Hello David,
  I met the same problem. Could you please show me what the corrupted line 
like, because i can't download the file zion uploaded. 

在 2013年10月23日星期三 UTC+8上午7:02:18,David Shteynberg写道:
>
> Hello again,
>
> I was able to replicate your problem on my computers.  It appears that 
> your file is corrupted in at least one place.  The first location I saw the 
> corrupted data was on line: 1644096.  There may be other corrupted parts. 
>  Please see try copying your file over from the Mascot server again in case 
> the corruption occurred during file transfer.
>
> Cheers,
> -David 
>
>
> On Mon, Oct 21, 2013 at 5:18 PM, zion <[email protected] <javascript:>> 
> wrote:
>
>> Hi David:
>>
>> I post my data on : 
>>
>> https://docs.google.com/file/d/0B-nLuoS-pq14Yl9NWFZoMnZtbmM/edit?usp=sharing
>>
>> Thanks a lot!!
>>
>> Peter
>>
>>
>>
>> On Tuesday, October 22, 2013 12:24:55 AM UTC+8, David Shteynberg wrote:
>>
>>> Actually the problem is this:  Error: 146354 identity scores, but 96591 
>>> ion scores read
>>>
>>>
>>> Is your dat file complete?  Can you post your dat file somewhere?
>>>
>>> -David
>>>
>>>
>>> On Mon, Oct 21, 2013 at 9:22 AM, David Shteynberg <David.Sh...@
>>> systemsbiology.org> wrote:
>>>
>>>> Hi Peter,
>>>>
>>>>
>>>> Can you see you if have the same error on a file that does not contain 
>>>> '-' in it's file name? 
>>>>
>>>> Thanks,
>>>> -David
>>>>
>>>>
>>>> On Mon, Oct 21, 2013 at 6:26 AM, zion <[email protected]> wrote:
>>>>
>>>>> Dear All:
>>>>>
>>>>> I have installed TPP4.6.3,
>>>>> and when converting .dat to .pepxml,
>>>>> there is a error message like this:
>>>>>
>>>>> variable modification 1, delta mass 45.9877 for Methylthio (C):
>>>>>  residues: C
>>>>>  nterm: 0
>>>>>  cterm: 0
>>>>>  protterm: 0
>>>>>
>>>>> variable modification 2, delta mass 15.9949 for Oxidation (M):
>>>>>  residues: M
>>>>>  nterm: 0
>>>>>  cterm: 0
>>>>>  protterm: 0
>>>>>
>>>>> Error: 146354 identity scores, but 96591 ion scores read
>>>>>
>>>>> command "c:\Inetpub\tpp-bin\Mascot2XML 
>>>>> c:/Inetpub/wwwroot/ISB/data/CL1-0.dat 
>>>>> -Dc:/Inetpub/wwwroot/ISB/data/SwissProt_57.8.fasta -Etrypsin" failed: 
>>>>> Operation not permitted
>>>>>
>>>>>
>>>>>
>>>>> *Command FAILED*
>>>>> RETURN CODE:256
>>>>>
>>>>> CAN anyone kindly provide solutions to this problem?
>>>>>
>>>>> Thanks a lot!!
>>>>>
>>>>> Peter
>>>>>
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