Commit b6b522f1 authored by peguerin's avatar peguerin
Browse files

cleaning metrics

parent 40dff249
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/home/pguerin/src/anaconda3/lib/python3.6/site-packages/quast-5.0.2-py3.6.egg/EGG-INFO/scripts/quast.py --min-contig 4000 --eukaryote --circos --output-dir metrics/serran/platanus /donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/platanus/assemblies/serran_mbb_gapClosed.fa
Version: 5.0.2, aa6e8430
System information:
OS: Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid (linux_64)
Python version: 3.6.8
CPUs number: 8
Started: 2019-07-19 13:45:37
Logging to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/quast.log
NOTICE: Maximum number of threads is set to 2 (use --threads option to set it manually)
CWD: /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection
Main parameters:
MODE: default, threads: 2, eukaryotic: true, min contig length: 4000, min alignment length: 65, \
min alignment IDY: 95.0, ambiguity: one, threshold for extensive misassembly size: 1000
Contigs:
Pre-processing...
/donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/platanus/assemblies/serran_mbb_gapClosed.fa ==> serran_mbb_gapClosed
2019-07-19 13:46:06
Running Basic statistics processor...
Contig files:
serran_mbb_gapClosed
Calculating N50 and L50...
serran_mbb_gapClosed, N50 = 613332, L50 = 352, Total length = 628172492, GC % = 40.32, # N's per 100 kbp = 3770.02
Drawing Nx plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/basic_stats/GC_content_plot.pdf
Drawing serran_mbb_gapClosed GC content plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/basic_stats/serran_mbb_gapClosed_GC_content_plot.pdf
Done.
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2019-07-19 13:46:28
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating Icarus viewers...
2 of 2: Creating PDF with all tables and plots...
Done
2019-07-19 13:46:33
RESULTS:
Text versions of total report are saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/report.html
PDF version (tables and plots) is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/report.pdf
Icarus (contig browser) is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/icarus.html
Log is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/metrics/serran/platanus/quast.log
Finished: 2019-07-19 13:46:35
Elapsed time: 0:00:58.284456
NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0
Thank you for using QUAST!
This diff is collapsed.
\documentclass[12pt,a4paper]{article}
\begin{document}
\begin{table}[ht]
\begin{center}
\caption{All statistics are based on contigs of size $\geq$ 4000 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}
\begin{tabular}{|l*{1}{|r}|}
\hline
Assembly & serran\_mbb\_gapClosed \\ \hline
\# contigs ($\geq$ 0 bp) & 177982 \\ \hline
\# contigs ($\geq$ 1000 bp) & 20164 \\ \hline
\# contigs ($\geq$ 5000 bp) & 2190 \\ \hline
\# contigs ($\geq$ 10000 bp) & 1713 \\ \hline
\# contigs ($\geq$ 25000 bp) & 1485 \\ \hline
\# contigs ($\geq$ 50000 bp) & 1355 \\ \hline
Total length ($\geq$ 0 bp) & 697914092 \\ \hline
Total length ($\geq$ 1000 bp) & 656076523 \\ \hline
Total length ($\geq$ 5000 bp) & 626940096 \\ \hline
Total length ($\geq$ 10000 bp) & 623752971 \\ \hline
Total length ($\geq$ 25000 bp) & 620167381 \\ \hline
Total length ($\geq$ 50000 bp) & 615500364 \\ \hline
\# contigs & 2469 \\ \hline
Largest contig & 2764103 \\ \hline
Total length & 628172492 \\ \hline
GC (\%) & 40.32 \\ \hline
N50 & 613332 \\ \hline
N75 & 397188 \\ \hline
L50 & 352 \\ \hline
L75 & 663 \\ \hline
\# N's per 100 kbp & 3770.02 \\ \hline
\end{tabular}
\end{center}
\end{table}
\end{document}
Assembly serran_mbb_gapClosed
# contigs (>= 0 bp) 177982
# contigs (>= 1000 bp) 20164
# contigs (>= 5000 bp) 2190
# contigs (>= 10000 bp) 1713
# contigs (>= 25000 bp) 1485
# contigs (>= 50000 bp) 1355
Total length (>= 0 bp) 697914092
Total length (>= 1000 bp) 656076523
Total length (>= 5000 bp) 626940096
Total length (>= 10000 bp) 623752971
Total length (>= 25000 bp) 620167381
Total length (>= 50000 bp) 615500364
# contigs 2469
Largest contig 2764103
Total length 628172492
GC (%) 40.32
N50 613332
N75 397188
L50 352
L75 663
# N's per 100 kbp 3770.02
All statistics are based on contigs of size >= 4000 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
Assembly serran_mbb_gapClosed
# contigs (>= 0 bp) 177982
# contigs (>= 1000 bp) 20164
# contigs (>= 5000 bp) 2190
# contigs (>= 10000 bp) 1713
# contigs (>= 25000 bp) 1485
# contigs (>= 50000 bp) 1355
Total length (>= 0 bp) 697914092
Total length (>= 1000 bp) 656076523
Total length (>= 5000 bp) 626940096
Total length (>= 10000 bp) 623752971
Total length (>= 25000 bp) 620167381
Total length (>= 50000 bp) 615500364
# contigs 2469
Largest contig 2764103
Total length 628172492
GC (%) 40.32
N50 613332
N75 397188
L50 352
L75 663
# N's per 100 kbp 3770.02
\documentclass[12pt,a4paper]{article}
\begin{document}
\begin{table}[ht]
\begin{center}
\caption{All statistics are based on contigs of size $\geq$ 4000 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}
\begin{tabular}{|l*{21}{|r}|}
\hline
Assembly & \# contigs ($\geq$ 0 bp) & \# contigs ($\geq$ 1000 bp) & \# contigs ($\geq$ 5000 bp) & \# contigs ($\geq$ 10000 bp) & \# contigs ($\geq$ 25000 bp) & \# contigs ($\geq$ 50000 bp) & Total length ($\geq$ 0 bp) & Total length ($\geq$ 1000 bp) & Total length ($\geq$ 5000 bp) & Total length ($\geq$ 10000 bp) & Total length ($\geq$ 25000 bp) & Total length ($\geq$ 50000 bp) & \# contigs & Largest contig & Total length & GC (\%) & N50 & N75 & L50 & L75 & \# N's per 100 kbp \\ \hline
serran\_mbb\_gapClosed & 177982 & 20164 & 2190 & 1713 & 1485 & 1355 & 697914092 & 656076523 & 626940096 & 623752971 & 620167381 & 615500364 & 2469 & 2764103 & 628172492 & 40.32 & 613332 & 397188 & 352 & 663 & 3770.02 \\ \hline
\end{tabular}
\end{center}
\end{table}
\end{document}
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length GC (%) N50 N75 L50 L75 # N's per 100 kbp
serran_mbb_gapClosed 177982 20164 2190 1713 1485 1355 697914092 656076523 626940096 623752971 620167381 615500364 2469 2764103 628172492 40.32 613332 397188 352 663 3770.02
All statistics are based on contigs of size >= 4000 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length GC (%) N50 N75 L50 L75 # N's per 100 kbp
serran_mbb_gapClosed 177982 20164 2190 1713 1485 1355 697914092 656076523 626940096 623752971 620167381 615500364 2469 2764103 628172492 40.32 613332 397188 352 663 3770.02
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