Please make sure the directory /tmp/ is writable for you

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tgrear
Posts: 2
Joined: Wed Sep 07, 2022 7:43 pm

Please make sure the directory /tmp/ is writable for you

Post by tgrear »

Hello Zhang Lab community,

In recent attempts to run I-Tasser on a new HPC we have run into an issue concerning the generation of the tmp directory during the execution of I-Tasser. There appears to be a conflict with the tmp directory created by I-Tasser and the HPC's tmp directory owned by root (verified). If anyone in the community is able to provide insights for a fix/workaround they would be greatly appreciated. Ideally, it would be a quick fix to adjust the tmp directory naming in I-Tasser but wanted to reach out to those more experienced with the software. Also on our HPC, /tmp is owned by root, and even though it has permissions 777, the program fails giving the error at the end of the log below.

LOG:

mkdir: cannot create directory ‘/tmp/cflcyd/ITcontigous_seq_cMoRFs_0_1fu’: Permission denied

Your setting for running I-TASSER is:
-pkgdir = /powerplant/workspace/cflcyd/software/I-TASSER/I-TASSER5.2
-libdir = /powerplant/workspace/cflcyd/software/I-TASSER/ITLIB
-java_home = /usr/lib/jvm/java-1.8.0
-seqname = contigous_seq_cMoRFs_0_1fu
-datadir = /powerplant/workspace/cflcyd/git/pepStream_DEV/Test3/strucutres/PDB/cMoRFs/cMoRF_0_1fu
-outdir = /powerplant/workspace/cflcyd/git/pepStream_DEV/Test3/strucutres/PDB/cMoRFs/cMoRF_0_1fu/iTASSER/iTasser
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 40
-nmodel = 10
-light = true
-hours = 6
-LBS = false
-EC = false
-GO = false

Fail make temporary directory /tmp/cflcyd/ITcontigous_seq_cMoRFs_0_1fu
Please make sure the directory /tmp/ is writable for you <---- I-Tasser error message

Thank you for your time,
Tyler J Grear | B.S. Physics | M.S. Physics
PhD Student in Bioinformatics and Computational Biology
University of North Carolina at Charlotte
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: Please make sure the directory /tmp/ is writable for you

Post by jlspzw »

Hi

1 Please check if you have folder /tmp/cflcyd?
2 If yes, then try to do something in /tmp/cflcyd, for example cd /tmp/cflcyd; touch test.txt; echo "aaa" >test.txt see if /tmp/cflcyd is a writeable folder, normally a folder with 777 permission should be OK for writing data. If no, try to mkdir -p /tmp/cflcyd and see if it works
3 if you continuously have this issue, you may need to change the I-TASSER program to let it write the temporary data in another place. you can go into I-TASSERmod folder, check each text file, and change the path "/tmp/xx/" to a place where you can write data. for example in MUSTERmod, change tmp in the line $work_dir="/tmp/!USER!/!TAG!"; to another place.

Best
IT team
tgrear
Posts: 2
Joined: Wed Sep 07, 2022 7:43 pm

Re: Please make sure the directory /tmp/ is writable for you

Post by tgrear »

Thank you very much for the rapid and effective troubleshooting steps. These ultimately led to the root issue (pun intended!), much appreciated Zhang Lab IT team.

Thank you for your time,
Tyler J Grear | B.S. Physics | M.S. Physics
BioMolecular Physics Group - Research Assistant
PhD Student in Bioinformatics and Computational Biology
University of North Carolina at Charlotte
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