Error when running reasoning_v1.0.py

[Jonathanyu2014]

Dear all, When I run reasoning_v1.0.py, there is an indexError as follows. However, the output file seems good. Dose this Error matter? What should I do?

Traceback (most recent call last): File "/home/user/softwares/SCcaller/reasoning_v1.0.py", line 118, in while a > d1p[pointer]: IndexError: list index out of range

[biosinodx]

Hi Jonathanyu2014,

Are the numbers of rows the same of your input and output files? If so, it should be OK. Could you share with me the last few rows of your mpileup file? That could be the reason of the error.

Best, Xiao

[Jonathanyu2014]

Hi biosinodx,

I find the numbers of the rows of my input files are the same with corresponding output files. I ran samtools (v1.5) with parameters "samtools mpileup -C50 -r chrM -Osf /home/user/hg19/hg19.fa /home/user/result/LE001-MM.mkdup.bam > /home/user/result/LE001/LE001-MM.chrM.mpileup".

Below is an example of my mpileup file from chrM of hg19 (last few lines):

chrM 16548 C 60 ,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >>>>>;EEBFFE0FFE<F@@FFF8EC6<EFFFFFF8DEA=AFFEFFEFFD?FFFDFDC SSSSSSSRSSSSSSSSSSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSOONLFGG=2$ 50,50,49,49,48,48,47,47,46,46,46,45,45,45,45,44,42,41,41,41,41,41,40,38,36,36,36,35,34,34,33,33,38,33,32,31,31,31,30,30,30,30,29,29,29,28,28,27,27,27,26,26,25,25,24,24,24,22,21,20 chrM 16549 C 59 ,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ;;;8B9CFFDEFFFF@F;FFF=CF:E@FFCFFFF8EF4;FFFCC<F?5FDFEE9F=> SSSSSRSSSSSSSSSSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,49,49,48,48,47,47,47,46,46,46,46,45,43,42,42,42,42,42,41,39,37,37,37,36,35,35,34,34,39,34,33,32,32,32,31,31,31,31,30,30,30,29,29,29,28,28,28,27,27,26,26 ,25,25,25,23,22,21 chrM 16550 C 55 ,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, :AAEFFEEFDGA@E47FFF6D@17D;F>FFEF4DE?;EFFDFFFCD?9EDFDFD> SSRSSSSSSSSSSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSOONLFGG=2$ 50,49,49,48,48,48,47,47,47,47,46,44,43,43,43,43,43,42,40,38,38,38,37,36,36,35,35,40,35,34,33,33,33,32,32,32,32,31,31,31,30,30,29,29,29,28,28,27,27,26,26,26,24,23,22 chrM 16551 C 55 ,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ??FFFFFFFGFBFBDFFFBEE;BFEFEF=FF<FFDAFFFFF?;FFF:EFFEFFF8 SRSSSSSSSSSSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,49,49,49,48,48,48,48,47,45,44,44,44,44,44,43,41,39,39,39,38,37,37,36,36,41,36,35,34,34,34,33,33,33,33,32,32,32,31,31,31,30,30,30,29,29,28,28,27,27,27,25,24,23 chrM 16552 T 49 ,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >>>ACEEGF.E8FEF0/F.>AF8;FFF0;;>>6EF8.FA:DCBFC>EF5 SSSSSSSSSSSRSSSSSSSSSSKSSSSSSSSSHSLSSSSSOONLFG=2$ 50,50,50,49,49,49,49,48,46,45,45,45,45,44,42,40,40,40,39,38,37,37,42,37,36,35,35,35,34,34,34,34,33,33,33,32,32,31,31,31,30,30,29,29,28,28,26,25,24 chrM 16553 T 49 ,$,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, BBBBEF>G31FFF<?E9/DF1?FEF6B?>F@FFBFEFFCF;EF?F<FE; SSSSSSSSSRSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,50,50,49,47,46,46,46,46,46,45,43,41,41,41,40,39,38,38,43,38,37,36,36,36,35,35,35,35,34,34,34,33,33,33,32,32,32,31,31,30,30,29,29,29,27,26,25 chrM 16554 A 46 ,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >E4F3@FFF;7>60CEFAFFEF3E=D:BBFFF;FEDF;9GFEDFE@ SSSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,48,47,47,47,47,47,46,44,42,42,42,41,40,40,39,39,44,39,38,37,37,37,36,36,36,36,35,35,35,34,34,34,33,33,33,32,32,31,31,30,30,30,28,27,26 chrM 16555 A 45 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, BBF0.FFF06C;19GFDEFFF>=EEE6FFDFD:E>F;2FEDCFF< SSSSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 49,48,48,48,48,48,47,45,43,43,43,42,41,41,40,40,45,40,39,38,38,38,37,37,37,37,36,36,36,35,35,35,34,34,34,33,33,32,32,31,31,31,29,28,27 chrM 16556 A 42 ,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @BF3FFF4:C5D;FFCGFE1D5F>FFCFAF@BEB;FA9F9D8 SSSSSSSSSSSSSSKSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,49,49,49,49,48,46,44,44,44,43,42,41,41,46,41,40,39,39,39,38,38,38,37,37,37,36,36,36,35,35,35,34,34,33,33,32,32,32,30,29,28 chrM 16557 T 43 ,$,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >DEEFFFDF6?4FFFEFFF<EFFDCFFFGEGCEFA?FDFBEE< SSRSSSSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,50,50,49,47,45,45,45,44,43,43,42,42,47,42,41,40,40,40,39,39,39,39,38,38,38,37,37,37,36,36,36,35,35,34,34,33,33,33,31,30,29 chrM 16558 A 38 ,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >G<>F/5@F:;FFFF;=EF51FFFFAFEAF9FCFCFE@ SSSSSSSSSSKSSSSSSSSSHSLSSSSSSONLFGG=2$ 50,48,46,46,46,45,44,44,43,43,48,43,42,41,41,41,40,40,40,40,39,39,39,38,38,38,37,37,37,36,35,35,34,34,34,32,31,30 chrM 16559 A 38 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, F::D37AFFFFFFF<B?F=7FFDFBFECEBDFEED9G> SSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 49,47,47,47,46,45,45,44,44,49,44,43,42,42,42,41,41,41,41,40,40,40,39,39,39,38,38,38,37,37,36,36,35,35,35,33,32,31 chrM 16560 G 38 ,$,,,,,,,,,$,,,,,,,,,,,,,,,,,,,,,,,,,,,, E8DF?D=FBEFGFF3>FFAFFGFG@>FCF:BFFFEFFE SSSSSSSSSKSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,48,48,48,47,46,46,45,45,50,45,44,43,43,43,42,42,42,42,41,41,41,40,40,40,39,39,39,38,38,37,37,36,36,36,34,33,32 chrM 16561 A 35 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, /9D1@FEFEFFF8DF5?FFDF7FDEE8;FFD@FG1 SSSSSSSSSSSSSSSSHSLSSSSSSOONLFGG=2$ 49,49,49,48,47,47,46,46,46,45,44,44,43,43,43,43,42,42,42,41,41,41,40,40,40,39,39,38,38,37,37,37,35,34,33 chrM 16562 C 36 ,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, CEEACFFF<FFC@FFF<FFFFF@FFFFFBFFFFFFF SSSSSSSSSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,50,49,48,48,47,47,47,46,45,45,45,44,44,44,44,43,43,43,42,42,42,41,41,41,40,40,39,39,38,38,38,36,35,34 chrM 16563 A 32 ,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, :<6CFFFF::ADF6FFFG;FF?F??FFEDFG< SSSSSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,49,49,48,48,48,47,46,46,46,45,45,45,44,44,44,43,43,43,42,42,42,41,41,40,40,39,39,39,37,36,35 chrM 16564 T 32 ,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, BAF6F:>.0?FA9EF?@<F=?D=FFD9FE7 SSSSSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,49,49,49,48,47,47,47,46,46,46,46,45,45,45,44,44,44,43,43,43,42,42,41,41,40,40,40,38,37,36 chrM 16565 C 30 ,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,, DDD=F<?EFFB>FFFFBFEFF@BFFFFFGF SSSSSSSSSSSHSLSSSSSSOONLFGG=2$ 50,50,50,49,48,48,48,47,47,47,47,46,46,46,45,45,45,44,44,44,43,43,42,42,41,41,41,39,38,37 chrM 16566 A 27 ,$,,,,,,,,$,,,,,,,,,,,,,,,,,, EF.5=:F.3D@CF@F<@EC6FF>@FFE SSSSSSSSHSLSSSSSSOONLFGG=2$ 50,49,49,49,48,48,48,48,47,47,47,46,46,46,45,45,45,44,44,43,43,42,42,42,40,39,38 chrM 16567 C 24 ,$,$,,,,,,$,,,,,,,,,,,,,,,, EBFFF8F1FG@FFFFFEFFFFFGF SSSSSSSLSSSSSSOONLFGG=2$ 50,50,49,49,49,49,48,48,47,47,47,46,46,46,45,45,44,44,43,43,43,41,40,39 chrM 16568 G 21 ,$,$,$,$,,,,,,,,,,,,,,,,, EEE7FFFAFFEFF@B222EEE SSSSSSSSSSSOONLFGG=2$ 50,50,50,50,49,48,48,48,47,47,47,46,46,45,45,44,44,44,42,41,40 chrM 16569 A 17 ,$,,,,,,,,,,,,,,,, EBFDFD6FE6?///?B? SSSSSSSOONLFGG=2$ 50,49,49,49,48,48,48,47,47,46,46,45,45,45,43,42,41 chrM 16570 T 13 ,$,$,$,,,,,,,,,, CECFD=CC2=<>5 SSSSSSOONL=2$ 50,50,50,49,49,49,48,48,47,47,44,43,42 chrM 16571 G 8 ,$,$,$,$,$,$,$,$ EED/0000 SSSNL=2$ 50,50,50,48,48,45,44,43

[biosinodx]

Hi Jonathanyu2014,

The mpileup looks OK. I will keep this issue in mind and see if I can revise the script in the next version. Thank you!

Best, Xiao

[biosinodx]

Hi Jonathanyu2014, This issue was resolved in the new version. Thanks! Xiao

[Jonathanyu2014]

Many thanks! I'll test and run the new version of SCcaller soon. Best, Jonathan