Open Will19902225 opened 7 months ago
visze
commented
7 months ago Hi,
Looks like no PE reads could be merged in the step PE_merge because counting of the merged reads is zero. Can you give me an example from the forward and reverse reads (e.g. the first 10 reads)?
I recommend to make sure that the input of MPRAflow is correct. Also the command with some example files will help to understand you issue.
Will19902225
commented
7 months ago Hi,
Thanks for your help. Here is a box link which you can download the raw reads data, R1, R2, R3. https://app.box.com/s/0l4tifwjzkdngtr96g82a3t030ihao41
Could you please take a look of these data? And if the data is not good, what can we do to fix it?
Thanks!
From: Max @.***> Sent: Sunday, February 25, 2024 2:10 AM To: shendurelab/MPRAflow Cc: Gao, Junfeng; Author Subject: ⚠ EXTERNAL: Re: [shendurelab/MPRAflow] map_element_barcodes (assign) [100%] 1 of 1, failed: 1 ✘ (Issue #81)
Hi,
Looks like no PE reads could be merged in the step PE_merge because counting of the merged reads is zero. Can you give me an example from the forward and reverse reads (e.g. the first 10 reads)?
I recommend to make sure that the input of MPRAflow is correct. Also the command with some example files will help to understand you issue.
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Will19902225
commented
6 months ago Hi,
Looks like no PE reads could be merged in the step PE_merge because counting of the merged reads is zero. Can you give me an example from the forward and reverse reads (e.g. the first 10 reads)?
I recommend to make sure that the input of MPRAflow is correct. Also the command with some example files will help to understand you issue.
Hi,
The R1 reads first 10 reads
@M01416:220:000000000-DN9DG:1:1101:17453:1773 1:N:0:TAGATCGC
TGGTTGCAAGGGACCGTCGACCTGAGGAGATCGGAAGAGCACACGTCTGATCTCCAGTCTCTTCTTGTTTTTTTTTTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTT
+
1>A>AAC1BFAAACAEAAEEAEEHG0FFCCGHFC?/ECFFFHFHGHHGE12DFF111D111221D111100B/>/>//>/<///0?1112??111//>A-----;---99--9-;------9-------9///9//--------;------99@@@?;---9-9--;-9--------;--@--=//9///------------;-@-9@@@--@-@---99-@?=@-99--9-=@@-@@
@M01416:220:000000000-DN9DG:1:1101:12921:1774 1:N:0:TAGATCGC
TCGAAATGAGGGAGGTTGGTCGCCGCAGATCGGAAGAAGCACACGTCTGATCTCCAGTCACCACTATTGTGTTTTTTTTTTTTGCTCTTCTTTCTTCTTTTCTTTTTTTTTTTTTTCTTTTTTTTTTCTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTGTTTTTTTTTTTT
+
3>A?AAAFFDB?2FC2FGEEEEEEEEECEGHHGGGCAGHHHHFFCGHFF55BF5FF3D33533?B3555B4?3B2B//>/////1B11112B12212BB11211?11/
3AAACB5FAFFGGGG?AEEFGHFHFHHGFDF?2FGGHHGHHHGHHHGHFCF5BA3D33D331B?35553B1B1F//>////?3B443BBF211/0BB11211?11//>-->-/00000=///.---;/-.;..00----9/;///;FF///;////.//;-///9;////////;--9---------//////.///////9-99-B//;/B////;/;@-;-9BF///--;-;= @M01416:220:000000000-DN9DG:1:1101:14363:1798 1:N:0:TTGATCGC TAAGTTGGGGACACACAAGCATCAAGGATACCCCTCACACTCCCCATCCTCCCTGCTCCGTTTCCTATTTTGTTTTTTTTTGCCTCTGTTTTTTTTTTGTTTTTTTTTTTTTATTCTTTTTTCCGTCCTCTTTCCTCTCTTTTTTTTTTTCTTCCTTTTCTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTCTTCTTTTTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTT + 1>>AAFF1>AADAF1EEFFCGGHHHBCH11GHF0AAFC1BBBGAEFGFHHGG/A1AF11//BAA212212220>0BF/>///1111B122B0/>EE/>/B0?0////-->-<.<00=000:-/0.<...00;00000;/00000-;-;@-//;///;9F/;/BFB-;;------9/;/BF/@---;@@--;9-;--/:B////9/-@----;-9-///9/99/;9///----@----- @M01416:220:000000000-DN9DG:1:1101:12672:1800 1:N:0:TTGATCGC TAACTCCAGTCACCACTAGAGGGTATATAATGGAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGTGCAATGTTTTTTTTTCTCTTTTCTTTTTTTTATTTTCTTTTTTTTCTGTCTGTTCTTCTTCATGTTTTGTTTTTGTTTTGTGCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT + 3>AAF4FCD4FFFGGF4F4GFCEGHFHGHFFDGBGCFGEEGEGHHF5FGHGEEF3F3210AEAFBF55555AD55210//>344B444444443/>//44?4444443///01222211@2211?111@11?1000000.-00000001100000--;-;--;-@=---;-;@-;--;B-9999---=9=?=?>@B?-;9>BBB>BBB??B;>=??@BB?=-;9;@?>;?BB?;@ @M01416:220:000000000-DN9DG:1:1101:15759:1815 1:N:0:TTGATCGC GTCGGAAACGGCGGCTCGGCGCGCAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTCTTGTGGGTTTTTTTTTTTAGCTCGACTTCTTTCTTTGCAATTTTTTTTTGTGCAATGTTTTTTCTTCGCTATGCTTTAGTTTTGTACCGCATTGTTCGTTTCGGTTGTCTCCTTTGTGTTTTTGGGTTTGGTTCCTTGTTTGTTTTCGTTTTCCTTTTTCTTTTTTTTTTTATTT + 1>>AAD1DFA1@CEGECEEGGAEC/EEF0FGFE/BEGCFG0FFEFHHGBB1GFHHHH11FF1BG1111/<?/?/<//>//>?<1?1<-><C111=1>G00000=0000<--:-9/00000;00/.-/0;0..;..;0000///;//-;///----9/;//-;/-/--;---/////;//;-9/-----------9-///////-/9;--/-;/;-///;/BB/9;/9;-------/// @M01416:220:000000000-DN9DG:1:1101:14344:1820 1:N:0:TTGATCGC
There are such instances in the remaining reads in R1 @M01416:220:000000000-DN9DG:1:1101:13255:1910 1:N:0:TAGATCGC CAAACAAACAAGCCTAAAATTTCCCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATATAATGGAAGCTCGACTTCCAGCTTGGCATTCCTTTACTGTGCAAAGTGAATACATCGCTAAGCGAAAGCTAAGTGTAGACGCGCTTAGACCGGTCGCCACCATGGTGTGCAAGGGCGAGGAGCCGAGGCTGATCTCGTATGCCGTCTTCTGCTTGTTAAAAA + BBBABFB??CAFFFF4FGDGGGHHHHHHHHHHFAGEGGHFHHCHHEGHHFHHHHGHHHHDGHFHAGHHFGFGE335D55D5FGHHGHHC//EFEB3FGHH3EHH3B4@44B3BEEGHHFHD3FB444BBDGBEEHG/3EB?//<0BDGHHHHH12DD@CCGGDB<G<<@C@-<<....:0/C:.;:0CCE.E---9-A.99-A?=EF.9//;.A.9///-ABFE;FFFFFF.////// @M01416:220:000000000-DN9DG:1:1101:14322:1910 1:N:0:TTGATCGC GACATACGAACCACTCGCTGATGCCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATATATTGTAAGCTCGACTTCCAGCTTGGCAATCCTGTTCTGTGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGCCAATCAATTTGGAAACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGCCGAGGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA +
