Graphical view of locBLAST is not working in Ubuntu

[akshaybioinfo]

I configured locBLAST in UBUNTU server with address http://14.139.224.59/BpGDB-BLAST/. The text view is working fine but graphical view is not working. While selecting graphical view it shows blank result page. Please suggest the modifications.

[AshokHub]

Set permission chmod 777 to the PHP file.

[AshokHub]

Grant permission to the locBLAST folder using sudo chmod -R 777 locBLAST command.

[akshaybioinfo]

I have already given full permission of 777 to locBLAST as well as all php and NCBI blast files. But did not get the graphical view, while text view is working fine. Thank you. *With Regards.* Akshay Singh PhD. *Research Associate* *NBPGR, New Delhi -110012*

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On Tue, Jun 11, 2024 at 9:50 PM Ashok Kumar T. ***@***.***> wrote: Grant permission to the locBLAST folder using sudo chmod -R 777 locBLAST command. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHE24FXEZUFAYFRWXKLB3XDZG4PUJAVCNFSM6AAAAABJDYJKGSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRRGE2TIOBUHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[akshaybioinfo]

The graphical view output of the configured locBLAST server is not working, while text view is working. My locBLAST address is http://14.139.224.59/BpGDB-BLAST/. I have given full permission of 777 to the locBLAST directory and all the php and blast files as suggested by you previously, but problem is not resolved yet. I am facing the same problem, kindly let me know what changes are required for the graphical view of the blast outputs.
Thank You.

[AshokHub]

Check whether the XML file is created while running the page in the Linux server. I don't have Linux OS in my system, so I can't verify.

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On Fri, 14 Jun, 2024, 3:28 pm akshaybioinfo, ***@***.***> wrote: The graphical view output of the configured locBLAST server is not working, while text view is working. My locBLAST address is http://14.139.224.59/BpGDB-BLAST/. I have given full permission of 777 to the locBLAST directory and all the php and blast files as suggested by you previously, but problem is not resolved yet. I am facing the same problem, kindly let me know what changes are required for the graphical view of the blast outputs. Thank You. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGN7QM6I7ZDVPIXBFEELGLZHK5DRAVCNFSM6AAAAABJDYJKGSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRXGY4DCNJUGA> . You are receiving this because you commented.Message ID: ***@***.***>

[akshaybioinfo]

yes XML file generated while running this page with lock symbol.
this is the structure and permission of the directory. Please check

