chunqijiang / jiang-azur

This is a repository for usage in server space 'jiang@azur'（For internal use）

This is a repository¹ for internal usage (Yoshizawa Group) in server space 'jiang@azur' (access necessary).

Start from 2023-02-28

For access to 'jiang@azur' at the first time, please contact Jiang².

It is possible to refer to all the usages listed here on your own terminal if you have a similar environment and OS. Free to ask if have any questions.

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Notes:

• ALWAYS enter your directory first cd user_name before any action!

• DO NOT install, update or modify anything without contact!

• CONTACT first if you want new packages or environments!

Currently released environments(env):

<env_id>	<env_name>	<create_date>	<update_date>	<env_description>
00	base	2023-02-28		basic environment, common usages
01	anvio-7.1	2023-02-28		anvi'o for pangenome / metagenome analyses
02	assembly	2023-02-28		tools for genome assembly: seqkit, fastqc, unicycler, flye, medaka, pilon ...
03	gtdbtk-2.1.1	2023-02-28	env 12	gtdbtk tool for GDTB
04	checkm	2023-02-28	env 13	genome quialty check (checkm or gunc), completeness and contamination
05	pydata	2023-02-28		data analysis using python
06	r-env	2023-02-28		data analysis using R
07	unicycler050	2023-02-13		only unicycler 0.5.0
08	qiime2-2023.2	2023-03-10	env 14	for qiime2 analyses
09	ncbi	2023-03-28	2023-07-12	local blast using blast+ or diamond
10	prokka	2023-07-03		rapid prokaryotic genome annotation
11	rna-seq	2023-11-02		RNA seq analysis: Trimmomatic, Trinity
12	gtdbtk-2.4.0	2024-05-14		gtdbtk-2.4.0 with new GTDB-Tk reference dataset R220 (ver202404)
13	checkm2	2024-06-04		MAGs quality check: checkM2, QUAST, GUNC
14	qiime2-amplicon-2024.5	2024-06-05		The 2024.5 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, q2cli and the following plugins: q2-alignment, q2-composition, q2-cutadapt, q2-dada2, ...
15	qiime2-metagenome-2024.5	2024-06-07		The 2024.5 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins: q2-assembly, q2-composition, q2-cutadapt, q2-demux, ...
16	metawrap	2024-06-10		MetaWRAP environment, a flexible pipeline for genome-resolved metagenomic data analysis: metawrap-mg, blast, concoct, maxbin2, megahit, metabat2, … Databases installed: checkm, ncbi_nt, ncbi_tax, SILVA 16S
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Shortcuts：

• Basic information on this space and the general list of environments please check here.

• Detailed list of environments and packages please check here.

Usages：

• Connection
  • 2023-03-06 created
• Env00-base
  • Introduction of common/basic commands
• Env01-anvio-7.1
  • 2023-05-15 updated
  • 2023-03-02 created
• Env02-assembly
  • 2023-05-15 updated
  • 2023-03-07 created
• Env03-gtdbtk-2.1.1
  • 2023-03-06 updated
  • 2023-03-02 created
• Env04-checkm
  • 2023-07-06 'gunc' was added for MAG check
  • 2023-03-06 created
• Env05-pydata
• Env06-r-env
• Env07-unicycler050
• Env08-qiime2-2023.2
• Env09-ncbi
  • 2023-07-12 'DIAMOND' was added for large scale blast
• Env10-prokka
  • 2023-07-28 created

Footnotes

1. All Rights Reserved. ↩

2. You should know where to find him^.^ ↩

jiang-azur's Issues

104, 'Connection reset by peer'

When I try to run
anvi-run-ncbi-cogs (COG20)
It has 'Config Error'
anvi-run-ncbi-cogs
usage: anvi-run-ncbi-cogs [-h] -c CONTIGS_DB [--cog-version COG_VERSION]
[--cog-data-dir COG_DATA_DIR] [-T NUM_THREADS]
[--sensitive] [--temporary-dir-path PATH]
[--search-with SEARCH_METHOD]
anvi-run-ncbi-cogs: error: the following arguments are required: -c/--contigs-db
(anvio-7.1) zhuoye@zhuoye-virtual-machine:/miniconda3/envs/anvio-7.1$ ^C
(anvio-7.1) zhuoye@zhuoye-virtual-machine:/miniconda3/envs/anvio-7.1$ anvi-setup-ncbi-cogs
COG version ..................................: COG20
COG data source ..............................: The anvi'o default.
COG base directory ...........................: /home/zhuoye/miniconda3/envs/anvio-7.1/lib/python3.6/site-packages/anvio/data/misc/COG

WARNING

This program will first check whether you have all the raw files, and then will
attempt to regenerate everything that is necessary from them.

Config Error: Something went wrong with your download attempt. Here is the problem for the url
ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data/cog-20.cog.csv: '<urlopen error ftp
error: ConnectionResetError(104, 'Connection reset by peer')>'

What is this problem?