Library installation error

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Newbie
Posts: 1
Joined: Wed May 05, 2021 2:29 pm

Library installation error

Post by Newbie »

Hello!

We received an error after testing I-TASSER, indicating the libraries downloaded were not complete and that we should use the download_lib.pl to obtain them.

When I executed the code, however, I received another error (log is pasted below)

ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz
=> ‘nr.tar.gz’
Resolving zhanglab.ccmb.med.umich.edu (zhanglab.ccmb.med.umich.edu)... 141.211.25.200
Connecting to zhanglab.ccmb.med.umich.edu (zhanglab.ccmb.med.umich.edu)|141.211.25.200|:21... failed: No route to host.

Could you please help me troubleshoot this problem? I tried pinging the IP address from two machines, both give me "no route to host" error.

Thank you!!
xiaogenz
Posts: 139
Joined: Sun Apr 25, 2021 12:02 am

Re: Library installation error

Post by xiaogenz »

Our FTP server is not working now which results in the problem of database downloading. You can change the line 102 in "download_lib.pl" to " system("wget -o log -c http://zhanglab.ccmb.med.umich.edu/library/nr.tar.gz") == 0 or die "System call failed: $!"; ". It will be working after the modification.
jed
Posts: 5
Joined: Mon Oct 25, 2021 3:32 am

Re: Library installation error

Post by jed »

Hello there,

I am having issues with installing the library. The error message I had was:

"bzip2: Data integrity error when decompressing.
Input file = (stdin), output file = (stdout)

It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.

You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.

tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
System call failed: at ./download_lib.pl line 191."

I ran the download_lib.pl again but the problem is still there. The script stops at ligand/2hgqZ_BS01.pdb.
Can you please help me troubleshoot this problem? Many thanks.

Jed
xiaogenz
Posts: 139
Joined: Sun Apr 25, 2021 12:02 am

Re: Library installation error

Post by xiaogenz »

Please download the newest "ligand.tar.bz2" updated on Oct 27, 2021. I have tested it and successfully uncompressed it. If the problem still persists, please manually download "ligand.tar.bz2" at "http://zhanglab.dcmb.med.umich.edu/BioL ... nd.tar.bz2" and uncompress it through "tar -xvf ligand.tar.bz2". Please let me know if you have any questions.
jed
Posts: 5
Joined: Mon Oct 25, 2021 3:32 am

Re: Library installation error

Post by jed »

Hello there,
Thank you for your help. I ran the download_lib.pl again and it downloaded everything successfully this time.
However, when I ran runI-TASSER.pl, I still got the error message:
"Your library files are not complete, please download library with the script download_lib.pl"

The command I used was:
'$pkgdir/I-TASSERmod/runI-TASSER.pl -libdir /home/yourname/ITLIB -seqname example -datadir /home/yourname/I-TASSER5.0/example'
To solve this problem, I tried to reinstall I-TASSER, but this didn't help. I double-checked that the directory for the library and runI-TASSER.pl are correct.
What should I do here?

Thanks,
Jed
jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Library installation error

Post by jlspzw »

Hi

Have you replace "yourname" in /home/yourname/ITLIB by real place? and please do 'ls" to your ITLIB path and let us check what exists in your folder

Best
IT team
jed
Posts: 5
Joined: Mon Oct 25, 2021 3:32 am

Re: Library installation error

Post by jed »

Hello there,
yes, I replaced the "yourname". When I used ls, I have "Bfactor CNT DEP download_lib.pl GO ligand map nr PSSM SIG summary
BPOCKET databases dotProfiles Enzyme home log MTX PDB receptor stride" in my ITLIB. The databases is my nr database.

Thanks,
Jed
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jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Library installation error

Post by jlspzw »

Hi Jed,

can you do ls to "/home/yourname/ITLIB/nr/nr" see if this file exist? (please replace "yourname as the real place of you, to make the conversation easily, can you tell us the real path next time? The issue you have is the script try to find the /home/yourname/ITLIB/nr/nr file (if you never change the runI-TASSER.pl), but the failed. so please first check if the file exist.

Best
IT team
jed
Posts: 5
Joined: Mon Oct 25, 2021 3:32 am

Re: Library installation error

Post by jed »

Hi there,
Thank you! I changed the "ITLIB/nr/nr" in runI-TASSER.pl to "ITLIB/nr/" and the problem is fixed.

But I got a new problem with blastpgp. The error is "/home/jed/I-TASSER5.1/blast/bin/blastpgp is not working properly, please check".

I read the runI-TASSER.pl and check the files in "/home/jed/I-TASSER5.1/blast/bin/". The directory has all applications that were mentioned in runI-TASSER.pl.

Thanks,
Jed
jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Library installation error

Post by jlspzw »

Hi

The issue major occurs after this step "$blastdir/blastpgp -b 1000 -j 3 -h 0.001 -d $db -i protein.fasta -C psitmp.chk -Q pssm.txt > blast.out"
you can add the command before this line

print "$blastdir/blastpgp -b 1000 -j 3 -h 0.001 -d $db -i protein.fasta -C psitmp.chk -Q pssm.txt > blast.out\n";

although you change the ITLIB/nr/nr to ITLIB/nr, the program runs, but it just means you folder ITLIB/nr exists, however, I still doubt the nr library is not correct downloaded, please do "ls /home/jed/ITLIB/nr" let us see what files exist in the folder

Best
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