGTCGTCAATGAAGGCCAGGTCATCAGGAAATCTCAATCCAATAGTATGTTTTAGAATCACGAGTCCCGGTCCCGGGTCGATAAAGTCTTCGAACAATGAGCATTTATCGTCAGTGAAAGGCCCCTCGAGATGCTTGCTCAGGCCAATCAGGCCAATAATCAAAATTCTGCGATAGGCCTTCTCCGCTCCAGGCCATGTTCCCGATATTTTCAGTCATGCTCTCTTCGACAGGAATTAAAACTCAATCTTCTCAGTGAGAATGAGAATGCAGCTCCTGTCGAGAAAAATGTTGGGCTCCATCAAACATCGTTCTCCATGGCCATCAATAATAACAATA
++
+$&%%%*&'%&'(&,()'((%%$'%-+-.'&''*&&'&'%$&%&))'**&)(&((+*0+',&'$'&&&21&,../,)).,('&&&)&''(.('&'%&&)'%&&'()%''&''',+()))''&&#%&&%)')'%%((&+-0'+&&''&&&'(%%%)),,)++,(,(),%(*,'171&)'+,(*''(&&)/+))),-.))($)(%((&('%+')('&(&*--&)%)*+-4&$%&&-,'&'&))(**:51,'('&%'$$')&$$&%%'%%$)&'&&'$('*&'()'%+'')&(&&$('(*)'&)&&*&)&(%&'-&&$$&+()%'*)+('&''%&%%%%$&'&(%'),.*+'&&&,),))*)*))(&+)*(,,%**''''&+((*'(&&'&'&&%*(%%&('(%(%%'$''(-('&+**'&''(%)(&*)%&$&%%.+('%%%%$%%$%%%$%&%&&%%&$%%%
+@15bdfe23-0646-4c89-b523-185bc14c3a2a runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12081 ch=399 start_time=2017-08-09T20:01:54Z
+GCATTATATACATTCGTGCATGTCCTTAAAAGCGCTAATGAGAAATGAAATATTCAAATGAAGCAGAAGTATATGCTCTTCACTAATTGTGAGCTCATAAATGTAATGACTCAAACTATACTATGATCTTGATCATAACTTTGCTCTTTAATCGGCTATTTCTGAAACTTATGACTCGAACATTTATCAACCGTATTTCATTTGAAGTGAAATTATACGTAAGTGGCGCTGCTCAGGCGAAATATATAGCAAAATTCTAGAACTCGAGCACATTACATCGGCATTTGAGGCCGGAATGGCTGGGAAAACGTGCGTGGCATCTCCATCGGTATAATATGAAATGCGGCCGTGCTTCAGCCTGAAATGAAACACTGATGTCAGCCTTCCGCGTGATGAAATCACTTCGAGAATTTCAGCGATATTGAAGGCCTGCTATGAAACAAGCGTGCTCGACCATAAGTATAAATGGCATGAAGAGAAGAAATGAAGGTAATGGTACTCATCAATTATATCAAATGCTTCTATTCCGGCGCGATGGCCTCGATATGCATTGAAATAACTCTTCATCTCGAGGCTTTCGATCTCGGCGCGGAAGCTTGCATCGAAATCAATTATGCAAAATCGTCAGGCATACCGTCTTCGAAGCGCGTCAGAATCATCATTTTGCCTCACTTTTAATAAATGAAGGCTGTCGAGGGTAATATGACATCAACAACTAACAATGCTCTGCCGAATGGAGCCAAACGTAATGGCGTAATCTTCAGTATCGCGAGAAGGCGTCTTCGGCGAAGGCTGAGATAATAATCGAGGCATCACCAAGTAACTAATATTTTGAAATCAATGCTGAGTACAAATGCGCTGGAAATAAAGAAAACTTCTCAGCTAAATGAAAGTATAATTGGCGAATATAGGCTAATCTCATATGCATCATCATATAAATGTTTCTCAGCTCGCATAGGCGCTCGCAGTAACATCTCGCTTGGCAAAGTAATTCTGAATCTCTCATGTCAATATACAACCATACAAATGACGTCATCCTCTTGAAATCAATCATCTTGCAAAAGTCTTCATTATAATCCGAGTATCAAGAGTAACTCTCCAACAAGCCATCCCAG
++
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
+@28daae22-d0dc-4fee-8453-3a2178b331c8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12175 ch=399 start_time=2017-08-09T20:02:22Z
