Subject: Re: [modeller_usage] Problem with alignment file
From: Modeller Caretaker <>
Date: Fri, 17 Sep 2004 17:15:35 -0700
Cc:
On Fri, Sep 17, 2004 at 09:06:09PM +0900, �?��?��??亮 wrote:
> Please help me. I cannot figure out this error.
> MODELLER 7v7, Sep 12, 2004 09:15pm
>
> Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power Macintosh
...
> Dynamically allocated memory at amaxseq [B,kB,MB]: 84067
> 82.097 0.080
> openf5__224_> Open 20 OLD SEQUENTIAL align.txt
> rdpir___270E> Error reading/processing file: align.txt
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
This error means that Modeller got to the end of the file without
reading in the whole sequence. As previously suggested, you should check
your alignment to make sure it is correct. (You can compare it with the
PDB sequence using the script at
http://salilab.org/modeller/FAQ.html#27)
Since you are using a Mac, you should also be aware that Modeller can
get confused by differences in line-end characters. Unix (and Mac OS X,
I believe) use the newline character to terminate lines. Windows uses a
carriage return followed by a newline. Macs prior to OS X used a
carriage return. If your alignment was created by an old-style Mac
program, it is possible it uses these old-style line-end characters, and
Modeller will refuse to read it. (A Unix text editor will probably show
this file all one line line with ^M characters in it.) You can fix a
file like this with the following:
tr '\r' '\n' < align.txt > align-new.txt
Ben Webb, Modeller Caretaker
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