AABAFFFAADBGGGCFGGGGGHBGGGFEFHFEECG2GCHGHHGHFHGHEFHFHHHHHFHHHGHHHDFGEEHHDF44B444@FFEHGG?EG4FGFFHHHGHHHH3243B3BBFFHHHHHHHHBGFFHEHH?EGGDHECD/B/<<F1CGHGGHHHHHHHFGEFF0FD---ACFGGCGFFBGHB./0CGEDAG?D--9C9B?DAFF..9/;BAEDFFFF-ADFFFFFFEFEF/9/99-9- @M01416:220:000000000-DN9DG:1:1101:12058:1914 1:N:0:TAGATCGC GGATCTATCAGTTTGCCTCCTTCAGCAATCGGAAGAGCACACGTCTGAATTCGAGTCACCACTAGAGGGTATATATTTTTTGCTCGACTTCCATCTTGGCTATCTGTTTCTGTGCAAAGTTTACACTTCGCTAAGCGAATGCTAATTTAAAATTAAATCTTTCCGGTCGCCACCATTTTTTGCAAGTTCGTGGAGCCTTTGCTGATTTCGTATCTTTTCTTCTGTTAGAAATTTTTTA + A@BBAFFFD55DGFFBGEE4GDFGGFGFGFEEG22B22B2BAEEGF25F5DG2BBFGFF3BABC333G1AFEBD55F5550>3FE1>EEE4334BFGF3B33BF444B44B4@B?4?3BB44B4433BBFDE//33<//11F221?2@211F1>122>22@1//AC/<...<.>11>1--00=0000<.....:C/000;00000<9F.//.000;0;C0;00=0000000000-. @M01416:220:000000000-DN9DG:1:1101:16586:1915 1:N:0:TAGATCGC CTGGAAGTTAGAAGGAAACAGACCACAGACCTGGTCCCCAAAAGAAATGGAGGCAATAGGTTTTGAGGGGCATTGTGTCGGGGTTCAGCTTCCAGTGTCCTACACACATATCAGTCAGTGTCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGCTGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTTTCCCCAACTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC + ?AA>CCCFFFF5GGA44BGFGCA4ECG4FDCHFEDB2FF2BGF223FGF32AEF1FFBFHFHGF1AGGGCCC33@5251/>?EEHFHH4B3@3B43B44GHHG03//33B4BFBFG?4F?4F?3F/B?BFFG?@/BA<AA/F1??/<CHHH?.A-.<.<.-.:CCFC0G..C::G00CF0BF0000BFFF//900999.CFB9CBB99.A?D..9;.B.-;.B;///;/9B/;BBB/ @M01416:220:000000000-DN9DG:1:1101:15876:1919 1:N:0:TAGATCGC GCCTAGAGCTGTGTCCATAGCCACCTGTCAAGAGGTCGAGTCAAGTCACTGTGAAAACTAAAAGTCCACAGTGCCATCTCGAGTGGAAAGTTATCCCCTCGCAGTGTGTCTTAGAAACTCCCCCAGCCCTGCTCTGTCTGGGCTGCTGTGTGGTCAGAGGTGACGCAGGCACCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATATAATGGAAGCTCGACTT + AABBBFFF5BC5FGCGGGGFGFFFGFGHHHBB4FGHHEGGHHHHF5GBF5G5DG5FBEBG3F3GAFBGFGG3F5B5F3FACGEG1AGHE1D5@F5@GFFGCEEE13B31BF4B@G4FG3?FG/EC/AAEGHHFBEFHHFGBHAG//FG1BGHD0DD0D1/<?DFD?C/A?HGF0FCGB.......//./<<..C:00:<CCH/;000;0C//900B?DFF000;;B0F0F?009;BGA @M01416:220:000000000-DN9DG:1:1101:12308:1920 1:N:0:TAGATCGC AGGTTATAGCATAACGATTGCGGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATATAATTGAAGCTCGACTTCCAGCTTGGCAATCCTTTACTGTGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGCTAGCGCAAGAACTGACCGGTCGCCACCATGTTGAGCAAGGGCGAGGAGCCGAGGCTGATCTCGTATGCCGTCTTCTGCTTGAATAATATA + ABABBFFFF5DFBFGFCFEE4EEGGGFF2GHHGAFEFGCHHHH0FHGG5DGGHF3GDFHEHHHFFGHEHGEBC4B44B443BBGHFA?/??433B3BF3F3GBG3244B33BBBFGBFFHF44BB32?FGGGHGAGB@////0?11?FG1FF@@@-AB0GGFBG/<-<-;-..:.;;00;:0/0<9/.AA-A9--9.;---@=E.;//;B.:.:///-A-9E/BF//BB.9/////// @M01416:220:000000000-DN9DG:1:1101:19516:1921 1:N:0:TAGATCGC GGACCTTTGGCTGTACCATTGCCAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATTTTTTTTTAGCTCGACTTTCAGCTTGGCAATTCTGTTCTGTGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGGCCGTGCTCTTAACGATCGGTCGCCACCATGTTGTGCAAGGGCGATGATCCGTGGCTGTTTTCGTATTCTGTCTTCTGCTTGTATAAATAA + AAAA3FBFFFFBGAGBFGGGFGBFAC4A4GHH?AAE222FHHHGHHFEDBCGHH3GGGFAFGEE3F3FGAEFC5D55>>//?BGEFGCE?E4B444BF3EFGBB3444B44BBF?E4B?GF12BBB0/BFD?F?BF0B///?0<11?0?GG--<>==GF11A...<<EG--...:GC00=0:.0;0C...B?-.9009..;?9A?.9/;;-99;/;/9;/FF/;//;FB.////;BF/ @M01416:220:000000000-DN9DG:1:1101:13109:1921 1:N:0:TAGATCGC CTGGAAGTTAGAAGGAAACAGACCACAGACCTGGTCCCCAAAAGAATTGGAGGCAATAGGTTTTGAGGGGCATTGGTACGGGGTTCAGCCTCCAGGGTCCTACACACTTATCAGTCAGTGTCCCAGTAGACCCCCCTCGTTATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTGGTGTGTCCCCAACTTTAGATCGGAAGAGCACACTTTTGAATTCCAGTCACC + 1>AA11BCD3FDF1GCFGGGFBF000G0BEFGHGHFHFF0EA0B/G1DGHFG?A/BG1FFF1FFH/FBE?GC0111112///>>/GEB10B0/010>0BGF>CC01/01BB12>2>1FGF>D111B11FGHH/?>/>A@///?<///>@CGGCECG.CG.<..@C.CFCG..:C.G000<90;09B0/;/EFFF0;./..;BF0CBB9..9-9---/9--///::9//;;//9/:/99 @M01416:220:000000000-DN9DG:1:1101:14831:1921 1:N:0:TAGATCGC GAGACCACCAAGGCAAGCAAGAGCCTGAACTCCAGTCACCACTAGAGGGTATATAATGGAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGTGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGACAACAGTAGAAAATACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGCCGAGGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACTTTTTATTTGTACTTTTCT + BBBBCCFBCCAFGGGGCGGGGFHHHCGHHHHHHHGHHHHGHHHHHDFGGAFGHFFHHHHHHHHHHGGGGGHHHB3FH3133BCGHGGE@>G4FFBEHBFGHFHB421B?//FEEGHGFEFGFHGHHEGHHHHH3FFHEGFHFHFG?CCGGFGGHHHGHDG1GFHFGGDFGGGGCGGFGC-??EGCF0CBAAEFG0:@ECFGGGGEFFF.09F.--;--.00000.00000000:000: @M01416:220:000000000-DN9DG:1:1101:15375:1922 1:N:0:TTGATCGC GGAGATAGATACAATCAGCCACTAGCTTGTACATGTGCACCACACACACACACACACACACACAAGATCGGAAGAGCATTCGTCTGAACTCCAGTCACCACTAGTTTGTTTATAATGGAAGCTCGACTTCCAGCTTGGCAATCCGTTACTGCGCAAAGTGAACACATCGCTAAGCGAAAGCTATGTATTGACATTAATCAACCGGTCTCCACCATGTTGAGCATGGGCGAGGAGCTGA + ABAA?FFFFFFFGC5FGCG4GGGF44DFGHE5B6FGCHDFFCGF?EE?FAEEGGCED1BA?EAF1AFGF1>B1111B3355B3B113434B333B3@3EDEG3ED444B0B44B?4F3BDC/3F<//?/B?GDFGB0/0?1?10?/1<<2>1?<<@@0??DDGG0FG1.<CD.0/-.-<.C000<;0G:00C:CCG0C0;::G---9.0;C/F.090900C0009C.9--9999..9/ @M01416:220:000000000-DN9DG:1:1101:19463:1922 1:N:0:TAGATCGC GGTGCCTGCGTCACCTCTGACCACACAGCAAGTTCGTTAGAAATGAATGAAGATAATGAGGCCTCGTGACTTTTATTTTTCACAGTGAGTGGGTTCACTGTGGGTTTTTTTGGCTATGTATACTGCTCTAGGCAGATCGGATGAGCACACGTCTGAACTCCAGTCACCACTAGTGGGTATATAATGGAAGCTCGATTTCCAGCTTTGCAATCCGGTACTTTGCTAAGTGAACACATCG + AAABACFB?DAA?EGFGGB5BAGFHC?GDGBGHFAFGBAFD55FG55FAA5BEFFFHBD531AFA?GHFFGHEA55DGGH3DDFFHHEF531?111@B4BF4BEE1111/>//?F3FGHH4444B3B3F3?222<FF2C/A//222<02?A0/?<GGBF1?<GGG111
