Entering edit mode
4.2 years ago
Doofania
▴
10
Hi, I had a bam file with me, I created the required .gtf using StringTie, but when I run tablemaker (https://github.com/leekgroup/tablemaker) on it, it produces the following error -
BAM error: CIGAR op has zero length (ch459_read36275_template_fail_FAH60712)
in half of the file, then I made it's sam file using samtools & saw something weird - It gave error in this read -
ch368_read8557_template_fail_FAH60712 16 1 4491430 56 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 * 0 0 CATGGATTTTAGGATGGCGTTGAATAGGTTGGAGTGGAATTTAATTCCAAATTATTAATTAAAGCACAACAAAATTTCCTCTTGATCAATACACTTCAAATGGAATAAGTCAGTGAGATATTTTAAAACTGGCTAAAACTGGACAGTGATTGTGGGGAGCAAGTCCCCTTAGGTATTTTAAAACAAAATCTCGTGTAGCCCCAACTGTTCAAAGGCAAGCGAAAGTATGATTACCATAATGTATTATATGCCAGGCAACTAAAAACAAAACAGCTTGACGCTAAGGATTCCTTAGCGCTTCCAGGTAGTAGTGTAACACTGCTTCTGGCCTCAGGTCGGGTCATTAACCGTCCAATGTCGGGGGTAATATGCAATAGTAAACCGCTGAGCTAGCGTCGGACACCACGGAAGGAATGGCTCCGTGGATTGTCCGAGTTCACTGCAGTCGTGCCCGGTAGGGAAGACCCATCTTCGGGCTTATACACAAAGAGGGCAATACTTATACAGAATTCCGTGACGAAAGCCACCCCCGGAGCTCAGTAAGGGCTGGTTGGAGATTCCGAAGCCATCCCGGCAGTAGGGCAAGCCTCGGGAGGGGCGAGGTTGCCTGTGCCGTGCGCTGGGTGCTGCCGCTGCGGTGGCGATGGCGGTGCCTGCGATGCAGCGGCTGCTGGGTTGCGCGTGAACCGCGCCCCGCACTTGCGGCGGGCGAGCCCATCGCGCTGTTGCTGGACAAGCGCTGGGGCGCCGTGATCCCCGGACGTCGCAAGGCCCGAGGGGAGTCCGGCCACTACTCGCGTGGCTGCGGGCGGCTCTTCGAGCACTGCGTTGCTGTACTGGAACGTAGAGTAGGTGCCGGCCGCCATATGCTCGCGCAGCGGGGCTGCAAAAGAAGCCGAGCCTGCTCCACGCCGCGCTGCGGGGATGTGGTCCGGTGATGGGCAGAGGTAGCCGTCGAGCGCGGGATGCACAGTCCTGGCAGCCGAATAATGAGGGGGCCCGAGCGGAACATCAGCGGAAGGACCGGCCGGATAGCCCGGCTCCGGGAAGGTGAAAGCAGACCAGGCCATCCATGGCCACGCAGCATTCGGGACCAGTAGCGCCGGCCTGGGGCTCGACGAAGCGTGCAGGAAGCCTCCACCTGCTTCATGCTTCACCTGCTTGCGCCGCCGCAACATCTCATGTTGGGTGGTCCTGATGCTGCACGCGCAGCCGCTCGGCCTCTTCCACGAGGGCCGCTTCTCTCTGCCAGGTCACGCCTTCCAGTGTCTTGCCTAGCGTTCTTGCTTAGCTCTGCGTTGTGCAGATCTGGGTTCTGCTGTGCCAACCGCTTGCGTTCGTCTAAGGCCCACCGATGAGCGTTCATCGGCCGCAACGGATGCAATGAGACTCCGCTTGGCTCGGCCCGACGTCCCGGCTGGCGCCCCGCTACTCGCCACCACCTCGCCTTTCACCTTTATCGTCTCGGTGGGCTCAGGACTGGCCAGGGACAGGCCCAACCTGCCATCACCGCGGGCTGCGCGCGCTCCGGGCTGGCCTTGTCGTCACTGGCGTATCCCGCATCCGGGCTGCCGGCTCTCCAGACCCCTAGCTCTGCTATGGCCGGACACGCCGCTTCCCGACCTTGGGAAACTGGCTGGAGCCGGGCGCTGGCGCCAAAACCTCTTGGGAAAGCGGAAGGCTGAATTCAGATGTCTGGAGGTGCTGCTCATTGTATCCATTGTGGTGACATGCTGTGTTTTCCTGTATTATTCAGTGACCAAATCTGGCTTACTAAATCCATACCTTCTGCTGACCATTCTCAGCAAATGAATACTTGGGATGTTGGGGCCACCGCACTTCAGACCCGCCAGCAGTGTTGTGTGGGCAACCAGTTTCTTCACTAAAATGGGAGGATGGAAGCCGAGCTCACGTTATCAGAGCCAA $$#(&$))'&&''$#%%"$&$#'%$&(%&#''&%$((%&(,))'*(+$.2),.