DANPOS3 runs but does not save?-- please help

[Stephan Baehr]

Hello,

I am trying to run danpos3 dpos on a series of .bam files. These bam files have paired end 75bp reads aligned to a genome with BWA. That (.sam) file was turned into a BAM file, sorted and indexed. the header remains present.

The Problem: When I run the standard dpos command (python danpos.py dpos sorted_pcaud1mnase.bam) I see a bunch of code stream through my terminal-- the bam file as it is being parsed, it appears. Great, I would think. However, when the code completes, I go to the new directory "result", but find that directory to be empty. No wig file, no anything. It makes me very sad.

I get no error prompt to chase, I have no exit files. It is as if danpos is parsing through the entire bam file and then not saving anything, or else, the parsing is failing somehow. Has this happened to anyone? I am at a loss. I suppose I could show the problem on a zoom call but I dont want to be such a burden.

Details:

I am a fairly new coder so I could be missing something. In the past I have successfully used danpos 2.2.2 on a server. However, now I cannot seem to make it work. :(

I did add the directories to the $PATH.  it would not have otherwise run.

I have set up a new linux partition (ubuntu 20.04) on my home desktop computer. I installed the pre-requisite files/programs, and when I run print_versions.py I get the following, correct output:

(base) thalion@Envinyatar:~/DANPOS3$ python print_versions.py

Python version
3.7.6 (default, Jan  8 2020, 19:59:22)
[GCC 7.3.0]
-------------------------------------------------

R version 4.0.1 (2020-06-06) -- "See Things Now"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

0
-------------------------------------------------

samtools 1.7
Using htslib 1.7
Copyright (C) 2018 Genome Research Ltd.
0
-------------------------------------------------

AVAILABLE python packages:
numpy: 1.18.5
pysam: 0.16.0.1
rpy2: 3.3.3
argparse: 1.1

Great job! No missing python packages!