>11<.<0<<==00D0<DG.0C.-/;:00;0:CC0::0<;:/.9D-.00;F00000;BBFB0/.;0. @M01416:220:000000000-DN9DG:1:1101:19606:1922 1:N:0:TAGATCGC GCCTAGAGCTGTGTCCATAGCCACCTTCCCCCACAAACTCCCCCAGCCCTGCTCTGTCTGGGCTGCTGTGTGGTCTTTGTTGACGCAGGCACCTGATCGGAAGATCACACGTCTGAACTCCAGTCACCACTATAGGGTCAATCCGTTACTGTGCAAAGTGAACACATCGCTAAGCGAAATCTAAGTTCCTATCATAATCCACCGGTCGCCACCATGTTGAGCATGGGCGAGGAGCCGA + AAAAFFCFFFFGFCGCBGGGGBGAGFHHBHCEEGGF2FFGEEEAEFGEEACFHHFGGHH32CFGAHFH3FEEG355555B?BDEF/EE1?1?3B33BE11?E0??3333/B?GF3?GFG3B3BB?32BEFH3BBD0FF02>>2?//FFFGF1@FGBDGB11F0><..>A<10-.--.<==0=DGD0G0;:0CH00:0C/.::AB--9.9..;00000/0009...-=A--;.9-- @M01416:220:000000000-DN9DG:1:1101:16661:1923 1:N:0:TAGATCGC GCCTAGAGCTGTGTCCATAGCCACCTTCCCCCACAGTGCCCCCTCTCACTGTGAAAACTAAAAGTCACGAGGCCTTATTTTCTTCATTCATTTCTAACGAACTTTCCTCTTTCAACTGATTTCTCGTCAGCCAGGGAGTGCCCCATGACGAAGCCACTCGAGTCAAGGGGTCGAATTTTCTACTTATGACCTCACTTTCTGTTGCTCTTTCTTTCCCTCCCTCCACAGTGCCTTCTCT + 3AAAAFFFFFFFFGGFGGGGC4FFCGHHG4FEEEAGFHHGFFEA2FG3FGFHFGGHBCG5BBBFBDF5E1A0E1@33DF5BGEF55@4F@B4FDFE4FAC?/GDF434343B44GHBG3DGG444/?//?BGHEHG/?/B1B0//B?<FD/@/<00F?0?/<F01?11<-<AC-.CCGH0==0DG0<00=<D0/.<CH0CGGG0;C0;0<CC;00;00/9.9/./9/.;0;00;0900 @M01416:220:000000000-DN9DG:1:1101:13793:1927 1:N:0:TAGATCGC GGAGATAGATACAATCAGCCACTAGCTTGTACATGTGCACCACACACACACACACACACACCAGATCGGAAGATCACACGTCTGAACTCCAGTCACCACTAGTGTTTATATTATGGAAGCTCGACTTCCAGCTTGGCATTCCGTTACTGTGCAAAGTGAACACATCTCTAAGCGAATTCTAATACCCTCCAAACACTAACCGGTCGCCACCATGGTGATCTTTGGCGAGGAGCCTAGG + AA3ABFFFBFDF5EGEFFFBGFHFGHGHBHFGGHFHFFFBGHHH2EFEGGCD2E11A111B1A11AF1E1F?15533330BBFFF4CGG3@3B333B@GFCE4BB@G4B4?4?BDG33FGGC/>/?EDFDFFH10/011B?F?1@?FHHHGFFB10@11F1F0/?11FFGB1<-.--.<<<111<0CGH?CG0<.<0<<G.--=:-@E....0C/000000009/C-;;9B?.;/9// @M01416:220:000000000-DN9DG:1:1101:14877:1929 1:N:0:TAGATCGC AAAGTCCCAAACCAACTGCTGGCCTGCCCAAGAAAGAAACCAAATTCATACAACCTCCGCAACTGAGATTGAAACCATGATAGATCGGAATCGCACACGTCTGAACTCTAGTCACCACTAGAGGGTCTATAATGGAAGCTCGATTCCAGCTTAGCAATCCGGAACTGTGCAAAGTGAACACATCGCTAAGCGACAGCTAAGAAAACTCTACTAATCAGTGTTCTCCACTATGGTGAGC + AA?AADF1DCC?111A1BGGGCGHCG00A1A00ABEGH000BAGF1FD2FGFFG/FFGC/AE?EGF11B11F111BF1D1DF@FGHEC?//10//>>0EGHB/F21F1111B121BGCC01B10/?00>22BF21F1GCFG//0212@101@11@FGGCGE@//>11>11>1><1111<10<C0..<.<<C-.--;.C00:00/:/;F009CB00900090;C009090;C000;F?/ @M01416:220:000000000-DN9DG:1:1101:17264:1930 1:N:0:TAGATCGC GGGTCTCACAGGGTCACGTCCGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTAGAGGGTATATAATGGAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGTGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGCGCTTGAACAATCCTACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGCCGAGTCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAG + A?AAAFDDFFBA2B4FFECFC?EEGDFGFHHHFGGGHCHGHCFGHHHGHFHHHHHHHHHGHBHHHGGHFDEFHFG55DD533BGGHGGGGGHE3FBGHGGFHFH?0//>><GFGDFHHHHHEHFG1BGGHGGHGFHHCEC//0GF1GFG/FFAHCGFGHGFHGG0<-@D?CEG?.GHHFGHGF/CG/EDG@@G@9E..-;@..;BB//9FFFFFF9/@A=FFFFFFFF/.;/;9@--. @M01416:220:000000000-DN9DG:1:1101:13847:1931 1:N:0:TAGATCGC GGTGCCTGCGTCACCTCTGACCACACAGCAGCCCAGACAGAGCAGGGCTGGGGGAGTTTCTTAGGCCCTCTGCGCGGGGTTCACTTTCCACTCGAGATGGCACTGTGGAGGGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTAGAGGGTATATAATGGAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGTGCAAAATGAACACATCGCTATGCGAATGCTAAGAACTG
The R3 reads, first 10 reads @M01416:220:000000000-DN9DG:1:1101:17453:1773 3:N:0:TAGATCGC TTTCTTGTCGTTTTTTCTTTTCTTCTTTTTTCTTTTGTTCGTCTTTTTTTTTTTTTTTTTTTTGTTTTTCTTGTTCTTTCTCTTTTTGTTTTNCTTNTTTTNTTTNTTTNNNNTNTNTTTTTTTNNNNTTNTTNNTNTTTNAATANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGNNGNNNNTNNTNNNNNNNNNGNTTCTCTTGTTGNNNNNN + 11>1131B11>111A001AB131333B311A011B11001/B//ADB1/////////>/>//>/0000?0>111112>1222?2111/<00?#//?#/>..#.<>#<.<####<#<#=<.=.--####..#.9##9#;9.#9...#9##################################################-9##-####-##9#########-#-:-;-9;/9/-###### @M01416:220:000000000-DN9DG:1:1101:12921:1774 3:N:0:TAGATCGC TTTTCTTTTATTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTNTTTNTTTTNTTTNTTTNNNNTNTNTTTTTTGNNNNGTNTANNTNTATNAGAANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCNNTNNNNTNNTNNNNNNNNNGNGGTTGTTGGTGNNNNNN + 1111113313333B310A00AAE//A///>01@111>///<//>/////-<-----:-9--9-----;-9----//////-;-9---9-=9-#---#9---#;:-#999####9#-#;----9-####--#-:##:#---#----#-##################################################--##9####9##9#########9#--9--------###### @M01416:220:000000000-DN9DG:1:1101:14672:1775 3:N:0:TTGATCGC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTNTTTTNTTTNTTTNNNNTNGNGCCCTGGNNNNAANGCNNGNTGGNGGTCNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGANNCNNNNTNNGNNNNNNNNNGNGCGTTGTGTGTNNNNNN + 11>111>1>0>0A/A/A/>/>/>/>//</////</<------:;----/;0;;B->=9-9-9-9-----9---99-----9--@-;9---9-#-9-#-;--#--9#-;9####-#-#----9--####--#99##9#-;;#;-;-#-##################################################:-##-####-##;#########-#--9--9--9--###### @M01416:220:000000000-DN9DG:1:1101:14624:1784 3:N:0:TTGATCGC TTTTTTTTCTTTTTTTTTTTTCTTTTCTTTTCCTTCTTTTTCTTTTCTTTTTTTTTTTTTGTGGTTTTTTTTTTTCTTGTTCTTTTTTTCTTNTTTNTTGTNTTTNTTTNNNNTNCNGTCTAGTNNNNGCNCTNNCNGAANTGCANGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGNNGNNNNTNNCNNNNNNNNNGNTGTTTTTGGGTNNNNNN + 111>1111>B3B1B000A///011112111121B21AB11B0D1112D11D1>E///////00/B/0///////-0111=<111110--/0=#.;.#....#...#.:.####.#.#9999;B0####:;#-9##;#999#9;9-#;##################################################--##9####-##-#########9#---9----9-9###### @M01416:220:000000000-DN9DG:1:1101:14078:1785 3:N:0:TTGATCGC TTTTTTTTCTTTTTTTTTTTCCTTCTTCCTCCTCTTTTTTTCTCTTTCTTTTTTTTTTTGTTTCTTTCTTTTCTTTTTTTTTTCTTTTCTTTNTTTNTTTTNTTTNTTTNNNNGNCNCCAGTTCNNNNGANCGNNGNGTANGGAANGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCNNTNNNNTNNTNNNNNNNNNTNTGTGTCTTTTTNNNNNN + 111>11110B3@1B000A//01121BA211100011A11>/012B21221111///>///B002B1122111211B11</>/>0=1111>11#.>.#..<.#...#...####.#.#..::.<0####..#.9##;#;;9#;9..#=##################################################--##;####-##-#########-#----9//9///###### @M01416:220:000000000-DN9DG:1:1101:13957:1791 3:N:0:TTGATCGC TTTTTTTGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTNTTTTNTTTNCTTNNNNTNTNGTGTGGGNNNNGGNAGNNTNGCGNGATGNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGNNTNNNNTNNGNNNNNNNNNGNTTAGCGGGTGTNNNNNN + 1111>111B1B0B000A0//A/A/>///>/>//<E//////?000<>-<?