download_lib.pl - Script Issues

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ahnaka
Posts: 2
Joined: Thu Mar 17, 2022 8:24 pm

download_lib.pl - Script Issues

Post by ahnaka »

Hello ITASSER Team,

I have been interested in testing out the CR-I-TASSER since its release, however, the web-version appears to take a bit of time to run samples. I wanted to install a local version and was trying to follow the instructions from https://zhanggroup.org/CR-I-TASSER/download.html

From following the MANUAL.txt, on step 2 it states to "'download_lib.pl' is provided in the package for automated library download and update of the libraries." I was able to input the directory and start running the script. However, I would hit an error in downloading the NR database.
'Downloading NR database...
System call failed: at ./download_lib.pl line 108'

Looking into this script, in line 108, it mentions 'ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz' as the location, but I don't believe I can access this. Would there be a potential workaround or way to update this?

Additionally, it looks like there are other downloads, some of them are from http://zhanglab.ccmd.med.umich.edu/BioLiP/ but are the updated links in https://zhanggroup.org/library/?

Thank you,
Andrew
XiZhang
Posts: 6
Joined: Tue May 04, 2021 5:06 pm

Re: download_lib.pl - Script Issues

Post by XiZhang »

Hello Andrew,

Thank you so much for pointing out the bug. We have updated the download_lib.pl and now should work fine. Please re-download the package and find the updated script. Also please do not concern about "zhanglab.ccmd.med.umich.edu" vs "zhanggroup.org". You could run a test like "wget -o log -c http://zhanglab.ccmb.med.umich.edu/BioL ... BSITES.bsr" which should be able to download BSITES.bsr to your local.

Best,
Xi
ahnaka
Posts: 2
Joined: Thu Mar 17, 2022 8:24 pm

Re: download_lib.pl - Script Issues

Post by ahnaka »

Hello Zhang,

Thank you for changing the script. I have tried again with the new download_lib.pl script, and most of the libraries were working/downloaded correctly. The one issue that I encountered with the new script is it complains about the metaclust_2017_05.fasta.gz file. In the log it states, 'ERROR: cannot verify metaclust.mmseqs.org's certificate, ... Issue certificate has expired.

It did suggest to attach --no-check-certificate to the call in order to download the .gz file, and this did get the file, but then it didn't extract the file. I believe that changing the extraction method (tar -zxvf to gzip -d) did allow the fasta file to download correctly. I think that after this change, CR-I-TASSER should have all of the libraries required to run. However, when doing a basic run:
"$pkgdir/I-TASSERmod/runI-TASSER.pl -libdir /home/yourname/ITLIB -seqname example -mapname yourmap.map -datadir /home/yourname/CR-I-TASSER-1.0/example"

I keep encountering 'error: without MSA file generate!'. This is early on in '2.0 run DeepMSA'. Are there any other steps that you could suggest?

Best Regards,
Andrew
ATVincentUL
Posts: 4
Joined: Fri Jan 28, 2022 12:14 am

Re: download_lib.pl - Script Issues

Post by ATVincentUL »

Hello,

I also have the same issue.

Antony
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