Error running quast

[deepBiomeDiego]

Hello,
I'm getting the following error when trying to run quast w/ even the most simple parameters (quast.log):

`/root/anaconda3/bin/quast.py ./test.fa -o /root/DeepBiome/SRR924736_out_dir/mega_out/combined_reference

Version: 4.6.3

System information:
OS: Linux-4.9.87-linuxkit-aufs-x86_64-with-debian-8.10 (linux_64)
Python version: 3.6.5
CPUs number: 3

Started: 2018-04-14 13:48:14

Logging to /root/DeepBiome/SRR924736_out_dir/mega_out/combined_reference/quast.log
NOTICE: Output directory already exists. Existing Nucmer alignments can be used
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /root/DeepBiome/SRR924736_out_dir/mega_out
Main parameters:
Threads: 1, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Contigs:
Pre-processing...
./test.fa ==> test

2018-04-14 13:48:15
Running Basic statistics processor...
Contig files:
test

'ascii' codec can't decode byte 0xef in position 14588: ordinal not in range(128)
Traceback (most recent call last):
File "/root/anaconda3/bin/quast.py", line 281, in
return_code = main(sys.argv[1:])
File "/root/anaconda3/bin/quast.py", line 140, in main
output_dirpath)
File "/root/anaconda3/lib/python3.6/site-packages/quast_libs/basic_stats.py", line 228, in do
html_saver.save_contigs_lengths(results_dir, contigs_fpaths, corr_lists_of_lengths)
File "/root/anaconda3/lib/python3.6/site-packages/quast_libs/html_saver/html_saver.py", line 475, in save_contigs_lengths
append(results_dirpath, json_fpath, 'contigsLengths')
File "/root/anaconda3/lib/python3.6/site-packages/quast_libs/html_saver/html_saver.py", line 220, in append
init(html_fpath)
File "/root/anaconda3/lib/python3.6/site-packages/quast_libs/html_saver/html_saver.py", line 115, in init
script_texts.append(js_html(aux_f_rel_path))
File "/root/anaconda3/lib/python3.6/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 "/root/anaconda3/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 0xef in position 14588: ordinal not in range(128)
`
Any help would be greatly appreciated.

[alexeigurevich]

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 quast.support@cab.spbu.ru

While we are debugging, you can try standalone version of Quast at https://downloads.sourceforge.net/project/quast/quast-4.6.3.tar.gz

[alexeigurevich]

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!

[olgabot]

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 quast.support@cab.spbu.ru
            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.

[alexeigurevich]

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.

[antonkulaga]

I have the same bug with latest docker

[rilango]

I have the same bug with latest docker

Please try
#70 (comment)

[alexeigurevich]

I am closing this issue since the solution was posted in #70 (comment) as mentioned above