Error in parsing

[tnn111]

I get the following errors:

Parsing assembly_graph_with_scaffolds.gfa...
Finish parsing.
Extracting edge sequences from assembly_graph_with_scaffolds.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
File "/global/homes/t/torben/opt/anaconda3/envs/AGB/bin/agb.py", line 153, in
main()
File "/global/homes/t/torben/opt/anaconda3/envs/AGB/bin/agb.py", line 145, in main
with open(TEMPLATE_PATH) as f: html = f.read()
File "/global/homes/t/torben/opt/anaconda3/envs/AGB/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 6389: ordinal not in range(128)

The command was

agb.py --graph assembly_graph_with_scaffolds.gfa -a spades

I installed everything exactly as in the instructions.

Any ideas?

[almiheenko]

Hi,

I couldn't reproduce this issue but added a workaround that should fix any encoding errors. Please let me know if you still have this problem. Thank you!

Best regards,
Alla

[asafpr]

I had the same issue. The solution that worked for me is to change all read/write to bytes instead of strings and then encoding/decoding. i.e. open(file, 'rb')

[TomHarrop]

I'm having the same issue with 9c1b39c. I've also tried export PYTHONIOENCODING=utf8 but it didn't help.

Extracting edge sequences from output/030_flye/denovo_full/assembly_graph.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/usr/local/bin/agb.py", line 154, in <module>
    main()
  File "/usr/local/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/usr/local/lib/python3.6/dist-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with open(fpath) as f: contents = f.read()
  File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 3300: ordinal not in range(128)

[almiheenko]

Hi Tom,
I've committed an additional fix for this issue and updated a conda package. Please let me know if you have any issues.

Thanks
Alla

[bestweicheng]

I have the same problem (download yesterday )

[TomHarrop]

Hi @almiheenko , thanks for the reply.

That doesn't fix it. Here's the error I get in a41ac9e:

Extracting edge sequences from output/030_flye/denovo_full/assembly_graph.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/usr/local/bin/agb.py", line 154, in <module>
    main()
  File "/usr/local/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/usr/local/lib/python3.6/dist-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()
AttributeError: module 'os' has no attribute 'io'

Is it a mistake here?

AGB/agb_src/scripts/utils.py

Line 221 in a41ac9e

with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()

[almiheenko]

This issue should be fixed by now, thanks to @kbseah.
Conda package is updated.

Please feel free to re-open if you still have any issues

[pbravakos]

Hi,
I tried to run the program today and got the following error:

Parsing assembly_graph_with_scaffolds.gfa...
Finish parsing.
Extracting edge sequences from assembly_graph_with_scaffolds.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/home1/pbravakos/Software/miniconda3/envs/AGB/bin/agb.py", line 154, in <module>
    main()
  File "/home1/pbravakos/Software/miniconda3/envs/AGB/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/home1/pbravakos/Software/miniconda3/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()
AttributeError: module 'os' has no attribute 'io'

[Dmitry-Antipov]

Messy workaround for this problem - install AGB from conda, activate environment as described in manual but run not conda's version but an AGB instance just cloned from github.

[hiroshisuga]

Manually removing "os.io." from that line worked for me.