QUAST synthax error

[DinizFerreira]

Hello,

Me and two colleagues have been trying to use QUAST (5.0.2) to assess assembly quality of a de novo genome sequencing. Unfortunately I am getting an error message. I am sending the log files attached to this email. Could you help me with this, please?

/quast-5.0.2/quast.py ../0-genome/purged.fa -t 20 --eukaryote --large --rna-finding --conserved-genes-finding --est-ref-size 500000000 --memory-efficient --pacbio ../0-genome/cmeg_raw_genome.fastq.gz

Version: 5.0.2

System information:
  OS: Linux-5.4.0-99-generic-x86_64-with-glibc2.29 (linux_64)
  Python version: 3.8.10
  CPUs number: 32

Started: 2022-12-01 19:41:26

Logging to /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/quast.log

CWD: /dados/home/blowflies/genome_annotation/cmeg/quast-error
Main parameters: 
  MODE: large, threads: 20, eukaryotic: true, minimum contig length: 3000, minimum alignment length: 500, \
  ambiguity: one, threshold for extensive misassembly size: 7000

Contigs:
  Pre-processing...
  ../0-genome/purged.fa ==> purged

2022-12-01 19:41:42
Running Reads analyzer...
Downloading gridss (file: gridss-1.4.1.jar)...
gridss successfully downloaded!
  Logging to files /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.log and /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
/usr/bin/bwa index -p /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/quast_corrected_input/purged.fa \
/dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/quast_corrected_input/purged.fa \
>> /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err \
2>> /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
/quast-5.0.2/quast_libs/minimap2/minimap2 -t 10 -ax map-pb /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/quast_corrected_input/purged.fa \
/dados/home/blowflies/genome_annotation/cmeg/0-genome/cmeg_raw_genome.fastq.gz > purged.pacbio1.sam \
2>> /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
/quast-5.0.2/quast_libs/sambamba/sambamba_linux view -t 10 -h -S -f bam purged.pacbio1.sam \
> purged.pacbio1.bam 2>> /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
  Done.
/quast-5.0.2/quast_libs/sambamba/sambamba_linux view -H -S quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.sam \
> quast_results/results_2022_12_01_19_41_26/reads_stats/purged.sam.header 2>> quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
  Sorting SAM-file...
/quast-5.0.2/quast_libs/sambamba/sambamba_linux view -t 10 -h -S -f bam quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.all.correct.sam \
> quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.bam 2>> \
quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
/quast-5.0.2/quast_libs/sambamba/sambamba_linux flagstat -t 10 quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.bam \
> quast_results/results_2022_12_01_19_41_26/reads_stats/purged.stat 2>> quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
/usr/bin/bamToBed -i quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.bam \
> quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.bed 2>> \
quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
sort -k1,1 -k2,2n quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.bed \
> quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.sorted.bed \
2>> quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
/usr/bin/bedtools genomecov -i quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.sorted.bed \
-g quast_results/results_2022_12_01_19_41_26/quast_corrected_input/purged.fa.fai > \
quast_results/results_2022_12_01_19_41_26/reads_stats/temp_output/purged.genomecov \
2>> quast_results/results_2022_12_01_19_41_26/reads_stats/reads_stats.err
  Analysis is finished.
  Creating total report...
    saved to /dados/home/blowflies/genome_annotation/cmeg/quast-error/quast_results/results_2022_12_01_19_41_26/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

invalid syntax (jsontemplate.py, line 1)
Traceback (most recent call last):
  File "/quast-5.0.2/quast.py", line 307, in <module>
    return_code = main(sys.argv[1:])
  File "/quast-5.0.2/quast.py", line 148, in main
    from quast_libs import basic_stats
  File "/quast-5.0.2/quast_libs/basic_stats.py", line 15, in <module>
    from quast_libs.circos import set_window_size
  File "/quast-5.0.2/quast_libs/circos.py", line 25, in <module>
    from quast_libs.icarus_utils import get_assemblies, check_misassembled_blocks, Alignment
  File "/quast-5.0.2/quast_libs/icarus_utils.py", line 15, in <module>
    from quast_libs.html_saver.html_saver import trim_ref_name
  File "/quast-5.0.2/quast_libs/html_saver/html_saver.py", line 18, in <module>
    from quast_libs.site_packages.jsontemplate import jsontemplate
  File "/quast-5.0.2/quast_libs/site_packages/jsontemplate/jsontemplate.py", line 1
    diniz@r540:~$ cd ..
                ^
SyntaxError: invalid syntax