Comments (7)
Hi!
Most probably it is an issue of anaconda integration of Quast. Could you please send us the content of "/root/anaconda3/lib/python3.6/site-packages/quast_libs/html_saver/static/" for debugging? You can put a link to an archive here or send it to us via [email protected]
While we are debugging, you can try standalone version of Quast at https://downloads.sourceforge.net/project/quast/quast-4.6.3.tar.gz
from quast.
Hopefully, the problem is solved already, so I am closing the issue now. Please reopen it (and send the requested files) if the problem persists!
from quast.
Hello,
I am having the same problem from the docker image: which I pulled with:
docker pull quay.io/biocontainers/quast:5.0.2--py35pl526ha92aebf_0
Here's the command and output. I'm using a fancy new workflow manager so I don't have access to the quast.log
files because they were on EC2 instances that were killed.
command:
quast-lg.py --output-dir {{output}} \
--threads 16 \
{{d}}/*.fasta.gz
where:
{{d}} =
dovetail_2018-05-06.fasta.gz sha256:3a72c5bb77cb0a133ce77b8055d79878c040bf34de2c7b4f513592d8070ac0ac 442.8MiB
jcvi_ise6.fasta.gz sha256:766bbd89408379f12e644f242511db72854c348f349db59e601d2c42bdcd7d1b 955.1MiB
stdout:
WARNING: Python locale settings can't be changed
/usr/local/lib/python3.5/site-packages/quast-5.0.2-py3.5.egg-info/scripts/quast-lg.py --output-dir /return/0 --threads 16 /arg/1/0/dovetail_2018-05-06.fasta.gz /arg/1/0/jc
vi_ise6.fasta.gz
Version: 5.0.2
System information:
OS: Linux-4.14.44-coreos-r1-x86_64-with-glibc2.2.5 (linux_64)
Python version: 3.5.5
CPUs number: 16
Started: 2018-12-03 18:39:58
Logging to /return/0/quast.log
CWD: /
Main parameters:
MODE: large, threads: 16, eukaryotic: true, minimum contig length: 3000, minimum alignment length: 500, \
ambiguity: one, threshold for extensive misassembly size: 7000
Contigs:
Pre-processing...
1 /arg/1/0/dovetail_2018-05-06.fasta.gz ==> dovetail_2018_05_06
2 /arg/1/0/jcvi_ise6.fasta.gz ==> jcvi_ise6
2018-12-03 18:43:23
Running Basic statistics processor...
Contig files:
1 dovetail_2018_05_06
2 jcvi_ise6
'ascii' codec can't decode byte 0xef in position 14588: ordinal not in range(128)
Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/quast-5.0.2-py3.5.egg-info/scripts/quast-lg.py", line 307, in <module>
return_code = main(sys.argv[1:])
File "/usr/local/lib/python3.5/site-packages/quast-5.0.2-py3.5.egg-info/scripts/quast-lg.py", line 149, in main
icarus_gc_fpath, circos_gc_fpath = basic_stats.do(ref_fpath, contigs_fpaths, os.path.join(output_dirpath, 'basic_stats'), output_dirpath)
File "/usr/local/lib/python3.5/site-packages/quast_libs/basic_stats.py", line 263, in do
html_saver.save_contigs_lengths(results_dir, contigs_fpaths, corr_lists_of_lengths)
File "/usr/local/lib/python3.5/site-packages/quast_libs/html_saver/html_saver.py", line 475, in save_contigs_lengths
append(results_dirpath, json_fpath, 'contigsLengths')
File "/usr/local/lib/python3.5/site-packages/quast_libs/html_saver/html_saver.py", line 220, in append
init(html_fpath)
File "/usr/local/lib/python3.5/site-packages/quast_libs/html_saver/html_saver.py", line 115, in init
script_texts.append(js_html(aux_f_rel_path))
File "/usr/local/lib/python3.5/site-packages/quast_libs/html_saver/html_saver.py", line 95, in js_html
return '<script type="text/javascript">\n' + open(get_real_path(script_rel_path)).read() + '\n</script>\n'
File "/usr/local/lib/python3.5/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 14588: ordinal not in range(128)
stderr:
ERROR! exception caught!
In case you have troubles running QUAST, you can write to [email protected]
or report an issue on our GitHub repository https://github.com/ablab/quast/issues
Please provide us with quast.log file from the output directory.
I've seen this error in Python 3 before and if I use the Python 2.7 image (5.0.2--py27pl526ha92aebf_0
) then it seems to run just fine.
from quast.
Hi Olga,
We will try to investigate the problem, so I am reopening this issue. We are not creating these docker images but the problem is probably related to our source code. I assume the dockers are created based on bioconda installations of Quast and we are taking care of them.
from quast.
I have the same bug with latest docker
from quast.
I have the same bug with latest docker
Please try
#70 (comment)
from quast.
I am closing this issue since the solution was posted in #70 (comment) as mentioned above
from quast.
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