-;-:-;--?--;-;-9-@-9----9@-;-9----9-;9-9-@#--9#-9--#9-9#-9-####;#-#;--9---####:-#-;##-#-;-#--;:#-##################################################-;##-####-##-#########-#---;-9---9-###### @M01416:220:000000000-DN9DG:1:1101:15225:1791 3:N:0:TTGATCGC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTCTTCTTTTTTTTTTTTTTTTGTTTTTTTTTTTNTTTNTTTGNTTTNTTTNNNNTNGNTCTTTCTNNNNTTNAGNNTNGCGNCGTGNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGNNGNNNNGNNGNNNNNNNNNGNGGTTTTGGCTGNNNNNN + 1>>11111>0>0//A/A/>/E/>//>/////<//<-----:--;--/9/;9:-9-;-9-9/;////9;/-;@-9-------;-B----9-9-#-9-#--9-#9--#-;9####-#-#-----//####;-#--##-#---#-9;-#-##################################################-;##-####-##9#########9#-:---9--;9-###### @M01416:220:000000000-DN9DG:1:1101:16193:1792 3:N:0:TTGATCGC TTTTCTCCGACTTTTTTTTTTCTTCCTTTTCGTTTTTTCGTCTTGTTTGGTTTTTTTGTCCTGCTTGTCTTTTTCGTTCCCTTTCTTTTTTTNTTTNTTTTNTTTNTTTNNNNTNTNTTTTTTGNNNNTTNTTNNTNTTCNAATANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGNNGNNNNGNNTNNNNNNNNNGNGTGTTGTGTTTNNNNNN + 11>1>131111113B1A000/01121122B2/00////0/B//AAB100///0///>/B21F11111B1B221>0/00001B11121111>/#///#?///#/?/#/<?####<#<#<....--####.<#<.##.#.:.#....#.##################################################9-##9####-##9#########9#:--;---99/;###### @M01416:220:000000000-DN9DG:1:1101:15141:1793 3:N:0:TAGATCGC TTTTCTTGCTTTTTTTTTTTCTTTTTTTTTGTCTTTTCTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTCTTNTTTNTTCTNTTTNTTTNNNNTNGNTCTCTGTNNNNTANGGNNGNTGTNGCTTNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTNNCNNNNGNNGNNNNNNNNNTNTTGTCAGTGTGNNNNNN + 11>>1B311BD31A1A0AAA011111/////B222B12111120B>//>>/////@<CC/@/@@----:----;--;//;.--;-9--;///#9;;#-;--#9-9#---####-#:#-----//####--#--##-#:9-#--9:#;##################################################99##-####-##-#########:#;:;A-//////###### @M01416:220:000000000-DN9DG:1:1101:17575:1798 3:N:0:TTGATCGC TTTTCTTTACTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTGTTTGTTTTTTTTTTTCTTTTCTTTTTTTTTTTTTTCTTTCTTTTTTTNTTTNTTTTNTTTNTTTNNNNTNTNTTGTGTGNNNNCCNCTNNTNTAGNGATANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTNNTNNNNGNNTNNNNNNNNNCNTTGTTTTTCTTNNNNNN + 11>11B3B31333311000AAAE//01DAA1//>//>//>///>/B?000??0/>/<---/=<000<=0=0------9--/00//9/9/:9;#--9#;---#-:-#-:9####;#-#--9:---####--#--##;#;9-#;9-;#-##################################################9-##-####-##-#########-#--9-----///###### @M01416:220:000000000-DN9DG:1:1101:14363:1798 3:N:0:TTGATCGC TTTTTTTTTATTTTTTTTTTTTCCTCTTTTCTTTTCCCCTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTGTTTTCTTTCTTNTTTNTCCTNTTTNTTTNNNNTNCNGTGGCCCNNNNGANCCNNCNCGGNATCGNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCNNTNNNNTNNGNNNNNNNNNGNGTAGGGAAAGGNNNNNN + 1>>1111>>03333300/////011111112D11D211000111//011111////>///>>CC------/0:000---9-//9B0000000#...#.--;#---#---####-#;#-;-;-9-####9-#--##9#;;;#--9A#-##################################################-;##9####9##;#########-#;;-;9E/;---###### @M01416:220:000000000-DN9DG:1:1101:12672:1800 3:N:0:TTGATCGC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTNTTTTNTTTNTTTNNNNTNTNTGTTATTNNNNTTNTANNCNCGCNTGCGNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGANNTNNNNGNNGNNNNNNNNNGNATGTTGGGGGGNNNNNN + 11>11>1>>0>0/AAAA////>/>>>/</</</<-----:-:---;A@@------9@-;99@9@?=-9-99--9-999==@-@9-@=-9-#-99#-9-:#99-#999####-#:#9--;-//####-9#--##-#99-#-;--#-##################################################;-##9####-##-#########-#-;-:-/-----###### @M01416:220:000000000-DN9DG:1:1101:15759:1815 3:N:0:TTGATCGC TTTCGCGCCGTTTTTTTTTTTTTTTCTGTTCGTTTTTTCTTCTTGTTGGTTTTTTTTGTCCTTCTTTTCTTTTGTGTTTCCTTTCTTTTTTTNTTGNTTTTNTTTNTTTNNNNTNTNTGTTTGGNNNNGTNCCNNTNTTANAAAANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGNNGNNNNGNNCNNNNNNNNNTNGGCTGTTGTTANNNNNN + 1>1111111>0000000/AAE////0122D2//0////01B22B1110///0//>/>/B2>F21111B2B11110000022?22121>11>/#...#>...#<<.#.<<####<#.#;..../.####..#.9##;#..9#..;.#.##################################################--##-####-##-#########-#-9-9--//--/###### @M01416:220:000000000-DN9DG:1:1101:14344:1820 3:N:0:TTGATCGC
There are such instances in the remaining reads in R3 @M01416:220:000000000-DN9DG:1:1101:8395:8719 3:N:0:TAGTTCGC GAATCCATGCATTCCATTCATAAAGGAGCACGCCAGACCGTCGTGTGCGGAAAGAGTGTCCTGCAGGTCTAGCGCGGGCCTTGCTTTACATGNATGNTGGCNCTGNGGCGNNGGNGNAAGTGCGNNNNGTNGGNNTNTAANATCCNGNNNNNNNNNNGNNNNNNNNNNNNNNNNNNCNNNNCNNCCNNANNNNNNNNTTNNTNNNNTNNGNNGTTNGNNTNTTTTTGGTAGTNNNGCN +
111>11@B113B3333FB33AF111BE000000A0B00EE///BG/1/A//A00BF1DG1FA1B100111B1>>F/EC//1>1>1111222#//?#??//#/?/#/?//##??#?#//?/?1/####.<#..##.#...#...<#.##########;##################.####.##9-##-########--##-####-##9##-9-#-##-#-;--9---///###9-# @M01416:220:000000000-DN9DG:1:1101:6706:8719 3:N:0:TAGATCGC AAGACCCGTTGTGTGTGCAGATAAGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCCTGCAGGTCTAGAGCGGGCCCTGGCAGAAATGNAGGNTGGCNTTCNTGTGNNGGNTNTCGCGGGNNNNGGNGTNNTNTTTNAATANANNNNNNNNNNGNNNNNNNNNNNNNNNNNNCNNNNANNCANNCNNNNNNNNGGNNGNNNNTNNCNNGTTNTNNCNTGTGGGGGGTGNNNTTN + BBBBBFBDB@AAAFGFGGGGGGHHHHHHHHH2E2EEHCGGEGGEEEFFBF3FGCGFHDFGHHEGGCFHFGFBGFHGFFFGCHHHHHFAFF4B#??/#??F/#///#/??/##?/#/#////?>/####..#.>##<#<..#....#<##########.##################.####:##;;##.########..##.####.##.##...#.##.#.;9...-----###.:# @M01416:220:000000000-DN9DG:1:1101:19369:8719 3:N:0:TAGATCGC AGCTAGCCGTATAAGGAGGCCTGAAGAGATCGGAAGAGCGTCGTGGAGGGAAAGAGTGTCCTGCAGGTCTAGAGCGGCCCTGGCAGAAATGCNGGCNGGCGNACTNAGTTNNTTNANTGGTGGGNNNNCTNTTNNTNTAANAAAANANNNNNNNNNNGNNNNNNNNNNNNNNNNNNCNNNNCNNCCNNCNNNNNNNNGANNGNNNNGNNTNNTTTNTNNGNGGCTTGTGGCTNNNAAN + 3AABBFFFBBAFGBGGGGGGGGGC4AEHHHHHGGGGHHHGGGGGGEEHGG1GHHFGHGHHHHHHHHHHHHHHHGHGGGCEHFFFFGGHHHFH#??F#??