+ACAAATCATCTCGATCGATCTTTATCTGAATCAAACCAGCAATCGAATCGGAAACAGAATGATGTCGAAGATCGAATAATCAAATATCTATCATCTATCAGGCCAAAATGGCATCCTTATAAATGAGAATGTCGGCTGAATCGAAATATCGGAAATAATGAACAAAATAATCGCGCAATAAAGAGAATAAATTAATCAGCAAGAAACCAGCCCTTCAGCTCCGCTCGCCATAAAACCGCTTTCTTCAAAACAATAAAACAAAGCAAGCAATAAACAAAGCTCTTTACTCAAATCCCAAACAAATTACCTTTCTCCCCAGCCGAATAAAACGGCCAACCAGCTAATGCCGCAAATACCCCGGCATCGAAACAAGCAAAGCAGCCAATACTCACGGCCAAAGCCATATAAACAATAAGGCCAAACCATCACCGTCGGCAAATAACAATCAGGCTGCAGATAAACAATGCAAATACTGCCAATCAAGCAACATGTCACATAATACTGTCCGCTATGAGAGAGGCATACCCAGAAATGCTAAAATAAATATTT
++
+((')'*&'(('''&)-&)++-.(&'%&&*('&*('*')$%',*(()*)()''(*&''+0/)**&()**+)*''(&((')'.-.)('*)(')().,+++,&&&.)+--*&(&%',,%&$%&'*'$%'''(%$%&'&'%%&(('&(*'&'(',(./.*.('%)''('&+)+))&$&$&(')*0,')'+)((,&(%&%&'+%*)+&,,'(+''2*'&'((%&%(&&)*+$''&$&'+(-'&'&&'&''&+,2.-1&%&&'()02*%%'(%'&'%'.,*-1-&%&&,,'&(()')&+(&&)'&()*)'&&*((&&&%&120+-/8'&%%)22++',-(-$&&&%)((%&$(%$%&3/,&,.-(+',&&(%&*$&&%$%)*&$&%&2.3+'$')('*%&()(+0*64+&&(//*++(&&%&$%%')'%%+&%&(%$&'&&'%'&$''%*''%%*$&$$&('&'&('&&&$%('**)*((+--.'&&&&(**)**&%&%&'&%&&%&(%$$&''&&%&%+')((((('(%))**(())$$$$%&&'&',))')($
+@86fd3e14-b5ee-4453-98fa-084d75821456 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12091 ch=399 start_time=2017-08-09T20:02:00Z
+CTGATGGTCGATCAAGCCAAATAGTCGATGAATCATATCATCGAATCAGGCTCAAACAATCTCGAATAAAACAATCATCCATCTTTCTCGAATCAGCAACAATCTTATCAAAACAATCAAGCAATCAAAGCCACACAAAATAATAACAACTCTTTACTCGCCCAAACAAAATAACAAAGCAAGCAATAATAAACAAGCTCTGCTCCAGCCCTCAAGCTTTCAATAAAACCATGTAGAATGCCTCTTCCCTAGTCAAAGCCAGCAACAGACTATATTCAG
++
+%%&%&%'(*+%&%%%''*)+&&'&%$&&$$&&((&&('&%%&%(''%'$#&%%()'&0512-+((('*-''%(((&&&)(&)(*+*((,&,/$%'%&%$&('&&%%)'')24+%&&%%-)&)++*&&'($,+%%$$*/5,)($($$&%%%%%'(&'$$$$'())&$'()*(''$%&&&%&)(&'0+*)&&')&(),)*+)$$%%%(&'*)((&'')&&$$%%%%%&'*((&&$%'&&&%$%%&&..,-($(#&&&'+$%%&$$%&%&#&$%()'(,&&%
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/workspace/pass/fastq_runid_d28f9f1c34b8f7416c367df1e0c4a864ba830c9c_0.fastq	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,16 @@
+@aabaf035-7aa8-439b-8773-523c69a350ca runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12103 ch=399 start_time=2017-08-09T20:02:04Z
