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HIT-ImmunologyLab / DBSCAN-SWA

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Error: Please add the DBSCAN-SWA installation directory to your $PATH environment variable before running the executable from another folder #4

Open dineshkumarsrk opened 3 years ago

dineshkumarsrk commented 3 years ago

I have followed all the instruction mentioned in your readme installed all the necessary dependencies and added the DBSCAN_SWA in my .bashrc and also added in terminal also using export option but still I am getting error as shown below,

ga@ga214:~$ python3 ~/Documents/tools/prophage_DBSCAN-SWA/bin/dbscan-swa.py --input ~/Documents/tools/prophage_DBSCAN-SWA/test/NC_007054.gb --output dinesh --prefix din
Warning:The parameter add_annotation default:PGPD,If you want to run fast, please set add_annotation to none
Error: Please add the DBSCAN-SWA installation directory to your $PATH environment variable before running the executable from another folder

my .bashrc file is shown below

export PATH=$PATH:/home/ga/ncbi-blast-2.8.1+/bin
export PATH=$PATH:/home/ga/Documents/tools/prokka/bin
export PATH=$PATH:/home/ga/Documents/tools/prophage_DBSCAN-SWA/software/blast+/bin:$PATH
export PATH=$PATH:/home/ga/Documents/tools/prophage_DBSCAN-SWA/bin
export PATH=$PATH:/home/ga/Documents/tools/prophage_DBSCAN-SWA/software/diamond

Please help me to fix this issue.

HIT-ImmunologyLab commented 3 years ago

@dineshkumarsrk I am sorry for the error. I have corrected the error in dbscan-swa.py and you could re-download the dbscan-swa.py. If you have any problem, welcome comment.

dineshkumarsrk commented 3 years ago

Thank you @HIT-ImmunologyLab . PATH variable issue has resolved now. But, now I am getting another error as follows,

ga@ga214:~$ python3 ~/Documents/tools/prophage_DBSCAN-SWA/bin/dbscan-swa.py --input ~/Documents/tools/prophage_DBSCAN-SWA/test/NC_007054.gb --output dinesh --prefix din
Warning:The parameter add_annotation default:PGPD,If you want to run fast, please set add_annotation to none
You are running DBSCAN-SWA first time, the database will be downloaded in /home/ga/Documents/tools/prophage_DBSCAN-SWA/db
--2021-03-01 14:55:30--  http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz
Resolving www.microbiome-bigdata.com (www.microbiome-bigdata.com)... 113.6.251.9
Connecting to www.microbiome-bigdata.com (www.microbiome-bigdata.com)|113.6.251.9|:80... failed: Connection timed out.
Retrying.

--2021-03-01 14:57:42--  (try: 2)  http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz
Connecting to www.microbiome-bigdata.com (www.microbiome-bigdata.com)|113.6.251.9|:80... failed: Connection timed out.
Retrying.

--2021-03-01 14:59:54--  (try: 3)  http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz
Connecting to www.microbiome-bigdata.com (www.microbiome-bigdata.com)|113.6.251.9|:80... failed: Connection timed out.
Retrying.

--2021-03-01 15:02:08--  (try: 4)  http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz
Connecting to www.microbiome-bigdata.com (www.microbiome-bigdata.com)|113.6.251.9|:80...

Even, I tried to open your site http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz on my google chrome but could not connect it. your site is having some issue.

HIT-ImmunologyLab commented 3 years ago

@dineshkumarsrk The website is correct(http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz). You can use other tool like axel. Alternatively, you could download the database manually from http://www.microbiome-bigdata.com/PHISDetector/index/download