/?#///#//?/##//#/#?/?/?//####//#<<##.#...#<<<E#<##########.##################;####.##;9##9########;;##.####.##.##.9.#:##.#...9.-./...###;.# @M01416:220:000000000-DN9DG:1:1101:4184:8719 3:N:0:TAGATCGC AATGTTGGGTAGACACAAGCATCAAGGATACGCTGCACACGCCCTATCCTCCCTGCTCCGAGTCCTATGGGGGTCTTCTGGGCCACTGACTGNTTTNTGTGNCGGNCTCTNNAGNCNGAACCCCNNNNCCNTGNNCNTCANAACCNANNNNNNNNNNTNNNNNNNNNNNNNNNNNNTNNNNGNNGTNNTNNNNNNNNTTNNTNNNNTNNGNNGAGNGNNTNGGTGGGAAAGGNNNTCN + 111>ABD111111A111AE10BA1A1A0A1A0A00A011B//AA/011A210/BB/1BFA///0B222110/>>/012B110///?BFF111#>>?#//>/#//?#?/?/##/?#/#?/?///?####??#/<##/#/<.#<...#.##########.##################.####9##..##.########99##-####;##;##---#9##-#;--;A@-/-;-###--# @M01416:220:000000000-DN9DG:1:1101:18776:8719 3:N:0:TAGATTGC AAAGGTTGGGACACGCAAGCATCAAGGATCCCCTTCACACTCCCCATCCTCCCTGCTCCGTTTCCGTGGGCGGCCTTCTGGCCCACTGCCTGNCTTNTCCGNAGGNCCCANNGGNCNGAACGCCNNNNCCNTCNNCNTCANAACCNANNNNNNNNNNTNNNNNNNNNNNNNNNNNNTNNNNTNNGTNNGNNNNNNNNTTNNANNNNTNNGNNAGCNGNNTNGTCGGGAAAGANNNTCN + 111>1B1>1A1>111A00E00F11ABG0F0A0B0FB112B00F//00B011AA0B/11B/A1BB2/1?>>/////?F1BF110?//B11011#/?/#</</#//?#??F/##/<#?#?///?//####<>#..##.#<..#<<.<#<##########;##################.####.##.;##-########;9##-####;##;##---#-##-#-;--9-----9###--# @M01416:220:000000000-DN9DG:1:1101:10910:8719 3:N:0:TAGATCGC ATCTTGGTTTCAATCTCAGTTTCGGAGGTTGTATGAATTTGGTTTCTTTCTTGGGCAGGCCAGCAGTTGGTTCGGGACTTTAGATCGGAAGANCGTNGTGTNGGGNAAGANNGTNANGCAGGTCNNNNGCNGGNNCNGGCNGAAANGNNNNNNNNNNTNNNNNNNNNNNNNNNNNNGNNNNGNNGGNNCNNNNNNNNACNNANNNNGNNTNNTGTNTNNTNGTGTTGTCTTTNNNTAN + AAABAFBFAFFFGGGFGFGFGGHEFEEEAFGGFFH5BFGHHHHHHHGHHEGFFEGHFDG?FGEG2GGGHHGHHGGGEGHHH4@FGFHGCAEF#??F#??F?#??F#??F/##??#?#?//FGGG####?<#??##?#??F#?/<F#?##########.##################.####.##..##9########..##.####.##.##.;.#.##9#..99A.B/;99###.9# @M01416:220:000000000-DN9DG:1:1101:20570:8720 3:N:0:TAGATCGC AAAGTTGGGGCACACAAGCATCAAGGATACCCCTCACACTCCCCATCCTCCCTGCTCCGATTCCGAGGGGGGTCTTCTGGGCCACTGACTGANTTGNGTGTNGGANCCTGNNGGNTNAACCCCGNNNNCANTCNNCNCAANACCTNTNNNNNNNNNNTNNNNNNNNNNNNNNNNNNGNNNNTNNTTNNCNNNNNNNNTCNNTNNNNCNNANNTGCNTNNTNTCGGGAAAGAGNNNCCN + 3A3>AD5C3AA@EFGECEGFGGBF4F4FFHHFEFECAFHFGFG22F3GFFHA2B1F5AA0BEFDF10>EC/<ACFHFH11F.CCCGC0<D=<#<<.#:;CC#;..#;;A.##9;#:#..9CEGB####;.#.;##.#;9.#.;99#;##########.##################.####.##.9##;########:.##.####.##.##...#.##9#;.9:.-9A;/9###;.# @M01416:220:000000000-DN9DG:1:1101:18223:8720 3:N:0:TAGATCGC CAGCCACGGCTGCTCGCCTGTCCTCCCCCTGGGGGCGACCGTGATTAAACGTTTAGTTCTTTGTTCTCGCTTTTTTATGTGTTCTCGTTGCANCGTNCCTGNGTTNCATCNNTTNTNTCGACCTNNNNTTNTANNCNCTCNTGTGNTNNNNNNNNNNCNNNNNNNNNNNNNNNNNNCNNNNGNNCCNNCNNNNNNNNGANNCNNNNCNNCNNGGGNTNNGNCCAAATTCATANNNCCN + 1A?1111>1A11A1AEEA00111A100B0///A//////>////BB@11@/BF0/11B2BF112B1>2//FE/11/<122220222/</B?1#///#///?#/?/#?//?##?/#.#.<><.>>####<.#..##<#...#....#;##########.##################;####-##-;##;########-9##-####-##;##9--#-##-#99--9/9//9/###;;# @M01416:220:000000000-DN9DG:1:1101:26484:8720 3:N:0:TAGATCGC ATCTTGGTTTCAATCTCAGTTTCGGAGGTTGCATGAATTTGGTTTCTTTCTCGGGCAGGCCAGCAGTTGGTTTGGGACTTTAGATCGGAAGANCGTNGTGTNGGGNAAGANNGTNCNGCAGGTCNNNNGCNGGNNCNGGCNGAAANGNNNNNNNNNNGNNNNNNNNNNNNNNNNNNGNNNNGNNGGNNTNNNNNNNNTCNNGNNNNTNNTNNGTTNTNNGNTTGGTTTTTTTNNNCGN + A>AAA5FF>FFFGFGGGBGEA5GEE2AE24F2A5FDGG5DGHFHHDGBGGB5EE2EE10E11112A5DFBFH1EFE1?FEGFHGF4FA1F1B#11?#????#??F#??F/##??#/#???FF0?####?/#??##/#??/#??CC#<##########.##################.####.##..##9########..##.####.##.##.9;#.##:#9:;..9.;.--###99# @M01416:220:000000000-DN9DG:1:1101:24218:8720 3:N:0:TAGATCGC CTTGGGCGCTGCATGGGTGAGTCAACGGCCCCTGCCCCTCAAGACAAGCAGAAGGCATGCGGGCAGCAGCAGGTAGGCGCCCCACCCCCCCCNCACNTCCTNCCANGCGCNNTGNCNGGGCGATNNNNCCNGGNNTNTGANGCGCNGNNNNNNNNNNCNNNNNNNNNNNNNNNNNNGNNNNTNNGGNNGNNNNNNNNTTNNTNNNNTNNCNNGGGNCNNTNCCCGAGCTGTCNNNCGN + 1A1AAA111ADA11FFG0AEGF11FBEE0E?////0ABAE011B0000/A00EGHEF1BB//>//?/B>000/011F1>EEC/<///<B/BC#///#///?#.>.#....##.<#<#.<<.C--####;.#.:##.#.:.#.9..#;##########.##################-####-##-9##-########9:##-####-##-##---#-##-#----;--99//###9-# @M01416:220:000000000-DN9DG:1:1101:19699:8720 3:N:0:TAGATCGC GCCTAGAGCTGGGCCTAAGAAACTCCCCCAGCCCTGCTCTGTCTGTGCTGCTGTGTGGCCAGAGGTGATGCAGGCACCAGATCGGAAGAGCGNCGTNTTGGNCAANAGTGNNCTNCNGGTCTAGNNNNGGNCCNNGNAGANATGCNGNNNNNNNNNNGNNNNNNNNNNNNNNNNNNGNNNNANNCANNTNNNNNNNNGCNNANNNNGNNANNGGGNGNNCNCTGTTTGTACANNNAAN + AAAAAF1BD11BEGGG1ECF1FCF1FGEC0EFF?GFHBGBGBEFHAFB21B11FGA0E/0BA0B/1/12BFB10E/EA0>0@F/E/>>0BF>#??>#>/>?#///#/?//##//#/#?//?FB2####</#??##/#/?/#??</#?##########.##################.####.##..##.########..##.####.##;##---#-##-#---9:/:;///###;-# @M01416:220:000000000-DN9DG:1:1101:5066:8721 3:N:0:TAGATCGC CTGGAAGTTAGAAGGAAACAGACCACAGACCTGGTCCCCAAAAGAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCNAGGNTCCTNCACNCAACNNAGNCNGTGGCCCNNNNGANCCNNCNCGGNATCGNANNNNNNNNNNGNNNNNNNNNNNNNNNNNNCNNNNCNNCTNNCNNNNNNNNACNNTNNNNTNNGNNCATNGNNTNGTAGGGAAAGGNNNTCN + 1>1>111B33131B1GFGC1EFEHHC0CGFH0A1A100F0B0A/0BAD11BFG/01FBHH1GAG/FFFCGCCEH/E//E@EE@EFB2FFGE#??F#//?/#??/#??//##/?#?#<?<FF0<####/<#??##?#/>>#<>.>#<##########.##################9####.##;.##.########-;##;####;##;##---#-##-#;;9AAE/--;-###--#
jcardwel
commented
3 months ago I'm seeing the same error, though I'm skipping the PE merge step (no fastq-insertPE input): Pipeline Name : MPRAflow Pipeline Version: 2.3.5 Fastq insert : /Schwartz/Schwartz/proj/MPRA/20240319_LH00407_0025_B22HHKLLT3/Plasmid_Ctrl_S1_L002_R1_001.fastq.gz fastq paired : null Fastq barcode : /Schwartz/Schwartz/proj/MPRA/20240319_LH00407_0025_B22HHKLLT3/cre_only.fastq.gz design fasta : /Schwartz/Schwartz/proj/MPRA/20240319_LH00407_0025_B22HHKLLT3/mpra_oligos.fasta minimum BC cov : 3 map quality : 30 base quality : 30 cigar string : n min % mapped : 0.5 Output dir : outs Run name : assoc Working dir : /home/cardwellj/MPRAflow/work Container Engine: null Current home : /home/cardwellj Current user : cardwellj Current path : /home/cardwellj/MPRAflow base directory : /home/cardwellj/MPRAflow Script dir : /home/cardwellj/MPRAflow Config Profile : standard
