Error parsing filemap:

[zillurbmb51]

Hello, I have admixture outputs which I want to plot using pong. My filemap are attached. No matter how I edit my filemap it always say that: `Error parsing filemap: check that the file is tab-delimited, that the columns are ordered properly, and that the '#' character is not used other than to indicate the start of a comment (i.e. it cannot be used as part of a runID).

filemap13.txt filemap15.txt ` Any help? Best, Zillur

[abehr]

Hi Zillur,

The filemap must be a 3-column file; it looks like you have an extra column for line numbers, and an extra non-commented row for column headers. Based on the example filemap depiction (Table 1 in the manual), I can see why this was confusing! I've attached a reformatted version of filemap13.txt that should work properly. You can also refer to the filemap provided with the pong example dataset. Hope that helps!

filemap13_reformatted.txt

Best, Aaron

[zillurbmb51]

Ohh! I was thinking about this error type. Thank you. Now I am getting a new error:

(base) [zillur@dutillab captured_regions]$ pong -m filemap17 -i snps_plot/pops_all2 -o pong2

Output dir pong2 already exists.
Overwrite? (y/n): y

-------------------------------------------------------------------
                            p o n g
      by A. Behr, K. Liu, T. Devlin, G. Liu-Fang, and S. Ramachandran
                       Version 1.4.7 (2016)
-------------------------------------------------------------------
-------------------------------------------------------------------

Parsing input and generating cluster network graph
Error parsing filemap: encountered duplicate Q matrix ID s1321.

Any help? filemap17.txt

[abehr]

Each run (i.e. each Q-matrix generated by running Admixture) listed in your filemap must be labeled with a unique runID. It looks like you have multiple runs in your filemap with the same ID, which is why pong is giving that error message. For example, you could change the names of the first two runs in your filemap to s1321_K=1 and s1321_K=9.

You can learn more about this in section 5.2 of the pong manual.

[zillurbmb51]

Thank you very much. It works now! I got the attached figure. Is there any way to customized order the plot (For example, in the attached figure at the top I have tcga_hg38_somatic; all test are not readable, I want this panel to the middle or bottom with full panel names).

[abehr]

Modes are sorted by how many runs they represent, with the major mode appearing first. Unfortunately there's no way to specify a second sort order beyond this. However, you can remove any tests from your filemap that are not necessary for analysis once you've identified as much, or you can download individual plots and then place them in any order.