+ACTCATTTAGCCGCTAATTCGTGTGTGCTAATCCTAATGGCTTTTGAAAGTGAGTAAGCAAGTATTTTCTAATAAATAATGAAGCGAAAGTTATATCTCTCAACTCTACTCGGCGTAATTGCTGCTCAAGCATATTGGCTGTTATACTGTACTTGTACGTCGTTGTACTTCCTTTATAGAAGCACATGAAGTATTTACCAAGAACACCATTTGCTTTGAGTACTCACTCAAATTATCGGCGTCTAGAACAAGTAATGATATCGTAAATTCGCGAAGTACTCGTCGAAAGAGCTGTGCATTTCTGACATCTCTGTGTAATCTCGAAGATAACGTGAATGCTCGCAGTAACTCTCTAGTAATGTCAGAATTTCTGGCCAAATCGAAAATGCATAAAGTAAACAATATGATATTGCCAGCCATTAATATGAATGCATTATTAAATAACAGAAACTCGCCTGATATGATATTATCATTATTCGTCATATCGATTAAACCATAATCGAGCAGAAGCGTAGTCGGCCTGAAATTATATCGGGCCTTACTGGTATAAATAACTCATATTTTAAAACCGGCTGTTTAAATGGCCGACGTGCTTGCTCTTACTCGCGGCCATCAATCAGGCATCTTCATTATCAATCTGCAAATCATTGCTGAGCATGCGAAAACGTCTACTCGAAACCCGGCGACCAGTGAATCCGTATTTGTCGCGCAACTTTTCGACTCATAAATGATA
++
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
+@2dd21811-c9af-4c4a-aaa0-4fd1f605abf8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12153 ch=399 start_time=2017-08-09T20:02:16Z
+GCAGTAATATGAGCCAGTCATGTCCAACATAGGCGGCGTGAGTGAGCGAGATGGTACCTAAATTGAAGCATGATATTGGCGTAAATTGCCTGATGTATTCTGGCTGTCGTCAATGTGCTGATAAATTTAAAATTTAATGCCCGGCGCTATTATGCATAACATCGGCGCAATATTTTATATGCATAGCGAGAATATTTGATGAATGATATCGTGAGATGGCATGCTGTCTCTGGCGCTGAGAATGAAGCCTCTCATCATCATGTCATTTCAATGATAAATTTTAAATGGCGATAATTATTTAATTTGCCGGTAGAATTGTATATGCATACAGCCAGCTAGCGATAACTATATTGGCGGCGCTGATGCGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGATATATCGGTAACTGTATATCATGGCCCGTGTATTTATTTTGCTTTTGGCGCCGCGCCGTGTTTAACCAGGTGGTAGTATGA
++
+$$&&'*.+,,**--(&'(&')&)0)*&**,*,0(*)&'&(%)**)&%(')-,,*,%)''()()*'*((*((&%+***.()(*+-,--(*'&''((%'*2.+3***:80).&)&)&('%%)%**.)25-(')&+--.41-25-.*+'&('*+,,+++-*('''./--('(&'&,'(&()+-&(+../1.-,../2278//1+*')&&&&&()0)&()/(++*.-03----+*,.,))))))*)**2-*+,*-/4+-('*.&(&+)*-.'&(+))+-*('*,-**-(*,5-,))(%*%&+01,*30.).(1))*%)'8*,0/0/1%&%'')))4,.'((*%('$&((')-.+.*&)'.)()('+%)&(+*-78+::/*:7+6.*--0220%'*+-*)&&&+)+*&,(*+0011,()&%'%)*+*'*%)%%(),,0('*''%'&'(%(()*,(,//,'(,1-&*''$,&').,12748<21-/*(*),(&&&),*(&&
+@3030a28d-1f16-4086-9ba1-ff31a97f434d runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12068 ch=399 start_time=2017-08-09T20:01:48Z
+ACGATAGCCTTAGATCGATCACGTATCATGCGGCATCGGCACTGGCGTGATAACGAAAACGTAATGAATTGACATATCGAAGCTCGGTGGGCCTAACTATGACATCGCAGGCATTAACGACCGAAATGTCACATTATCGATAAGCAAGAATCTCATCCCTAAAGAGAAGAGGCGGCGCTCGTGGGCGTCGGGGCGACGCTGAAGCGTGTCAGGCGGGAATTGCCAGAGAGAAATCCCATCGAAGCATCAAAATGATATAACATACTCGCCTAACTGGCGGACTCGAGAATATCGAGAACTGGTCATGTCATGCCCGAAAACCCGAAAATGTGAGCTCATCAAAGAATGGGCCGACGTCTTGAATATGAGCATCATGAAAAGCAAACTCGGTATGTTTCGGTAAGCTTCGGCCGTCAATATATCGGAAGCATCGCCGAAAAGAGAGCATA
++
