Commit 40dff249 authored by peguerin's avatar peguerin
Browse files

supernova second try

parent 0fe02518
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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/supernova_try2 /donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/chromium/try_2/serranus2.1.fasta /donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/chromium/try_2/serranus2.2.fasta
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 14:27:08
Logging to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/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/measuring
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...
1 /donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/chromium/try_2/serranus2.1.fasta ==> serranus2.1
2 /donnees/RESERVEBENEFIT/whole_genome_assembly/assemblage_serran/mbb/chromium/try_2/serranus2.2.fasta ==> serranus2.2
2019-07-19 14:27:29
Running Basic statistics processor...
Contig files:
1 serranus2.1
2 serranus2.2
Calculating N50 and L50...
1 serranus2.1, N50 = 129974, L50 = 1253, Total length = 608570381, GC % = 40.45, # N's per 100 kbp = 1079.82
2 serranus2.2, N50 = 129974, L50 = 1253, Total length = 608452956, GC % = 40.45, # N's per 100 kbp = 1079.94
Drawing Nx plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/basic_stats/GC_content_plot.pdf
Drawing serranus2.1 GC content plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/basic_stats/serranus2.1_GC_content_plot.pdf
Drawing serranus2.2 GC content plot...
saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/basic_stats/serranus2.2_GC_content_plot.pdf
Done.
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2019-07-19 14:28:11
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 14:28:19
RESULTS:
Text versions of total report are saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/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/measuring/metrics/serran/supernova_try2/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/measuring/metrics/serran/supernova_try2/report.html
PDF version (tables and plots) is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/report.pdf
Icarus (contig browser) is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/icarus.html
Log is saved to /home/pguerin/working/reservebenefit/genome_assembly/projets/genome_assemblies_collection/measuring/metrics/serran/supernova_try2/quast.log
Finished: 2019-07-19 14:28:19
Elapsed time: 0:01:11.743638
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*{2}{|r}|}
\hline
Assembly & serranus2.1 & serranus2.2 \\ \hline
\# contigs ($\geq$ 0 bp) & 37930 & 37929 \\ \hline
\# contigs ($\geq$ 1000 bp) & 37930 & 37929 \\ \hline
\# contigs ($\geq$ 5000 bp) & 11581 & 11578 \\ \hline
\# contigs ($\geq$ 10000 bp) & 7525 & 7522 \\ \hline
\# contigs ($\geq$ 25000 bp) & 4839 & 4839 \\ \hline
\# contigs ($\geq$ 50000 bp) & 3387 & 3387 \\ \hline
Total length ($\geq$ 0 bp) & {\bf 656292939} & 656174363 \\ \hline
Total length ($\geq$ 1000 bp) & {\bf 656292939} & 656174363 \\ \hline
Total length ($\geq$ 5000 bp) & {\bf 599452940} & 599327150 \\ \hline
Total length ($\geq$ 10000 bp) & {\bf 571549453} & 571420023 \\ \hline
Total length ($\geq$ 25000 bp) & {\bf 530507219} & 530432349 \\ \hline
Total length ($\geq$ 50000 bp) & {\bf 476900835} & 476835395 \\ \hline
\# contigs & 13621 & 13620 \\ \hline
Largest contig & 1404557 & {\bf 1411736} \\ \hline
Total length & {\bf 608570381} & 608452956 \\ \hline
GC (\%) & 40.45 & 40.45 \\ \hline
N50 & 129974 & 129974 \\ \hline
N75 & 57329 & {\bf 57354} \\ \hline
L50 & 1253 & 1253 \\ \hline
L75 & 3006 & 3006 \\ \hline
\# N's per 100 kbp & {\bf 1079.82} & 1079.94 \\ \hline
\end{tabular}
\end{center}
\end{table}
\end{document}
Assembly serranus2.1 serranus2.2
# contigs (>= 0 bp) 37930 37929
# contigs (>= 1000 bp) 37930 37929
# contigs (>= 5000 bp) 11581 11578
# contigs (>= 10000 bp) 7525 7522
# contigs (>= 25000 bp) 4839 4839
# contigs (>= 50000 bp) 3387 3387
Total length (>= 0 bp) 656292939 656174363
Total length (>= 1000 bp) 656292939 656174363
Total length (>= 5000 bp) 599452940 599327150
Total length (>= 10000 bp) 571549453 571420023
Total length (>= 25000 bp) 530507219 530432349
Total length (>= 50000 bp) 476900835 476835395
# contigs 13621 13620
Largest contig 1404557 1411736
Total length 608570381 608452956
GC (%) 40.45 40.45
N50 129974 129974
N75 57329 57354
L50 1253 1253
L75 3006 3006
# N's per 100 kbp 1079.82 1079.94
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 serranus2.1 serranus2.2
# contigs (>= 0 bp) 37930 37929
# contigs (>= 1000 bp) 37930 37929
# contigs (>= 5000 bp) 11581 11578
# contigs (>= 10000 bp) 7525 7522
# contigs (>= 25000 bp) 4839 4839
# contigs (>= 50000 bp) 3387 3387
Total length (>= 0 bp) 656292939 656174363
Total length (>= 1000 bp) 656292939 656174363
Total length (>= 5000 bp) 599452940 599327150
Total length (>= 10000 bp) 571549453 571420023
Total length (>= 25000 bp) 530507219 530432349
Total length (>= 50000 bp) 476900835 476835395
# contigs 13621 13620
Largest contig 1404557 1411736
Total length 608570381 608452956
GC (%) 40.45 40.45
N50 129974 129974
N75 57329 57354
L50 1253 1253
L75 3006 3006
# N's per 100 kbp 1079.82 1079.94
\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
serranus2.1 & 37930 & 37930 & 11581 & 7525 & 4839 & 3387 & 656292939 & 656292939 & 599452940 & 571549453 & 530507219 & 476900835 & 13621 & 1404557 & 608570381 & 40.45 & 129974 & 57329 & 1253 & 3006 & 1079.82 \\ \hline
serranus2.2 & 37929 & 37929 & 11578 & 7522 & 4839 & 3387 & 656174363 & 656174363 & 599327150 & 571420023 & 530432349 & 476835395 & 13620 & 1411736 & 608452956 & 40.45 & 129974 & 57354 & 1253 & 3006 & 1079.94 \\ \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
serranus2.1 37930 37930 11581 7525 4839 3387 656292939 656292939 599452940 571549453 530507219 476900835 13621 1404557 608570381 40.45 129974 57329 1253 3006 1079.82
serranus2.2 37929 37929 11578 7522 4839 3387 656174363 656174363 599327150 571420023 530432349 476835395 13620 1411736 608452956 40.45 129974 57354 1253 3006 1079.94
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
serranus2.1 37930 37930 11581 7525 4839 3387 656292939 656292939 599452940 571549453 530507219 476900835 13621 1404557 608570381 40.45 129974 57329 1253 3006 1079.82
serranus2.2 37929 37929 11578 7522 4839 3387 656174363 656174363 599327150 571420023 530432349 476835395 13620 1411736 608452956 40.45 129974 57354 1253 3006 1079.94
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