a big bug? the tmpClyJgf exists, but it is empty, so can not read. how should I reviese it?

[kobejamescurry]

thanks a lot, urgent for help

[ambj]

This seems as an error occurring from NetMHCpan.
try running MuPeXI with the -t (temp file option) and look at the NetMHCpan output.

[kobejamescurry]

I ran with that -f -t -n
this use the allele HLA-A01:01,HLA-B08:01 you supplied in the manual, though there is error in pepmatch * file , it can give the result TCRBOA1.mupexi

but when I use other alleles, the pepmatch * file has the errors and there can not give the result TCRBOA1.mupexi

if I use the example.vcf you supplied, the pepmatch * file is ok, also it can give the result TCRBOA1.mupexi

[ambj]

what about the NetMHCpan output file, any error reported here.
Just to clarify - the '*' is not allowed in the input HLA alleles.

[kobejamescurry]

after replace , give the result TCRBOA1.mupexi
but all the pepmatch_ is still wrong, HOW to solve this, thanks a lot

this is the netMHCpan_EL.txt

this is the netMHCpan_BA.txt

[ambj]

What is the MuPeXI output error?
Do you have permission to the /tmp dir?

[kobejamescurry]

when I run the command, just through python MuPeXI.py, the stdout is like following , gives no error

[kobejamescurry]

permissoin is 600

[ambj]

If MuPeXI runs without error and you get the output file and the corresponding normal peptide sequences for frame-shifts and indels - then it is not clear to me what your problem is?
The error regarding HLA-B40:02 is solved?

[kobejamescurry]

in your MuPeXI.py code, you change the file permission

[kobejamescurry]

it seems that The error regarding HLA-B40:02 is solved after replace *, I need to test more

[kobejamescurry]

as the ower, I have R and W, it should be totally ok for the file,

[kobejamescurry]

1 in the final result, sometimes can has FS/X in the column of Amino_Acid_Change , it means frame-shifts and indels or other things , thanks a lot.

the following two columns all are FS/X, X means random amino, is FS short for frame-shifts, if so, if it is
indel, what should be in the column of Amino_Acid_Change

VPPAGTWAL	VKPAPTWAL
PESTPSTL	NTSTPSTL

2 without getting the right pepmatch * file, but give the .mupexi file, is the .mupexi file can be used?

thanks a lot

[kobejamescurry]

here you change the permission, in your MuPeXI.py

I think the permission maybe can only changed by you, because all the file generated by your procedure, thanks a lot

[kobejamescurry]

I tried to revise the origin code, I make the tmp_dir in the my own defined out_dir, and comment the # clean_up(tmp_dir), so I can keep al the tmp file.
but still get the same error, I really can not undestand.

I just ran python MuPeXI.py, the stdout is ok, but the inner is wrong,
I guess you leak some extreme conditions

the tmpClyJgf exists, but it is empty, so can not read. how should I reviese it ?

[kobejamescurry]

here is another extreme condition you may not considered

when there is no missense, fs , deletion, insertion, you lose this

[kobejamescurry]

2 without getting the right pepmatch * file, but give the .mupexi file, is the .mupexi file can be used?

like following

thanks a lot

[kobejamescurry]

I do not know how the tmp file is used, hope you can give me help , thanks a lot

[ssudhaman]

Hi,
I was wondering if you had a fix for this yet, I seem to be getting the same error on my "pepmatch.txt" files.
"Error. Cannot read peplist from /tmp/MuPeXI_G_Iql4/tmpibkyxs"