Question: DANPOS2 - index out of bounds error
0
gravatar for ckcollings11
3.6 years ago by
United States
ckcollings110 wrote:

Hello,

I am running into an error using DANPOS2.  I do not understand why the error is occurring.
I also posted this on the DANPOS2 help forum but I thought that I might be able get help from here - perhaps from some random python expert who just happens to know about DANPOS2.


I used the following 6 commands.  I have 4 groups (A,B,C,D) with 2 replicates each.
I am trying to obtain the 'ref_adjust.xls' files for each of the 4 samples in the 6 possible pair-wise comparisons (AB,AC,AD,BC,BD,CD)

**********
danpos.py dpos AB/A/A1.bam,AB/A/A2.bam,AB/B/B1.bam,AB/B/B2.bam -e 1 --frsz 150 --clonalcut 0 -o AB/AB_output -b AB/E/E.bam
danpos.py dpos AC/A/A1.bam,AC/A/A2.bam,AC/C/C1.bam,AC/C/C2.bam -e 1 --frsz 150 --clonalcut 0 -o AC/AC_output -b AC/E/E.bam
danpos.py dpos AD/A/A1.bam,AD/A/A2.bam,AD/D/D1.bam,AD/D/D2.bam -e 1 --frsz 150 --clonalcut 0 -o AD/AD_output -b AD/E/E.bam
danpos.py dpos BC/B/B1.bam,BC/B/B2.bam,BC/C/C1.bam,BC/C/C2.bam -e 1 --frsz 150 --clonalcut 0 -o BC/BC_output -b BC/E/E.bam
danpos.py dpos BD/B/B1.bam,BD/B/B2.bam,BD/D/D1.bam,BD/D/D2.bam -e 1 --frsz 150 --clonalcut 0 -o BD/BD_output -b BD/E/E.bam
danpos.py dpos CD/C/C1.bam,CD/C/C2.bam,CD/D/D1.bam,CD/D/D2.bam -e 1 --frsz 150 --clonalcut 0 -o CD/CD_output -b CD/E/E.bam
**********

All comparisons printed out a 'reference_positions.xls' file in the main output folder.
All comparisons printed out wig files for the 4 samples and for the background sample in the 'pooled' subfolder.
All comparisons printed out the 4 .xls files in the 'pooled' subfolder that did not contain 'ref_adjust' in the file name.
3 of these comparisons worked fine (AB,BC,CD) and also printed out the 4 'ref_adjust.xls' files in the 'pooled' subfolder.
However, 2 of these comparisons (AC, AD) generated all of the output except the 4 'ref_adjust.xls' files.
And, strangely, the remaining comparison (BD) generated all of the output except 2/4 of the 'ref_adjust.xls' files.


We received the following error message associated with the missing 'ref_adjust.xls' files.

%%%%%%%%%%
Traceback (most recent call last):
  File "/group/bioinfo/apps/apps/danpos-2.2.2/danpos.py", line 1352, in <module>
    if sys.argv[1]=='dpos':runDANPOS(command='dpos')
  File "/group/bioinfo/apps/apps/danpos-2.2.2/danpos.py", line 411, in runDANPOS
    pcfer=0)#args.pcfer)#0)                  
  File "/group/bioinfo/apps/apps/danpos-2.2.2/functions.py", line 375, in danpos
    pooledgroups[groupname].fillPositions(dic=tdic,file=os.path.join(opath,'pooled',groupname+addname+"positions.ref_adjust.xls"),width=width,distance=distance,edge=edge,pcut=pheight,height=height,calculate_P_value=1,mode='w',title_line=1,poscal=1,rd=rd)
  File "/group/bioinfo/apps/apps/danpos-2.2.2/wig.py", line 484, in fillPositions
    smts.fetchValueFromWig(twig)
  File "/group/bioinfo/apps/apps/danpos-2.2.2/summits.py", line 34, in fetchValueFromWig
    smt.data[cr]['v'][i]=wig.data[cr][tp]
IndexError: index out of bounds
%%%%%%%%%%


We performed md5sum checks on all of the files and found that
AB/A/A1.bam = AC/A/A1.bam = AD/A/A1.bam
AB/A/A2.bam = AC/A/A2.bam = AD/A/A2.bam
AB/B/B1.bam = BC/B/B1.bam = BD/B/B1.bam
AB/B/B2.bam = BC/B/B2.bam = BD/B/B2.bam
AC/C/C1.bam = BC/C/C1.bam = CD/C/C1.bam
AC/C/C2.bam = BC/C/C2.bam = CD/C/C2.bam
AD/D/D1.bam = BD/D/D1.bam = CD/D/D1.bam
AD/D/D2.bam = BD/D/D2.bam = CD/D/D2.bam
AB/E/E.bam = AC/E/E.bam = AD/E/E.bam = BC/E/E.bam = BD/E/E.bam = CD/E/E.bam


So, we do not believe that there is a problem with the input files.
Also, all of the 8 samples were involved in at least one of the three comparisons that worked.


Please let me know if I am doing something wrong or if there is something I can do to fix the problem.

Thanks for your time.

Sincerely,
Clayton
 

software error • 1.3k views
ADD COMMENTlink written 3.6 years ago by ckcollings110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1584 users visited in the last hour