executor > local (15) [95/ae488f] process > count_bc_nolab [100%] 1 of 1 ✔ [f8/14031f] process > create_BWA_ref [100%] 1 of 1 ✔ [5a/cbe2e6] process > align_BWA_S [100%] 11 of 11 ✔ [3d/7dab8e] process > collect_chunks [100%] 1 of 1 ✔ [6d/5d3399] process > map_element_barcodes [ 0%] 0 of 1 [- ] process > filter_barcodes - Error executing process > 'map_element_barcodes (assign)'
Caused by:
Process map_element_barcodes (assign) terminated with an error exit status (1)
Command executed:
echo "test assign inputs" echo 30 echo 30 echo cre_only.fastq.gz zcat cre_only.fastq.gz | head
echo count_fastq.txt echo count_merged.txt cat count_fastq.txt cat count_merged.txt
python /home/cardwellj/MPRAflow/src/nf_ori_map_barcodes.py /home/cardwellj/MPRAflow cre_only.fastq.gz count_fastq.txt s_merged.bam count_merged.txt assoc 30 30 n
Command exit status: 1
Command output: test assign inputs 30 30 cre_only.fastq.gz @barcode1 aggacaattc + ########## @barcode2 aatcaccact + ########## @barcode3 agttcatgaa count_fastq.txt count_merged.txt 280800 20286799 /home/cardwellj/MPRAflow cre_only.fastq.gz s_merged.bam count_fastq.txt count_merged.txt counts 20286799 280800 280800 start bad pairs: 0 poor quality: 14441481 start
Command error: paired-end reads: 84%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 17118697/20286799.0 [00:25<00:03, 1026300.14it/s] paired-end reads: 85%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ | 17224110/20286799.0 [00:25<00:02, 1034491.69it/s] paired-end reads: 85%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 17327586/20286799.0 [00:25<00:02, 1033269.75it/s] paired-end reads: 86%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 17433476/20286799.0 [00:25<00:02, 1040668.39it/s] paired-end reads: 86%|██████████████████████████████████████████████████████████████���███████████████████████████████████████████████████████▍ | 17537569/20286799.0 [00:25<00:02, 1036193.63it/s] paired-end reads: 87%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 17643852/20286799.0 [00:25<00:02, 1043995.91it/s] paired-end reads: 87%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 17748282/20286799.0 [00:25<00:02, 1041911.78it/s] paired-end reads: 88%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 17852495/20286799.0 [00:25<00:02, 1041797.23it/s] paired-end reads: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ | 17956690/20286799.0 [00:25<00:02, 1038566.28it/s] paired-end reads: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ | 18060560/20286799.0 [00:25<00:02, 1034613.93it/s] paired-end reads: 90%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 18166215/20286799.0 [00:26<00:02, 1041096.61it/s] paired-end reads: 90%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 18270344/20286799.0 [00:26<00:01, 1035524.37it/s] paired-end reads: 91%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 18373917/20286799.0 [00:26<00:01, 1008475.76it/s] paired-end reads: 91%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 18474934/20286799.0 [00:26<00:01, 984875.22it/s] paired-end reads: 92%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 18578713/20286799.0 [00:26<00:01, 1000133.87it/s] paired-end reads: 92%|█████████████████████████████████████████████████████████████████████████████████████████████��████████████████████████████████▏ | 18680741/20286799.0 [00:26<00:01, 1006093.25it/s] paired-end reads: 93%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 18783770/20286799.0 [00:26<00:01, 1013230.24it/s] paired-end reads: 93%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 18885222/20286799.0 [00:26<00:01, 1005339.30it/s] paired-end reads: 94%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 18985860/20286799.0 [00:26<00:01, 1002843.27it/s] executor > local (15) [95/ae488f] process > count_bc_nolab [100%] 1 of 1 ✔ [f8/14031f] process > create_BWA_ref [100%] 1 of 1 ✔ [5a/cbe2e6] process > align_BWA_S [100%] 11 of 11 ✔ [3d/7dab8e] process > collect_chunks [100%] 1 of 1 ✔ [6d/5d3399] process > map_element_barcodes [100%] 1 of 1, failed: 1 ✘ [- ] process > filter_barcodes - Error executing process > 'map_element_barcodes (assign)'
Caused by:
Process map_element_barcodes (assign) terminated with an error exit status (1)
Command executed:
echo "test assign inputs" echo 30 echo 30 echo cre_only.fastq.gz zcat cre_only.fastq.gz | head
echo count_fastq.txt echo count_merged.txt cat count_fastq.txt cat count_merged.txt
python /home/cardwellj/MPRAflow/src/nf_ori_map_barcodes.py /home/cardwellj/MPRAflow cre_only.fastq.gz count_fastq.txt s_merged.bam count_merged.txt assoc 30 30 n
Command exit status: 1
Command output: test assign inputs 30 30 cre_only.fastq.gz @barcode1 aggacaattc + ########## @barcode2 aatcaccact + ########## @barcode3 agttcatgaa count_fastq.txt count_merged.txt 280800 20286799 /home/cardwellj/MPRAflow cre_only.fastq.gz s_merged.bam count_fastq.txt count_merged.txt counts 20286799 280800 280800 start bad pairs: 0 poor quality: 14441481 start