*1+1()&,+($&%'+-*0/5/,6+))&()&&.)(&((&%'*)*$(--(1+*-()(&&*++)+'()*(29260154-125-*('11--4;0.*(%%)*5&#-2)''-.0:1..-2)&''*&$%++1(,++*-.,40,1.,+,*)('/.'--4..)-)&'()()'((%$$0/*&&&,)+25++(('('()(-21**%%&.'*(('.*)&*/:9-12002..,.0112112121-(%1)./+-,&%+*.0*5/,)&%%'()+**(&%)*%'&.*/03110(*+1,++194//$&'024**)/+-*$&'',970)+(&%$&,,40.-+(-3,1,)(+%(*/.2678899976/7.++.*'%*&+,)/1---+(%(($+*%&&$$#%0-+)(%%&'*.,)'%,,%'(&%(3.(+'()3++,*+&*'-8*'(*+/02-/),&,/9,,-&),++'#$$%'&*+32//,'*&(&()&%1'$/210'()'**)((&%%%,8+++2/11,+))*3;25&&*')')).6+4-*(&'&06/**('(.%(-2')-71)'''&*),','&'$,--.(&++*')*.*/*+)+$()%&(($$-1,,&&&'$/1-.1+(()+%/*,)++/6,*))(./,+,++*'($$))5).-)/42)-.)()(+,262-453%$%%&.01-,)'%%&((('&(&&0-('(&(*06:,''''$#%('*5:.++'0'/,'$)*,5)4,),115/&*+1+*'.)%'$%(($'%'#*%*"'&(/10*)'''+/-/&&,++,-,-1,((*'&12'1..&))))%'))*/4()*0-30/+0)(&$#$,%,(%$'&'3.863-+-%,+*)#,0,/80*)/,)3325;11/,.$#$)%'%-.3)%()(),*4)3*$%&'&1))*&%1)))**.-00060--+-0)(&''#'%$#+)')/(*(++')*&)'(')*3750*1,%)+/481,.,,.(&(,.'+).*,%')))*(&)('*-)%%$)0%/4(()*)%%()&$%'%(0+-4,6,/1.())/)3-#'$%(('%%'&1/*(52(%$%%(),+,.*4*(:5*+,,,/))+'&+,,-3-/0,-()+').)/2%(),(&&&',14//71.,*+)')+2,+/,*(*,)'((&'$$&3+8:1++'%+)%%$'(-'')&*'((((+6+++,-,4-1)(,(1)+'((*4+0*-),)(&$&'&&+*'%%#(%&&,)+(*&'%&$#(,('.)%&)($',*-.**+*(**,.($$&*2/,2122868-7;877,,*)*--,+*''.('(*,*,/2622+**('.)((*(,+('(&+(+034./1012*+%%%'(,((-++,-$$*%'+,,2*,*2//,--/2./-*,-,+/1+-**+97+*,73--1,-,,,/20-1/)0,('&+)-+((-(3,56''*+,-&&)$#/72+-++20-2(+'*(()-(%(&/,*77001.*,+)()'*-(())3/+,,,,*()'&+*1/::0).,*))))+5500.+(+0(+*''08+-0./06475/-(,+,-.,++01+*(,,2.&*,/-((('(+,-,0++4,+*+*/-)(+(+*&))0+((-/(16*8,7..*5*-(--3:4/2124-,).%('-')*&()*1<(--'$%+*%%+8'&&5*/6,(*+,/-.),*&',)/,+)+%,).+'%),0)&(--')(#$#**(),)(&)-2;1+2&*)110-21)(($,(+23764/./4.5.,,'+(2&&(*#'&+*-,*+,//558*.,()*(((,)()%(')#'($,.($'(-3685(/**0.,*&('&(*$'17),.71,-('%$%&&&++09-.*-,(&'054146336,)*,''3/*%)%$'.+,)+310++)(''$$%(*+--%'&-(($ NM:i:269 ms:i:1922 AS:i:1922 nn:i:0 ts:A:+ tp:A:P cm:i:62 s1:i:489 s2:i:372 dv:f:0.1088
& not this -