drwxrwxrwx 5 root root 12288 Jun 19 10:26 .
drwxr-xr-x 7 root root 4096 Jun 11 15:42 ..
-rw-r--r-- 1 www-data www-data 338 Jun 19 10:24 blast2024.06.19.10.24.25.fas
-rw-r--r-- 1 www-data www-data 3870 Jun 19 10:24 blast2024.06.19.10.24.25.xml
-rw-r--r-- 1 www-data www-data 338 Jun 19 10:24 blast2024.06.19.10.24.46.fas
-rw-r--r-- 1 www-data www-data 3870 Jun 19 10:24 blast2024.06.19.10.24.46.xml
-rw-r--r-- 1 www-data www-data 338 Jun 19 10:26 blast2024.06.19.10.26.29.fas
-rw-r--r-- 1 www-data www-data 3870 Jun 19 10:26 blast2024.06.19.10.26.29.xml
-rwxrwxrwx 1 root root 26920560 Jun 11 10:39 blastdb_aliastool
-rwxrwxrwx 1 root root 28680304 Jun 11 10:40 blastdbcheck
-rwxrwxrwx 1 root root 36085616 Jun 11 10:40 blastdbcmd
-rwxrwxrwx 1 root root 40512880 Jun 11 10:40 blast_formatter
-rwxrwxrwx 1 root root 40591216 Jun 11 10:40 blastn
-rwxrwxrwx 1 root root 13244 Jun 11 10:23 blastn.php
-rwxrwxrwx 1 root root 40583024 Jun 11 10:40 blastp
-rwxrwxrwx 1 root root 12020 Jun 11 10:23 blastp.php
-rwxrwxrwx 1 root root 40583024 Jun 11 10:40 blastx
-rwxrwxrwx 1 root root 12556 Jun 11 10:23 blastx.php
-rwxrwxrwx 1 root root 6243 Jun 11 10:41 cleanup-blastdb-volumes.py
-rwxrwxrwx 1 root root 28967976 Jun 11 10:41 convert2blastmask
drwxrwxrwx 3 root root 4096 Jun 11 11:47 db
-rwxrwxrwx 1 root root 40664944 Jun 11 10:41 deltablast
-rwxrwxrwx 1 root root 12654 Jun 11 10:23 deltablast.php
-rwxrwxrwx 1 root root 1135 Jun 11 10:34 download.php
-rwxrwxrwx 1 root root 27406960 Jun 11 10:41 dustmasker
-rwxrwxrwx 1 root root 37399 Jun 11 10:23 footer.php
-rwxrwxrwx 1 root root 4752 Jun 11 10:41 get_species_taxids.sh
-rwxrwxrwx 1 root root 347 Jun 11 10:23 header.php
-rwxrwxrwx 1 root root 789 Jun 11 10:23 help.php
drwxrwxrwx 2 root root 4096 Jun 11 10:23 images
-rwxrwxrwx 1 root root 38414 Jun 11 10:50 index.php
-rwxrwxrwx 1 root root 51346 Jun 11 10:41 legacy_blast.pl
-rwxrwxrwx 1 root root 35147 Jun 11 10:36 LICENSE
-rwxrwxrwx 1 root root 31243888 Jun 11 10:42 makeblastdb
-rwxrwxrwx 1 root root 28452720 Jun 11 10:42 makembindex
-rwxrwxrwx 1 root root 30556784 Jun 11 10:42 makeprofiledb
drwxrwxrwx 2 root root 4096 Jun 11 10:23 paper
-rwxrwxrwx 1 root root 27945 Jun 11 10:23 parameters.php
-rwxrwxrwx 1 root root 40558192 Jun 11 10:42 psiblast
-rwxrwxrwx 1 root root 13730 Jun 11 10:23 psiblast.php
-rwxrwxrwx 1 root root 11558 Jun 11 10:36 README.md
-rwxrwxrwx 1 root root 40632432 Jun 11 10:42 rpsblast
-rwxrwxrwx 1 root root 9767 Jun 11 10:23 rpsblast.php
-rwxrwxrwx 1 root root 40644720 Jun 11 10:42 rpstblastn
-rwxrwxrwx 1 root root 9496 Jun 11 10:23 rpstblastn.php
-rwxrwxrwx 1 root root 28108144 Jun 11 10:43 segmasker
-rwxrwxrwx 1 root root 15440 Jun 11 10:25 style.css
-rwxrwxrwx 1 root root 40619888 Jun 11 10:43 tblastn
-rwxrwxrwx 1 root root 12677 Jun 11 10:23 tblastn.php
-rwxrwxrwx 1 root root 40492656 Jun 11 10:43 tblastx
-rwxrwxrwx 1 root root 11529 Jun 11 10:23 tblastx.php
-rwxrwxrwx 1 root root 25985 Jun 11 10:43 update_blastdb.pl
-rwxrwxrwx 1 root root 1191 Jun 11 10:34 update.php
-rwxrwxrwx 1 root root 32020336 Jun 11 10:43 windowmasker
-rwxrwxrwx 1 root root 40842 Jun 11 10:23 xml.php

And suggest me the necessary changes.
while running blast in text view mode the XML files generated and disappears after result page display and in graphical view mode XML files will not disappears, XML files will be available in the directory.

[AshokHub]

Check the file size of the XML file.

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On Wed, 19 Jun, 2024, 11:21 am akshaybioinfo, ***@***.***> wrote: while running blast in text view mode the XML files generated and disappears after result page display and in graphical view mode XML files will not disappears, XML files will be available in the directory. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGN7QIHKAZSSIJQIDSVGQTZIEL6LAVCNFSM6AAAAABJDYJKGSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZXHAYDGNBYGY> . You are receiving this because you commented.Message ID: ***@***.***>

[akshaybioinfo]

The size of XML file is 3.9 KB and another file name with extension .fas is 338 bytes.

[AshokHub]

Do the following

1. Copy Linux executable BLAST+ to the server
2. Grant 777 permission to the directory