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 Date and time of compilation : 09/14/2004 09:31:49 Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 20:55:55.058
TOP_________> 109 749 SET ALNFILE = 'align.txt'
TOP_________> 110 750 SET KNOWNS = '1stc'
TOP_________> 111 751 SET SEQUENCE = 'pkcAcat'
TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './'
TOP_________> 113 753 SET STARTING_MODEL = 1
TOP_________> 114 754 SET ENDING_MODEL = 1
TOP_________> 115 755 SET HETATM_IO = ON
TOP_________> 116 756 CALL ROUTINE = 'model'
TOP_________> 117 419 CALL ROUTINE = 'getnames'
TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 120 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 121 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 122 538 SET ROOT_NAME = SEQUENCE
TOP_________> 123 539 RETURN
TOP_________> 124 420 CALL ROUTINE = 'homcsr'
TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
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
Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2004/09/17 20:55:55.058 Closing time : 2004/09/17 20:55:57.131 Total CPU time [seconds] : 1.88
-- >P1;1stc structureX:1stc:15::350::::: GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG KEFSEF*
>P1;pkcAcat sequence:pkcAcat:1::336::::: EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ SDFEGF*
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
participants (2)
-
Modeller Caretaker
-
柳田 亮