+()*%)*&'&%&&'%-*+,,'#&)*..'()&(+,+)23'$(%')8*)+&'%%(*.(*.('&%&.'&*&&.)++)&'$',*)'%%&'''(&())+)'%%')&(%,),),9..86)4*.&-,+-2'()(&&&'&(&,()(''&$-.&*)'&)2*+$$%%%*-(,/)*,--)((-,5460())'&&)&'.-1/)-.-,($%%%$()(('&&%''(/-**-+'&,&('+(+*,-,.14/)5-$%*()'))'*)(,/*&%(()''&%')&))+*+(&&%'&)''('%&'&&)'+)+*+.++)''*((+-.*.)+*.0)()('*9;3-2''+.*-+-,*(''()%&'(')-'+*+*+2+.*0143.2*&+,'%'&*2240%'%+.01(*69.312,2.1.)%(&%'*)*)&')(&'&..11016(('%&)()'&&(%+,/30-156,&)&(&&&&%
+@310f7b48-a3e0-4cdc-b396-09f4b86081dd runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12113 ch=399 start_time=2017-08-09T20:02:08Z
+AACATTGTGCTTAGGTAGAGCGTAACTAATCTGAAAGCAGCGCGAGTGGTAAGCAGTATTTATCGCTAAATAATTCAGCGAGATTTACTCGCTCTCCGGCTCTGCTCGGCGTAATTGAAACAATAAGCGTCTCTGTTGAAGCTATTCTCTGTGTTGCTAATGTGGCAGCGATCGGCCGCTCAATTTCGCCAAAACTTGCGCTCAGTATTGCTGCCAGCACAAAACTGGGAGGCGAGAATGCCATGCTGGCGGCGTGTAATTTCGCTCGACTGTGATACGTAAATTGCATTAAAATGCTCATCGAGGGGCTTTGATATTTCAGGCATCTCGTCAATGTAATATGAAGAGAAGCCAGCGTGTTGCTCACCATTAACCATAACTTCTGTAAAGTACAATGACCGTAGATTTCTGGCGTCATCGCTGAAAGTAAACACCGACCATATGATATTTGCCAATGGTATTAACAATGCGTGCAATGCGAGGCGCAGCTTCTGTTGGTATGACGCATCAGGCAATCATCGGCCATCGTCATATCGGTCGTATGGTAGCGTAGAGCAGAAGCGGCTAGTAAATGCAAGTGCTCAAATTATACTCTAAATCGCTCATATCTATTTTACGCGCGATATTTCTTTAAATGTCCGGAGCCCGAAATGCCTGTGCTCTTGCGCCAGAACCTGATGCGGCGGCCATCGAGGCGGTGCTCGATGCTGCCAATCGTGCGAGCATGCTTGAAAACGTCTACTCGAAAGCTCTGACGCGTGTCAAAAGCTAAAGTATGTTTTTGTCGCATATTTCTCCGCGCCAG
++
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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_data_nofilt.fastq	Mon Jun 18 12:20:28 2018 -0400
@@ -0,0 +1,32 @@
+@aabaf035-7aa8-439b-8773-523c69a350ca runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12103 ch=399 start_time=2017-08-09T20:02:04Z
+ACTCATTTAGCCGCTAATTCGTGTGTGCTAATCCTAATGGCTTTTGAAAGTGAGTAAGCAAGTATTTTCTAATAAATAATGAAGCGAAAGTTATATCTCTCAACTCTACTCGGCGTAATTGCTGCTCAAGCATATTGGCTGTTATACTGTACTTGTACGTCGTTGTACTTCCTTTATAGAAGCACATGAAGTATTTACCAAGAACACCATTTGCTTTGAGTACTCACTCAAATTATCGGCGTCTAGAACAAGTAATGATATCGTAAATTCGCGAAGTACTCGTCGAAAGAGCTGTGCATTTCTGACATCTCTGTGTAATCTCGAAGATAACGTGAATGCTCGCAGTAACTCTCTAGTAATGTCAGAATTTCTGGCCAAATCGAAAATGCATAAAGTAAACAATATGATATTGCCAGCCATTAATATGAATGCATTATTAAATAACAGAAACTCGCCTGATATGATATTATCATTATTCGTCATATCGATTAAACCATAATCGAGCAGAAGCGTAGTCGGCCTGAAATTATATCGGGCCTTACTGGTATAAATAACTCATATTTTAAAACCGGCTGTTTAAATGGCCGACGTGCTTGCTCTTACTCGCGGCCATCAATCAGGCATCTTCATTATCAATCTGCAAATCATTGCTGAGCATGCGAAAACGTCTACTCGAAACCCGGCGACCAGTGAATCCGTATTTGTCGCGCAACTTTTCGACTCATAAATGATA
