panacus report

[zhangyehao]

[zhangyehao@login ~]$ panacus report ~/test.yaml
Error: Failed to parse template.

Caused by:
Template "report": No such file or directory (os error 2)

Why the above problems occur and how to solve them? Thanks!

[heringerp]

What's inside the test.yaml? Does the command panacus report --help work?

[zhangyehao]

like:

• !Hist
  graph: ../simple_files/simple_graphs/t_groups.gfa
• !Hist
  name: testing this
  count_type: Bp
  graph: ../simple_files/simple_graphs/t_group2.gfa
  display: false
  is:
• !Hist
  name: command-hist
  count_type: Bp
  graph: ../panthera23.chroms/chr19.gfa
  display: true

[zhangyehao@login ~]$ panacus report test.yaml
Error: Failed to parse template.
Caused by:
Template "report": No such file or directory (os error 2)

The help output for panacus report --help is displayed correctly.
[zhangyehao@login ~]$ panacus report --help
Create an html report from a YAML config file
Usage: panacus report [OPTIONS] [yaml_file]
Arguments:
[yaml_file] Specifies yaml config
Options:
-d, --dry-run If set, no actual computation is done, only the planned computation will be shown
-t Set the number of threads used (default: use all threads) [default: 0]
-h, --help Print help

in addition,sometimes:
thread 'main' panicked at src/graph_broker/graph.rs:45:18:
internal error: entered unreachable code: expected '+' or '-', but got >
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

In conclusion, I can't get html results with panacus report.
I look forward to your answers to my doubts.

[heringerp]

Do you have the files ../simple_files/simple_graphs/t_groups.gfa and ../simple_files/simple_graphs/t_group2.gfa? If not could try removing these two hist blocks?

So the total file is:

- !Hist
  name: command-hist
  count_type: Bp
  graph: ../panthera23.chroms/chr19.gfa
  display: true

[zhangyehao]

I have removed these two Hist blocks.
My .yaml file looks like this:

- !Hist  
  name: command-hist  
  count_type: Bp  
  graph: /panthera23.chroms/chr19.gfa  
  display: true

I don't know what the cause of this error is.

Error: Failed to parse template.
Caused by:
Template "report": No such file or directory (os error 2)

[heringerp]

Is the path /panthera23.chroms/chr19.gfa correct? It needs to be either absolute or relative to the directory where you are executing panacus

[zhangyehao]

Yes, I know that.

[heringerp]

Can you run the command with RUST_LOG=debug panacus report ~/test.yaml

[zhangyehao]

test.log

[heringerp]

I've just created a new release (v0.3.1) that should fix this problem. Could you try it with the new version?

[zhangyehao]

My pleasure

[zhangyehao]

Thank you for releasing panacus v0.3.1. I am now able to use panacus report to generate HTML reports. However, it seems that there is an issue with the results. In the statistics for bp, the expected results are not appearing. I believe this might be due to an accidental modification of the code.

chr22.zip

For more details on the issue, I have attached the HTML results. The file chr22.hprc-v1.0-pggb.histgrowth.html is an example result from the examples, while chr22_1.html is the result from my own run.

Additionally, there are some small issues in the figure. I have set the values to 0.1, 0, and 1 instead of 0.1%, 0%, and 1%. Although this doesn't affect the statistics, the display might be misleading.

Thank you very much for your help, and I look forward to your response.

Best regards

[heringerp]

Thanks for the descriptions. Version 0.3.2 (release) should fix these issues.

Best regards