ch380_read3068_template_fail_FAH60712 16 1 4774317 60 68S6M1I4M1D15M1D15M2D6M3D3M1D14M2D14M2D6M2I10M5D8M1D18M2D14M1D13M1D6M1D2M1D3M4D15M3008N18M4D27M2D2M1I2M3D3M3D30M2D7M1D4M1I5M1D10M4919N20M2I4M1D2M1I33M1I16M4I15M1I5M1I21M1D3M1I14M1D7M2D1M1I20M1217N8M1I27M3D2M4D1M2D9M3D5M3I21M2I5M1D12M1D7M2D5M2D3M2D12M1I18M1467N5M2D4M1D10M3I17M1D37M1D15M3I10M18S * 0 0 AGATTTTCCATAGGTGATTGGATAATAATAACAATTGCGGAATAGTTGGATAGGTATTTAACGAGTTTTCTTACCTTTAAAATGGGATGTGGGGCAGATGCAGGCACACGGAGGCATTAGGCACACATGGAGCTGATGCAGGCACATGGAGGGCCCAGATGCTGATGTCTTTCTCAATGGCTTTTGCATTTTGATGTGTATTGATATCTTCTTGAAATCTATGAATCAAGTGCATCAAGTGCCCTAGACTTCTTGGGTCATGGCTGTAGTAAAGTTACCGCCATTTTTCAGATAGCGGCTAATTCTTAAGCCAGCTGCACTTCAATTAATTTTGCTTTGGTAATATCAGCACCCTCTTCAACCAGCTGGACTCTCCATATCTCCTCTTAAACGGCTGGATGGTCACACCTCTCCCCATTCACAAGCTGGTTTGGATAGGTCAATAGGTTGTTGTTGGTATCAACTCGACCTAAATCTATAGAATACTGTAGTCTCCTAGACTCAGTGCTGATACTGGTGCCTGAAACTATGTCCCTTCATTAAATCCATATTTTTGGAGGCCGTTAGTCTGCCCCTCAATAAAGCCCAGCCTTGGCCGGGTTCTACTCTCGCCTTTCTCCAGATGGCCTGCCACTTCACCTCTTCTCCATATCTCTGGTGCGTCTTTCCCATTCTGGGTTTGGACTGCCGGGCTTCAGGTTGGCCCGCTCACTCTCGGCAAGAACCACAGCAGGTCCAGGCTGACCCACAGCCGCGCGCGACCGTGCCAGCCTAAACACAATACGACTCA #$$$(,*#"&%&)($$%%%'&%%&($)$&&&&*(*'&#*&'%$%#&$)($%$**$*%6+/+'$'$*-&''&%&&*&.*,1/**.7/('(),090*+(&%'*)31,)*)))*%(%&%$$,70,+**)-+.(*&''%%%%*%0.*+*)(,*'*/)+.'&&*'&&$#'((*)192*+)+,)-)&/:4)&%),43,%$&(',*('%%&''')2($('$$*(+,'%$$&&/$%$$#$$$&%)&&$)/4)()'**2,++,+22'&&%(9(*'''&''&&#&()+-,..+3;74)&&$&$'%&(/0.7,1,*'$&)&*1)$%+)*(),.--/---(10+'((-4--)&&*()*-2+*'21)(*/44494/,,)'-,''&))++(%'('%-')+00.+*+.1./3((')('**+&+'%&%,39,,4-+.+-,'('+($$$,-))*/.(.20..//.+),*(*.'1*/2-3.--./+,+'/5+-&$$'%%*',+,)($((.+..2*,)*)+))&%-+')+*,**(,)*)0'%+,*&'()*)-2)-4--0112006,))(+473+**$++,,%&%$&&'&#)*,(&%&(&')'%,,+*)2),++('+'-,)+'&%'((&&(,*.6*('$$&#'+2.+)&&**''&&'$),)+/*))1,&&'''&$%'(#*++,+-51(2,'00*+,-)&4+5.+,+&'%').*.++(--,..,.-$#%%'&'()()$&'(($*/,,*,-5516/,04-13/,*).,(&%%'0(((''&'%#/''$&*()%(%#&)(+(&%&$'%%$'&$" NM:i:141 ms:i:690 AS:i:690 nn:i:0 ts:A:+ tp:A:P cm:i:19 s1:i:148 s2:i:132 dv:f:0.1114
Commands I used were -
1) stringtie -L RNA_nanopore.brain.C1R1_mapping_E94_minimap2_primary_no_read_less_than_80QC_genome_convert.sorted.bam -o RNA_nanopore.brain.gtf -p 6 -v
2) tablemaker -p 4 -q -W -G RNA_nanopore.brain.gtf -o sample01_output mapped.bam --library-type fr-firststrand
Any help would be appreciated.
Hi Doofania,
next time please use the code option to highlight code, data examples and error messages. Simply pasting a large chunk of those without any formatting looks rather unorganized and typically does not motivate people to even have a closer look at this question. Highlighting therefore increases a chance of a good answer.
Ok sure, I'll keep it in mind next time :)