++
+%%'%$).&&+2+()+**3+''+%&%+%%'&*,()',((),&%''%&%)*&%&(').7,-*/..-/4.+%+'('-20,1*+)+/*))+-,'*'(/..,+)*')3...-+)-+)*((++),&('&()&',*()%&%$$&(((*-*''&&&'&%%&%%(%&&('&+'(($)''+'.2(%)&*'(%&%&#%%%%%*&)'&%&%'(&(&'&(*&*0*&%%%$&'%)'(&%'$''''$%%%%&'&$$%#'*%1(+()%%)**'+0.01&)(,*)+*)()+1%+*,-.*''&.0(((,,0/--0-42)'(*)0+100-*()&+)'(*/+&.)&(+)%,)*&((*%%(,).,(.)(%&%&%),$&'''%()*0&1(49,(%))+&)''(&()*-)''%((02,14(&&('('&&'*')*'*)('1201.1,(('')()*.-22,.2*/-)*&()%*(&(*/*-+'&%&&&&*(*81--)))(%%&%,02-,++.+$+((,-)'*'*(*''('+(&(&&'%&(%)',)1*,(+)&''((&&&'()+(('%''%&%((+,*%(&$''%(&058*)(('(()*''%)*(+2//(,0.*%$'%%&)''*)+5/+)('&&-(4**((*(&&'*3/0/,*)%().-/0-,+''%&(+*'%&1''&%&'$'(&%&(-40'.-)*)'%&'()-+*.''%'&'*&(%+&(*)'&%&$*./*-/((%)*'*047-*(,/70&(((&'%$'&
+@921ea44a-1215-4f98-9f38-bf36b1bdf69c runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12085 ch=399 start_time=2017-08-09T20:01:58Z
+ACGCGGGTGTGGATCGATCCATGATGTCGAAACCTCATTCATGAGATCGTCAGAAATAGAATGTCAGACAGTATCAGATAATGACCGATGGCGTTAATGATGCGTCATCGAAGGAATCGAACCGTCGTCAATGAAGGCCAGGTCATCAGGAAATCTCAATCCAATAGTATGTTTTAGAATCACGAGTCCCGGTCCCGGGTCGATAAAGTCTTCGAACAATGAGCATTTATCGTCAGTGAAAGGCCCCTCGAGATGCTTGCTCAGGCCAATCAGGCCAATAATCAAAATTCTGCGATAGGCCTTCTCCGCTCCAGGCCATGTTCCCGATATTTTCAGTCATGCTCTCTTCGACAGGAATTAAAACTCAATCTTCTCAGTGAGAATGAGAATGCAGCTCCTGTCGAGAAAAATGTTGGGCTCCATCAAACATCGTTCTCCATGGCCATCAATAATAACAATA
++
+$&%%%*&'%&'(&,()'((%%$'%-+-.'&''*&&'&'%$&%&))'**&)(&((+*0+',&'$'&&&21&,../,)).,('&&&)&''(.('&'%&&)'%&&'()%''&''',+()))''&&#%&&%)')'%%((&+-0'+&&''&&&'(%%%)),,)++,(,(),%(*,'171&)'+,(*''(&&)/+))),-.))($)(%((&('%+')('&(&*--&)%)*+-4&$%&&-,'&'&))(**:51,'('&%'$$')&$$&%%'%%$)&'&&'$('*&'()'%+'')&(&&$('(*)'&)&&*&)&(%&'-&&$$&+()%'*)+('&''%&%%%%$&'&(%'),.*+'&&&,),))*)*))(&+)*(,,%**''''&+((*'(&&'&'&&%*(%%&('(%(%%'$''(-('&+**'&''(%)(&*)%&$&%%.+('%%%%$%%$%%%$%&%&&%%&$%%%
+@15bdfe23-0646-4c89-b523-185bc14c3a2a runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12081 ch=399 start_time=2017-08-09T20:01:54Z
+GCATTATATACATTCGTGCATGTCCTTAAAAGCGCTAATGAGAAATGAAATATTCAAATGAAGCAGAAGTATATGCTCTTCACTAATTGTGAGCTCATAAATGTAATGACTCAAACTATACTATGATCTTGATCATAACTTTGCTCTTTAATCGGCTATTTCTGAAACTTATGACTCGAACATTTATCAACCGTATTTCATTTGAAGTGAAATTATACGTAAGTGGCGCTGCTCAGGCGAAATATATAGCAAAATTCTAGAACTCGAGCACATTACATCGGCATTTGAGGCCGGAATGGCTGGGAAAACGTGCGTGGCATCTCCATCGGTATAATATGAAATGCGGCCGTGCTTCAGCCTGAAATGAAACACTGATGTCAGCCTTCCGCGTGATGAAATCACTTCGAGAATTTCAGCGATATTGAAGGCCTGCTATGAAACAAGCGTGCTCGACCATAAGTATAAATGGCATGAAGAGAAGAAATGAAGGTAATGGTACTCATCAATTATATCAAATGCTTCTATTCCGGCGCGATGGCCTCGATATGCATTGAAATAACTCTTCATCTCGAGGCTTTCGATCTCGGCGCGGAAGCTTGCATCGAAATCAATTATGCAAAATCGTCAGGCATACCGTCTTCGAAGCGCGTCAGAATCATCATTTTGCCTCACTTTTAATAAATGAAGGCTGTCGAGGGTAATATGACATCAACAACTAACAATGCTCTGCCGAATGGAGCCAAACGTAATGGCGTAATCTTCAGTATCGCGAGAAGGCGTCTTCGGCGAAGGCTGAGATAATAATCGAGGCATCACCAAGTAACTAATATTTTGAAATCAATGCTGAGTACAAATGCGCTGGAAATAAAGAAAACTTCTCAGCTAAATGAAAGTATAATTGGCGAATATAGGCTAATCTCATATGCATCATCATATAAATGTTTCTCAGCTCGCATAGGCGCTCGCAGTAACATCTCGCTTGGCAAAGTAATTCTGAATCTCTCATGTCAATATACAACCATACAAATGACGTCATCCTCTTGAAATCAATCATCTTGCAAAAGTCTTCATTATAATCCGAGTATCAAGAGTAACTCTCCAACAAGCCATCCCAG
++
+$*(.*,+)+()42,,&,%&)0--)')'&&%%$&$&(+-***(**&$''&&'&**%(,(&&('&&(&,)&(&)))&&('*&%'%%/14.)(('&'(**)*0-)&''(.*((.(*/)((*()))(&$)-*-,)')'&&&&&'--&(.,,1(+-//-843,5:.,+(((%(3/-.*/-:8*(&%%)('%)*+'/+&(&&')'$(*((,*)''(-,,-+**'%'$$&%)-'$$)$%&'&('+(()0)..-(('(+1/**+'*(&*&(/30.$%'&&)*'((**(&*))0)(%(&'%(('&'''$%&),++'$&&'..,*'')')*+,)*30)'/*'*)('$&''&*&%''&&)(%'(*((%&'&%&('&'*-**&&&&%&%''%++&-)+((++'()(%--(+*$(,('&)')',,()'(/)+%#''%((**+/'%%$%$%,*'%'&&'&($%&%'%(&''--%&&%&11--,)%&*+,))&,-%.15-)(('&'(+&$%&%))-+1++,-,(*&('(,*(&&%(')'-/+&('('''*)''+&&&++1,+$((/.-16-'(&')&)*''(&(&'&('''+*&&'.*+))((&'))'(&%$%%)(('%((''')*((''$'%'(.+2+-+''''''%$%%%'&&&&)'&(+(')&'&(%()*+(&*46/&+,)+%&('(&)'&,.)&('()&%)%)&&&*($(&)&'%'%*(+(&%%'%'%*)'*-*&&++*&)&'())0/((*&,-%&$%'+-1+*&%%&&+++'%$%'%&)),)&(&%%%%'&*,(&')+,)((('+(%'(&(')(((,&,)0054*.*-)%&'&&'(&()384,*)))-',*('(%&%$&$%&*('&%$$'(&)*+/241'**-*&)')()()-,*0()$*-+*+0-./2-0(%(((.('&%$$%)(()+,))'&$))+.&(*'(%'%((*(5?5211(&**,%()'(''''((*%%&%%%$&&'&'(&&'%)&'*0*(*)'&'&&&(+)+()&))+&(%(')&'&'))-,'*'&&)(('''&((()))*''&%-+1*(&%)'&*)'*&&'1,*$&%+,/&))),-4,0*+%$%&%'('&'&')+/12/0--*&+*$&%(-.,)(&
+@28daae22-d0dc-4fee-8453-3a2178b331c8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12175 ch=399 start_time=2017-08-09T20:02:22Z
+ACAAATCATCTCGATCGATCTTTATCTGAATCAAACCAGCAATCGAATCGGAAACAGAATGATGTCGAAGATCGAATAATCAAATATCTATCATCTATCAGGCCAAAATGGCATCCTTATAAATGAGAATGTCGGCTGAATCGAAATATCGGAAATAATGAACAAAATAATCGCGCAATAAAGAGAATAAATTAATCAGCAAGAAACCAGCCCTTCAGCTCCGCTCGCCATAAAACCGCTTTCTTCAAAACAATAAAACAAAGCAAGCAATAAACAAAGCTCTTTACTCAAATCCCAAACAAATTACCTTTCTCCCCAGCCGAATAAAACGGCCAACCAGCTAATGCCGCAAATACCCCGGCATCGAAACAAGCAAAGCAGCCAATACTCACGGCCAAAGCCATATAAACAATAAGGCCAAACCATCACCGTCGGCAAATAACAATCAGGCTGCAGATAAACAATGCAAATACTGCCAATCAAGCAACATGTCACATAATACTGTCCGCTATGAGAGAGGCATACCCAGAAATGCTAAAATAAATATTT
