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>
File "/group/bioinfo/apps/apps/danpos-2.2.2/danpos.py", line 411, in runDANPOS
File "/group/bioinfo/apps/apps/danpos-2.2.2/functions.py", line 375, in danpos
File "/group/bioinfo/apps/apps/danpos-2.2.2/wig.py", line 484, in fillPositions
File "/group/bioinfo/apps/apps/danpos-2.2.2/summits.py", line 34, in fetchValueFromWig
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.