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error when running i-tasser

Posted: Tue Jul 06, 2021 8:38 pm
by fatin_izz
Hi, I've encountered an error when running i-tasser which says that the length of my sequence is not within the range even though the sequence is only around 70 residues. What do you think might be the problem?

Here's what I've wrote:
user@LamSD:~/Desktop/fatin/I-TASSER5.1/I-TASSERmod$ ./runI-TASSER.pl -libdir /home/us
er/Desktop/fatin/I-TASSER5.1/ITLIB -seqname LAN_01_018,1.10.20.10-FF-000011,564-639 -
datadir /home/user/Desktop/fatin/I-TASSER5.1 -outdir /home/user/Desktop/fatin/I-TASSE
R5.1

Your setting for running I-TASSER is:
-pkgdir = /home/user/Desktop/fatin/I-TASSER5.1
-libdir = /home/user/Desktop/fatin/I-TASSER5.1/ITLIB
-java_home = /usr
-seqname = LAN_01_018,1.10.20.10-FF-000011,564-639
-datadir = /home/user/Desktop/fatin/I-TASSER5.1
-outdir = /home/user/Desktop/fatin/I-TASSER5.1
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false

1. make seq.txt and rmsinp
error: the sequence length is not in the range [10, 1500]

The sequence:
>LAN_01_018,1.10.20.10-FF-000011,564-639
SKGRTASKRKIRELVESVDPEERLNDEVEDLLLEIADEFIDSITRFGCQLAKHRKSDRLEVKDLALHLERSYGMRI

Re: error when running i-tasser

Posted: Wed Jul 07, 2021 1:26 pm
by jlspzw
can you attach you sequence here? we can not find problem from the pasted sequence, Than you.

Re: error when running i-tasser

Posted: Wed Jul 07, 2021 3:42 pm
by fatin_izz
sure! here's the sequence

Re: error when running i-tasser

Posted: Thu Jul 08, 2021 4:15 pm
by jlspzw
Can you make a folder that named as "Test" or others instead of "LAN_01_018,1.10.20.10-FF-000011,564-639" and put you sequence in that folder, rename the sequence file as seq.fasta, do not just put LAN_01_018,1.10.20.10-FF-000011,564-639 into the folder, I am not sure the problem is caused by the path that contains "," or you didn't put the seq.fasta file in the folder, but you can try first.

From the sequence itself, seems no problem, let me know if it works or not

Re: error when running i-tasser

Posted: Thu Jul 08, 2021 4:20 pm
by jlspzw
also, when you do like what said, then run commands like the following

~/Desktop/fatin/I-TASSER5.1/I-TASSERmod$ ./runI-TASSER.pl -libdir /home/user/Desktop/fatin/I-TASSER5.1/ITLIB -seqname Test -datadir /home/user/Desktop/fatin/I-TASSER5.1/Test -outdir /home/user/Desktop/fatin/I-TASSER5.1/Test

if your folder named as Test

Re: error when running i-tasser

Posted: Wed Jul 14, 2021 5:36 pm
by fatin_izz
It worked! Thank you so much for your help.