我是直接使用conda安装的
conda create -n interproscan
conda activate interproscan
conda install interproscan -y
安装完会提示
# First time usage please README !!! #
######################################
The databases are huge and consequently not shipped within this installation.
Please download and install the Databases manually by following the commands below:
!!! /!\ Edit the 2 first lines to match the wished version of the DB /!\ !!!
Commands:
=========
# See here for latest db available: https://github.com/ebi-pf-team/interproscan or http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/
# Set versions
version_major=5.59
version_minor=91.0
CONDA_PREFIX=/the/path/to/your/interproscan/conda/env/
# get the md5 of the databases
wget http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz.md5
# get the databases (with core because much faster to download)
wget http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz
# checksum
md5sum -c interproscan-${version_major}-${version_minor}-64-bit.tar.gz.md5
# untar gz
tar xvzf interproscan-${version_major}-${version_minor}-64-bit.tar.gz
# remove the sample DB bundled by default
rm -rf $CONDA_PREFIX/share/InterProScan/data/
# copy the new db
cp -r interproscan-${version_major}-${version_minor}/data $CONDA_PREFIX/share/InterProScan/
INFO:
====
Phobius (licensed software), SignalP, SMART (licensed components) and TMHMM use
licensed code and data provided by third parties. If you wish to run these
analyses it will be necessary for you to obtain a licence from the vendor and
configure your local InterProScan installation to use them.
(see more information in $CONDA_PREFIX/share/InterProScan/data/<db>)
大体的意思就是需要配置数据库
按照提示去指定的参考链接下载，然后解压出来放到指定的位置就可以了
试着运行一下，命令是
interproscan.sh -i ../ys.pep.fa -f tsv --goterms -dp -cpu 48
有报错
Error: Failed to open binary auxfiles for data/superfamily/1.75/hmmlib_1.75: use hmmpress first
https://github.com/ebi-pf-team/interproscan/issues/221
这个链接里也提到了这个问题，暂时没有看懂是什么意思
我是把 data/superfamily/ 这个目录删除了，然后把同组的另外一个人的账号下的这个文件下复制到我这里，没有报错了
运行过程的输出
10/06/2023 23:15:05:969 Welcome to InterProScan-5.59-91.0
10/06/2023 23:15:05:970 Running InterProScan v5 in STANDALONE mode... on Linux
10/06/2023 23:15:10:221 RunID: tcu21_20230610_231509668_7jyb
10/06/2023 23:15:18:078 Loading file /home/myan/my_data/raw_data/pome/ys.Genome/02.genome.annotation/05.evm/ys/interproscan/../ys.pep.fa
10/06/2023 23:15:18:080 Running the following analyses:
[AntiFam-7.0,CDD-3.18,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
10/06/2023 23:15:24:667 Uploaded 28774 unique sequences for analysis
10/06/2023 23:44:09:196 25% completed
11/06/2023 00:10:37:434 50% completed
11/06/2023 00:25:07:522 75% completed
11/06/2023 00:36:57:263 90% completed
11/06/2023 01:36:57:409 90% completed
11/06/2023 02:36:57:623 99% completed
11/06/2023 03:36:57:693 99% completed
11/06/2023 03:44:25:881 100% done: InterProScan analyses completed
2023-06-11 03:44:26,394 [main] [uk.ac.ebi.interpro.scan.jms.main.Run:1801] WARN - deleteWorkingDirectoryOnCompletion : false
不知道为啥删除临时文件夹会失败
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