++
+((')'*&'(('''&)-&)++-.(&'%&&*('&*('*')$%',*(()*)()''(*&''+0/)**&()**+)*''(&((')'.-.)('*)(')().,+++,&&&.)+--*&(&%',,%&$%&'*'$%'''(%$%&'&'%%&(('&(*'&'(',(./.*.('%)''('&+)+))&$&$&(')*0,')'+)((,&(%&%&'+%*)+&,,'(+''2*'&'((%&%(&&)*+$''&$&'+(-'&'&&'&''&+,2.-1&%&&'()02*%%'(%'&'%'.,*-1-&%&&,,'&(()')&+(&&)'&()*)'&&*((&&&%&120+-/8'&%%)22++',-(-$&&&%)((%&$(%$%&3/,&,.-(+',&&(%&*$&&%$%)*&$&%&2.3+'$')('*%&()(+0*64+&&(//*++(&&%&$%%')'%%+&%&(%$&'&&'%'&$''%*''%%*$&$$&('&'&('&&&$%('**)*((+--.'&&&&(**)**&%&%&'&%&&%&(%$$&''&&%&%+')((((('(%))**(())$$$$%&&'&',))')($
+@2dd21811-c9af-4c4a-aaa0-4fd1f605abf8 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12153 ch=399 start_time=2017-08-09T20:02:16Z
+GCAGTAATATGAGCCAGTCATGTCCAACATAGGCGGCGTGAGTGAGCGAGATGGTACCTAAATTGAAGCATGATATTGGCGTAAATTGCCTGATGTATTCTGGCTGTCGTCAATGTGCTGATAAATTTAAAATTTAATGCCCGGCGCTATTATGCATAACATCGGCGCAATATTTTATATGCATAGCGAGAATATTTGATGAATGATATCGTGAGATGGCATGCTGTCTCTGGCGCTGAGAATGAAGCCTCTCATCATCATGTCATTTCAATGATAAATTTTAAATGGCGATAATTATTTAATTTGCCGGTAGAATTGTATATGCATACAGCCAGCTAGCGATAACTATATTGGCGGCGCTGATGCGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGATATATCGGTAACTGTATATCATGGCCCGTGTATTTATTTTGCTTTTGGCGCCGCGCCGTGTTTAACCAGGTGGTAGTATGA
++
+$$&&'*.+,,**--(&'(&')&)0)*&**,*,0(*)&'&(%)**)&%(')-,,*,%)''()()*'*((*((&%+***.()(*+-,--(*'&''((%'*2.+3***:80).&)&)&('%%)%**.)25-(')&+--.41-25-.*+'&('*+,,+++-*('''./--('(&'&,'(&()+-&(+../1.-,../2278//1+*')&&&&&()0)&()/(++*.-03----+*,.,))))))*)**2-*+,*-/4+-('*.&(&+)*-.'&(+))+-*('*,-**-(*,5-,))(%*%&+01,*30.).(1))*%)'8*,0/0/1%&%'')))4,.'((*%('$&((')-.+.*&)'.)()('+%)&(+*-78+::/*:7+6.*--0220%'*+-*)&&&+)+*&,(*+0011,()&%'%)*+*'*%)%%(),,0('*''%'&'(%(()*,(,//,'(,1-&*''$,&').,12748<21-/*(*),(&&&),*(&&
+@3030a28d-1f16-4086-9ba1-ff31a97f434d runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12068 ch=399 start_time=2017-08-09T20:01:48Z
+ACGATAGCCTTAGATCGATCACGTATCATGCGGCATCGGCACTGGCGTGATAACGAAAACGTAATGAATTGACATATCGAAGCTCGGTGGGCCTAACTATGACATCGCAGGCATTAACGACCGAAATGTCACATTATCGATAAGCAAGAATCTCATCCCTAAAGAGAAGAGGCGGCGCTCGTGGGCGTCGGGGCGACGCTGAAGCGTGTCAGGCGGGAATTGCCAGAGAGAAATCCCATCGAAGCATCAAAATGATATAACATACTCGCCTAACTGGCGGACTCGAGAATATCGAGAACTGGTCATGTCATGCCCGAAAACCCGAAAATGTGAGCTCATCAAAGAATGGGCCGACGTCTTGAATATGAGCATCATGAAAAGCAAACTCGGTATGTTTCGGTAAGCTTCGGCCGTCAATATATCGGAAGCATCGCCGAAAAGAGAGCATA