Command error: paired-end reads: 84%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 17118697/20286799.0 [00:25<00:03, 1026300.14it/s] paired-end reads: 85%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ | 17224110/20286799.0 [00:25<00:02, 1034491.69it/s] paired-end reads: 85%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 17327586/20286799.0 [00:25<00:02, 1033269.75it/s] paired-end reads: 86%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 17433476/20286799.0 [00:25<00:02, 1040668.39it/s] paired-end reads: 86%|██████████████████████████████████████████████████████████████���███████████████████████████████████████████████████████▍ | 17537569/20286799.0 [00:25<00:02, 1036193.63it/s] paired-end reads: 87%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 17643852/20286799.0 [00:25<00:02, 1043995.91it/s] paired-end reads: 87%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 17748282/20286799.0 [00:25<00:02, 1041911.78it/s] paired-end reads: 88%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 17852495/20286799.0 [00:25<00:02, 1041797.23it/s] paired-end reads: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ | 17956690/20286799.0 [00:25<00:02, 1038566.28it/s] paired-end reads: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ | 18060560/20286799.0 [00:25<00:02, 1034613.93it/s] paired-end reads: 90%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 18166215/20286799.0 [00:26<00:02, 1041096.61it/s] paired-end reads: 90%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 18270344/20286799.0 [00:26<00:01, 1035524.37it/s] paired-end reads: 91%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 18373917/20286799.0 [00:26<00:01, 1008475.76it/s] paired-end reads: 91%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 18474934/20286799.0 [00:26<00:01, 984875.22it/s] paired-end reads: 92%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 18578713/20286799.0 [00:26<00:01, 1000133.87it/s] paired-end reads: 92%|█████████████████████████████████████████████████████████████████████████████████████████████��████████████████████████████████▏ | 18680741/20286799.0 [00:26<00:01, 1006093.25it/s] paired-end reads: 93%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 18783770/20286799.0 [00:26<00:01, 1013230.24it/s] paired-end reads: 93%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 18885222/20286799.0 [00:26<00:01, 1005339.30it/s] paired-end reads: 94%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 18985860/20286799.0 [00:26<00:01, 1002843.27it/s] paired-end reads: 94%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 19086219/20286799.0 [00:27<00:01, 988198.17it/s] paired-end reads: 95%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 19185140/20286799.0 [00:27<00:01, 976406.82it/s] paired-end reads: 95%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 19284941/20286799.0 [00:27<00:01, 982788.51it/s] paired-end reads: 96%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ | 19387405/20286799.0 [00:27<00:00, 994881.30it/s] paired-end reads: 96%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 19493042/20286799.0 [00:27<00:00, 1012561.83it/s] paired-end reads: 97%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ | 19596306/20286799.0 [00:27<00:00, 1018381.69it/s] paired-end reads: 97%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 19701573/20286799.0 [00:27<00:00, 1028429.46it/s] paired-end reads: 98%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 19804515/20286799.0 [00:27<00:00, 1024902.68it/s] paired-end reads: 98%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 19907552/20286799.0 [00:27<00:00, 1026534.87it/s] paired-end reads: 99%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ | 20012411/20286799.0 [00:27<00:00, 1033052.94it/s] paired-end reads: 99%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 20115762/20286799.0 [00:28<00:00, 1024386.73it/s] paired-end reads: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌| 20218250/20286799.0 [00:28<00:00, 1019430.41it/s] paired-end reads: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20286799/20286799.0 [00:28<00:00, 719871.27it/s]
barcodes: 0%| | 0/70200.0 [00:00<?, ?it/s]
barcodes: 64%|████████████████████████████████████████████████████████████████████████████████████████████████▊ | 44703/70200.0 [00:00<00:00, 447025.10it/s]
barcodes: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 70200/70200.0 [00:00<00:00, 453737.34it/s]
Traceback (most recent call last):
File "/home/cardwellj/MPRAflow/src/nf_ori_map_barcodes.py", line 157, in
Work dir: /home/cardwellj/MPRAflow/work/6d/5d3399f7da422d10aa82e749dcd45e
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
jcardwel
commented
3 months ago Oddly, if I go to the work directory and try to run the python command outside of the nextflow pipeline, it appears to compete without error: (MPRAflow) [cardwellj@e00 5d3399f7da422d10aa82e749dcd45e]$ python3 /home/cardwellj/MPRAflow_batch_test/MPRAflow/src/nf_ori_map_barcodes.py /home/cardwellj/MPRAflow_batch_test/MPRAflow cre_only.fastq.gz count_fastq.txt s_merged.bam count_merged.txt assoc 30 30 n /home/cardwellj/MPRAflow_batch_test/MPRAflow cre_only.fastq.gz s_merged.bam count_fastq.txt count_merged.txt counts 20286799 280800 filtered barcodes: 0it [00:00, ?it/s]
However, if I manually take that output file to the next, filter_barcodes step, I can't get it to complete:
(MPRAflow) [cardwellj@e00 5d3399f7da422d10aa82e749dcd45e]$ python3 /home/cardwellj/MPRAflow_batch_test/MPRAflow/src/nf_filter_barcodes.py assoc assoc_coords_to_barcodes.pickle assoc_barcodes_per_candidate-no_repeats-no_jackpots.feather 3 0.5 /home/cardwellj/MPRAflow/work/95/ae488f924b13641b61162714bb2d76/label_rmIllegalChars.txt
Traceback (most recent call last):
File "/home/cardwellj/MPRAflow_batch_test/MPRAflow/src/nf_filter_barcodes.py", line 24, in
Hi,
I hope you are all doing well. I have an issue below. Could you please help me fix it? Thanks.
