pigx-scrnaseq [AttributeError - 'NoneType' object has no attribute 'items']

[Somesh]

Hi pigx team,

I installed pigx-scrnaseq via guixr on my profile and when I try to execute it with the following command; pigx-scrnaseq -s settings.yaml sample_sheet.csv , I get the following Python error -

I am trying to run this on data from CEL-Seq2 protocol for which I found parameters in the settings file when I run pigx-scrnaseq --init

Any idea what's going on here ?

Somesh (somes...@mdc-berlin.de),

Bioinformatics PhD Student,

Genomics Technology Platform, BIMSB

[vedran...@gmail.com]

Dear Somesh, 

Could you please provide the sample sheet and the settings file you were using?

Best, 

Vedran

[Somesh]

Hi Vedran,

You can download both files from here -> https://mdcsft.mdc-berlin.de/download.php/5672227922/pigx-scrnaseq-celseq2-files.zip

Best,

Somesh

[Mathias Dahlmann]

Hi Vedran,

a similar error is thrown when I try to run the pigx-chipseq command with the settings and sample file generated by --init.

I've upgraded to the recent guixr version and installed  pigx-chipseq version 0.0.43

$ pigx-chipseq --init

Generated settings.yaml template.
Generated sample_sheet.csv template.

$ pigx-chipseq -s settings.yaml sample_sheet.csv -n

Traceback (most recent call last):
  File "/home/dahlmann/.guix-profile/bin/pigx-chipseq", line 338, in <module>
    generate_config(args.configfile,
  File "/home/dahlmann/.guix-profile/bin/pigx-chipseq", line 153, in generate_config
    update_config(settings,yaml.safe_load(open(settingsfile, 'r')))
  File "/gnu/store/wyvks69r3fb2xm3rnifdzz1hcymrqzq7-snakemake-5.7.1/lib/python3.8/site-packages/snakemake/utils.py", line 468, in update_config
    _update(config, overwrite_config)
  File "/gnu/store/wyvks69r3fb2xm3rnifdzz1hcymrqzq7-snakemake-5.7.1/lib/python3.8/site-packages/snakemake/utils.py", line 461, in _update
    for (key, value) in u.items():
AttributeError: 'NoneType' object has no attribute 'items'

[Vedran Franke]

Hey Mathias, 

Ill invite Alex, who is the current developer/maintainer of the ChIP pipeline:

v

[Gianni Carraro]

Hi Vedran,

I just installed pigx 1.1.7 using Guix in Ubuntu.

I tried to run the minimal test dataset and I get the same exact error as Somesh posted.

pigx-scrnaseq -s settings.yaml sample_sheet.csv -n

Traceback (most recent call last):

  File "/home/gc/.guix-profile/bin/pigx-scrnaseq", line 362, in <module>
    generate_config(args.configfile,
  File "/home/gc/.guix-profile/bin/pigx-scrnaseq", line 167, in generate_config
    update_config(settings,yaml.safe_load(open(settingsfile, 'r')))
  File "/gnu/store/6v5h60wjdslsbv0skrdi7v3q6y6qj553-snakemake-5.32.2/lib/python3.8/site-packages/snakemake/utils.py", line 480, in update_config
    _update(config, overwrite_config)
  File "/gnu/store/6v5h60wjdslsbv0skrdi7v3q6y6qj553-snakemake-5.32.2/lib/python3.8/site-packages/snakemake/utils.py", line 473, in _update

    for (key, value) in u.items():
AttributeError: 'NoneType' object has no attribute 'items'

I used the provided setting and sample sheet (see attached).

I also tried with my data and setting and the error message was the same.

Any idea?

Thank you,

Gianni

[Ricardo Wurmus]

Hi Gianni,

> I used the provided setting and sample sheet (see attached).

You will at least need to uncomment the “locations” section in the
settings.yaml. Remove the leading “# ” from that first block.

You may also need to specify more than that first section, though
there are defaults for others. (For example, you will rarely ever
have to provide your own “tools” section, because the defaults are
perfect when using Guix.)

The documentation at
https://bioinformatics.mdc-berlin.de/pigx_docs/ documents these
sections and provides guidance on how to pick appropriate values.

--
Ricardo Wurmus

System administrator
BIMSB - Scientific Bioinformatics Platform
Max Delbrueck Center for Molecular Medicine

email: ricardo...@mdc-berlin.de
tel: +49 30 9406 1796