/public/home/zhaichaoyu/.conda/envs/quast/opt/quast-5.3.0/quast.py --rna-finding --conserved-genes-finding --gene-finding --no-read-stats --no-snps --threads 8 --mgm --min-identity 90.0 /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/nextpolish/genome.nextpolish.fasta -o /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out --labels genome.nextpolish

Version: 5.3.0

System information:
  OS: Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17 (linux_64)
  Python version: 3.11.9
  CPUs number: 56

Started: 2025-05-23 11:23:22

Logging to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!

CWD: /public/home/zhaichaoyu/project/LR-seq/metaproject
Main parameters: 
  MODE: meta, threads: 8, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/nextpolish/genome.nextpolish.fasta ==> genome.nextpolish

2025-05-23 11:23:24
Running Basic statistics processor...
  Contig files: 
    genome.nextpolish
  Calculating N50 and L50...
    genome.nextpolish, N50 = 7483, L50 = 503, auN = 35192.2, Total length = 16503761, GC % = 41.18, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/basic_stats/GC_content_plot.pdf
  Drawing genome.nextpolish GC content plot...
    saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/basic_stats/genome.nextpolish_GC_content_plot.pdf
Done.

2025-05-23 11:23:51
WARNING: GeneMark tool can't be started because of license limitations!

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2025-05-23 11:23:51
Running Barrnap...
Logging to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/predicted_genes/barrnap.log...
/public/home/zhaichaoyu/.conda/envs/quast/lib/python3.11/site-packages/quast_libs/barrnap/bin/barrnap \
--quiet -k bac --threads 8 result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/quast_corrected_input/genome-nextpolish.fasta \
> result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/predicted_genes/genome-nextpolish.rna.gff \
2>> result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/predicted_genes/barrnap.log
    Ribosomal RNA genes = 30
    Predicted genes (GFF): /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/predicted_genes/genome-nextpolish.rna.gff
Done.

2025-05-23 11:24:00
Running BUSCO...
  running BUSCO with augustus from /public/home/zhaichaoyu/.conda/envs/quast/lib/python3.11/site-packages/quast_libs/augustus3.2.3
Logs and results will be saved under /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats...
WARNING: BUSCO did not fail explicitly but found nothing for all assemblies! Possible reasons and workarounds:
  1. Provided assemblies are so small that they do not contain even a single partial BUSCO gene. Not likely but may happen -- nothing to worry then.
  2. Incorrect lineage database was used. To run with fungi DB use --fungus, to run with eukaryota DB use --eukaryote, otherwise BUSCO uses bacteria DB.
  3. Problem with BUSCO dependencies, most likely Augustus. Check that the binaries in /public/home/zhaichaoyu/.conda/envs/quast/lib/python3.11/site-packages/quast_libs/augustus3.2.3/bin/ are working properly.
     If something is wrong with Augustus, you may try to install it yourself (https://github.com/Gaius-Augustus/Augustus or `conda install -c bioconda augustus`) and make sure "augustus" binary is in PATH.
     Please install the PROPER VERSION of Augustus, we tested BUSCO with augustus-3.2.3, it may also work with augustus-3.3, the newer/older versions are not supported.
  4. Some other problem with BUSCO. Check the logs (you may need to rerun QUAST with --debug to see all intermediate files).
     If you cannot solve the problem yourself, post an issue at https://github.com/ablab/quast/issues or write to alexey.gurevich@helmholtz-hips.de
Done.

2025-05-23 11:26:02
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2025-05-23 11:26:08
RESULTS:
  Text versions of total report are saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/report.html
  PDF version (tables and plots) is saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/report.pdf
  Icarus (contig browser) is saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/icarus.html
  Log is saved to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB47445/ERR6713789/2.Analysis/Assemblybased/2.Polish/metaquast_out/quast.log

Finished: 2025-05-23 11:26:08
Elapsed time: 0:02:46.570980
NOTICEs: 2; WARNINGs: 2; non-fatal ERRORs: 0

Thank you for using QUAST!