(MPRAflow) nextflow run --w /home/huanglabdell/Documents/MPRAflow/work02232024 association.nf --name HH_01092024as_1 --fastq-insert "/media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R1_001.fastq.gz" --fastq-insertPE "/media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R3_001.fastq.gz" --fastq-bc "/media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R2_001.fastq.gz" --design "/media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/mIL13_hTNF_hIL6_hIL1B_remove_adaptor.fa" -dsl1 N E X T F L O W ~ version 22.04.2 Launching
association.nf[chaotic_picasso] DSL1 - revision: 087b40d39fMPRAflow v2.3.1"
Pipeline Name : MPRAflow Pipeline Version: 2.3.1 Fastq insert : /media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R1_001.fastq.gz fastq paired : /media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R3_001.fastq.gz Fastq barcode : /media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/3_S3_L001_R2_001.fastq.gz design fasta : /media/huanglabdell/596F-E992/02212024/BCL2/Data/Intensities/BaseCalls/HH_01092024as/mIL13_hTNF_hIL6_hIL1B_remove_adaptor.fa minimum BC cov : 3 map quality : 30 base quality : 30 cigar string : n min % mapped : 0.5 Output dir : outs Run name : HH_01092024as_1 Working dir : /home/huanglabdell/Documents/MPRAflow/work Container Engine: null Current home : /home/huanglabdell Current user : huanglabdell Current path : /home/huanglabdell/Documents/MPRAflow base directory : /home/huanglabdell/Documents/MPRAflow Script dir : /home/huanglabdell/Documents/MPRAflow Config Profile : standard
executor > local (6) [99/2602b6] process > count_bc_nolab (count) [100%] 1 of 1 ✔ [53/c27b7f] process > create_BWA_ref (make ref) [100%] 1 of 1 ✔ [3b/2d3496] process > PE_merge (merge) [100%] 1 of 1 ✔ [c7/e14a7f] process > align_BWA_PE (align) [100%] 1 of 1 ✔ [00/ec1417] process > collect_chunks [100%] 1 of 1 ✔ [02/caf11f] process > map_element_barcodes (assign) [ 0%] 0 of 1 [- ] process > filter_barcodes - Error executing process > 'map_element_barcodes (assign)'
Caused by: Process
map_element_barcodes (assign)terminated with an error exit status (1)Command executed:
echo "test assign inputs" echo 30 echo 30 echo 3_S3_L001_R2_001.fastq.gz zcat 3_S3_L001_R2_001.fastq.gz | head
echo count_fastq.txt echo count_merged.txt cat count_fastq.txt cat count_merged.txt
python /home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py /home/huanglabdell/Documents/MPRAflow 3_S3_L001_R2_001.fastq.gz count_fastq.txt s_merged.bam count_merged.txt HH_01092024as_1 30 30 n
Command exit status: 1
Command output: test assign inputs 30 30 3_S3_L001_R2_001.fastq.gz @M01416:220:000000000-DN9DG:1:1101:15719:1611 2:N:0:TTTCCTCT TTTTTTTTTTTTTTT + 111111>1000>EAE @M01416:220:000000000-DN9DG:1:1101:17284:1628 2:N:0:TTTCCTCT TTTTTCTTTTTTTTT + 1>1>>1B3311>10A @M01416:220:000000000-DN9DG:1:1101:15709:1633 2:N:0:TTTCCTCT TTTTTTTTTTTTTTT count_fastq.txt count_merged.txt 1310484 0 /home/huanglabdell/Documents/MPRAflow 3_S3_L001_R2_001.fastq.gz s_merged.bam count_fastq.txt count_merged.txt counts 0 1310484 1310484 start bad pairs: 0 poor quality: 0 start
Command error:
paired-end reads: 0it [00:00, ?it/s] paired-end reads: 0it [00:00, ?it/s]
barcodes: 0%| | 0/327621.0 [00:00<?, ?it/s] barcodes: 11%|███████████████▌ | 34592/327621.0 [00:00<00:00, 345912.91it/s] barcodes: 21%|███████████████████████████████▌ | 70236/327621.0 [00:00<00:00, 349002.57it/s] barcodes: 32%|███████████████████████████████████████████████▏ | 105901/327621.0 [00:00<00:00, 351260.75it/s] barcodes: 43%|███████████████████████████████████████████████████████████████▍ | 142333/327621.0 [00:00<00:00, 355077.52it/s] barcodes: 55%|███████████████████████████████████████████████████████████████████████████████▋ | 178835/327621.0 [00:00<00:00, 358000.26it/s] barcodes: 66%|████████████████████████████████████████████████████████████████████████████████████████████████▏ | 215784/327621.0 [00:00<00:00, 361370.54it/s] barcodes: 77%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 252876/327621.0 [00:00<00:00, 364181.15it/s] barcodes: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 290323/327621.0 [00:00<00:00, 367206.76it/s][W::bgzf_read_block] EOF marker is absent. The input is probably truncated
executor > local (6) [99/2602b6] process > count_bc_nolab (count) [100%] 1 of 1 ✔ [53/c27b7f] process > create_BWA_ref (make ref) [100%] 1 of 1 ✔ [3b/2d3496] process > PE_merge (merge) [100%] 1 of 1 ✔ [c7/e14a7f] process > align_BWA_PE (align) [100%] 1 of 1 ✔ [00/ec1417] process > collect_chunks [100%] 1 of 1 ✔ [02/caf11f] process > map_element_barcodes (assign) [100%] 1 of 1, failed: 1 ✘ [- ] process > filter_barcodes - Error executing process > 'map_element_barcodes (assign)'
Caused by: Process
map_element_barcodes (assign)terminated with an error exit status (1)Command executed:
echo "test assign inputs" echo 30 echo 30 echo 3_S3_L001_R2_001.fastq.gz zcat 3_S3_L001_R2_001.fastq.gz | head
echo count_fastq.txt echo count_merged.txt cat count_fastq.txt cat count_merged.txt
python /home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py /home/huanglabdell/Documents/MPRAflow 3_S3_L001_R2_001.fastq.gz count_fastq.txt s_merged.bam count_merged.txt HH_01092024as_1 30 30 n
Command exit status: 1
Command output: test assign inputs 30 30 3_S3_L001_R2_001.fastq.gz @M01416:220:000000000-DN9DG:1:1101:15719:1611 2:N:0:TTTCCTCT TTTTTTTTTTTTTTT + 111111>1000>EAE @M01416:220:000000000-DN9DG:1:1101:17284:1628 2:N:0:TTTCCTCT TTTTTCTTTTTTTTT + 1>1>>1B3311>10A @M01416:220:000000000-DN9DG:1:1101:15709:1633 2:N:0:TTTCCTCT TTTTTTTTTTTTTTT count_fastq.txt count_merged.txt 1310484 0 /home/huanglabdell/Documents/MPRAflow 3_S3_L001_R2_001.fastq.gz s_merged.bam count_fastq.txt count_merged.txt counts 0 1310484 1310484 start bad pairs: 0 poor quality: 0 start
Command error:
paired-end reads: 0it [00:00, ?it/s] paired-end reads: 0it [00:00, ?it/s]
barcodes: 0%| | 0/327621.0 [00:00<?, ?it/s] barcodes: 11%|███████████████▌ | 34592/327621.0 [00:00<00:00, 345912.91it/s] barcodes: 21%|███████████████████████████████▌ | 70236/327621.0 [00:00<00:00, 349002.57it/s] barcodes: 32%|███████████████████████████████████████████████▏ | 105901/327621.0 [00:00<00:00, 351260.75it/s] barcodes: 43%|███████████████████████████████████████████████████████████████▍ | 142333/327621.0 [00:00<00:00, 355077.52it/s] barcodes: 55%|███████████████████████████████████████████████████████████████████████████████▋ | 178835/327621.0 [00:00<00:00, 358000.26it/s] barcodes: 66%|████████████████████████████████████████████████████████████████████████████████████████████████▏ | 215784/327621.0 [00:00<00:00, 361370.54it/s] barcodes: 77%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 252876/327621.0 [00:00<00:00, 364181.15it/s] barcodes: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 290323/327621.0 [00:00<00:00, 367206.76it/s][W::bgzf_read_block] EOF marker is absent. The input is probably truncated
barcodes: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉| 327469/327621.0 [00:00<00:00, 368472.31it/s] barcodes: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 327621/327621.0 [00:00<00:00, 363754.83it/s] Traceback (most recent call last): File "/home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py", line 157, in
save_barcodes_per_candidate(coords_to_barcodes, f'{prefix}_barcodes_per_candidate.feather')
File "/home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py", line 134, in save_barcodes_per_candidate
pd.Series(d, name = 'n_barcodes')
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/generic.py", line 5063, in getattr
return object.getattribute(self, name)
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/accessor.py", line 171, in get
accessor_obj = self._accessor(obj)
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib | 34592/327621.0 [00:00<00:00, 345912.91it/s]
barcodes: 21%|███████████████████████████████▌ | 70236/327621.0 [00:00<00:00, 349002.57it/s]
barcodes: 32%|███████████████████████████████████████████████▏ | 105901/327621.0 [00:00<00:00, 351260.75it/s]
barcodes: 43%|███████████████████████████████████████████████████████████████▍ | 142333/327621.0 [00:00<00:00, 355077.52it/s]
barcodes: 55%|███████████████████████████████████████████████████████████████████████████████▋ | 178835/327621.0 [00:00<00:00, 358000.26it/s]
barcodes: 66%|████████████████████████████████████████████████████████████████████████████████████████████████▏ | 215784/327621.0 [00:00<00:00, 361370.54it/s]
barcodes: 77%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 252876/327621.0 [00:00<00:00, 364181.15it/s]
barcodes: 89%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 290323/327621.0 [00:00<00:00, 367206.76it/s][W::bgzf_read_block] EOF marker is absent. The input is probably truncated
barcodes: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉| 327469/327621.0 [00:00<00:00, 368472.31it/s] barcodes: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 327621/327621.0 [00:00<00:00, 363754.83it/s] Traceback (most recent call last): File "/home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py", line 157, in
save_barcodes_per_candidate(coords_to_barcodes, f'{prefix}_barcodes_per_candidate.feather')
File "/home/huanglabdell/Documents/MPRAflow/src/nf_ori_map_barcodes.py", line 134, in save_barcodes_per_candidate
pd.Series(d, name = 'n_barcodes')
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/generic.py", line 5063, in getattr
return object.getattribute(self, name)
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/accessor.py", line 171, in get
accessor_obj = self._accessor(obj)
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/strings.py", line 1796, in init
self._validate(data)
File "/home/huanglabdell/Documents/MPRAflow/work/conda/mpraflow_py36-1978c54da7aacd41df3c7a4cb7639795/lib/python3.6/site-packages/pandas/core/strings.py", line 1818, in validate
raise AttributeError("Can only use .str accessor with string "
AttributeError: Can only use .str accessor with string values, which use np.object dtype in pandas
Work dir: /home/huanglabdell/Documents/MPRAflow/work/02/caf11fd327ea7f39e2b5ecfe90187f
Tip: when you have fixed the problem you can continue the execution adding the option
-resumeto the run command line