++
+()*%)*&'&%&&'%-*+,,'#&)*..'()&(+,+)23'$(%')8*)+&'%%(*.(*.('&%&.'&*&&.)++)&'$',*)'%%&'''(&())+)'%%')&(%,),),9..86)4*.&-,+-2'()(&&&'&(&,()(''&$-.&*)'&)2*+$$%%%*-(,/)*,--)((-,5460())'&&)&'.-1/)-.-,($%%%$()(('&&%''(/-**-+'&,&('+(+*,-,.14/)5-$%*()'))'*)(,/*&%(()''&%')&))+*+(&&%'&)''('%&'&&)'+)+*+.++)''*((+-.*.)+*.0)()('*9;3-2''+.*-+-,*(''()%&'(')-'+*+*+2+.*0143.2*&+,'%'&*2240%'%+.01(*69.312,2.1.)%(&%'*)*)&')(&'&..11016(('%&)()'&&(%+,/30-156,&)&(&&&&%
+@86fd3e14-b5ee-4453-98fa-084d75821456 runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12091 ch=399 start_time=2017-08-09T20:02:00Z
+CTGATGGTCGATCAAGCCAAATAGTCGATGAATCATATCATCGAATCAGGCTCAAACAATCTCGAATAAAACAATCATCCATCTTTCTCGAATCAGCAACAATCTTATCAAAACAATCAAGCAATCAAAGCCACACAAAATAATAACAACTCTTTACTCGCCCAAACAAAATAACAAAGCAAGCAATAATAAACAAGCTCTGCTCCAGCCCTCAAGCTTTCAATAAAACCATGTAGAATGCCTCTTCCCTAGTCAAAGCCAGCAACAGACTATATTCAG
++
+%%&%&%'(*+%&%%%''*)+&&'&%$&&$$&&((&&('&%%&%(''%'$#&%%()'&0512-+((('*-''%(((&&&)(&)(*+*((,&,/$%'%&%$&('&&%%)'')24+%&&%%-)&)++*&&'($,+%%$$*/5,)($($$&%%%%%'(&'$$$$'())&$'()*(''$%&&&%&)(&'0+*)&&')&(),)*+)$$%%%(&'*)((&'')&&$$%%%%%&'*((&&$%'&&&%$%%&&..,-($(#&&&'+$%%&$$%&%&#&$%()'(,&&%
+@310f7b48-a3e0-4cdc-b396-09f4b86081dd runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12113 ch=399 start_time=2017-08-09T20:02:08Z
+AACATTGTGCTTAGGTAGAGCGTAACTAATCTGAAAGCAGCGCGAGTGGTAAGCAGTATTTATCGCTAAATAATTCAGCGAGATTTACTCGCTCTCCGGCTCTGCTCGGCGTAATTGAAACAATAAGCGTCTCTGTTGAAGCTATTCTCTGTGTTGCTAATGTGGCAGCGATCGGCCGCTCAATTTCGCCAAAACTTGCGCTCAGTATTGCTGCCAGCACAAAACTGGGAGGCGAGAATGCCATGCTGGCGGCGTGTAATTTCGCTCGACTGTGATACGTAAATTGCATTAAAATGCTCATCGAGGGGCTTTGATATTTCAGGCATCTCGTCAATGTAATATGAAGAGAAGCCAGCGTGTTGCTCACCATTAACCATAACTTCTGTAAAGTACAATGACCGTAGATTTCTGGCGTCATCGCTGAAAGTAAACACCGACCATATGATATTTGCCAATGGTATTAACAATGCGTGCAATGCGAGGCGCAGCTTCTGTTGGTATGACGCATCAGGCAATCATCGGCCATCGTCATATCGGTCGTATGGTAGCGTAGAGCAGAAGCGGCTAGTAAATGCAAGTGCTCAAATTATACTCTAAATCGCTCATATCTATTTTACGCGCGATATTTCTTTAAATGTCCGGAGCCCGAAATGCCTGTGCTCTTGCGCCAGAACCTGATGCGGCGGCCATCGAGGCGGTGCTCGATGCTGCCAATCGTGCGAGCATGCTTGAAAACGTCTACTCGAAAGCTCTGACGCGTGTCAAAAGCTAAAGTATGTTTTTGTCGCATATTTCTCCGCGCCAG
++
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