Unable to open(r) file when running netMHCpan --version _MHCTOOLS_VERSION_SNIFFING #170
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Sounds like you don’t have write permission in the tmp dir?
…On Sat, Oct 19, 2024 at 5:13 AM Trevor Pfizenmaier ***@***.***> wrote:
{"detail":"Command '['netMHCpan', '--version',
'_MHCTOOLS_VERSION_SNIFFING']' returned non-zero exit status 1."}
# /opt/netMHCpan-4.1/Linux_x86_64/bin/netMHCpan --version _MHCTOOLS_VERSION_SNIFFING
# Sat Oct 19 09:11:42 2024
# User: ec2-user
# PWD : /opt/netMHCpan-4.1/test
# Host: Linux ip-xxx.ec2.internal xxx.amzn2023.x86_64 x86_64
# Command line parameters set to:
# [-rdir filename] /opt/netMHCpan-4.1/Linux_x86_64 Home directory for NetMHpan
# [-syn filename] /opt/netMHCpan-4.1/Linux_x86_64/data/synlist.bin Synaps file
# [-v] 0 Verbose mode
# [-dirty] 0 Dirty mode, leave tmp dir+files
# [-tdir filename] /opt/netMHCpan-4.1/tmp/netMHCpanXXXXXX Temporary directory (made with mkdtemp)
# [-hlapseudo filename] /opt/netMHCpan-4.1/Linux_x86_64/data/MHC_pseudo.dat File with MHC pseudo sequences
# [-hlaseq filename] File with full length MHC sequences
# [-a line] HLA-A02:01 MHC allele
# [-f filename] File name with input
# [-w] 0 w option for webface
# [-s] 0 Sort output on descending affinity
# [-p] 0 Use peptide input
# [-rth float] 0.500000 Rank Threshold for high binding peptides
# [-rlt float] 2.000000 Rank Threshold for low binding peptides
# [-l string] 8,9,10,11 Peptide length [8-11] (multiple length with ,)
# [-xls] 0 Save output to xls file
# [-xlsfile filename] NetMHCpan_out.xls Filename for xls dump
# [-t float] -99.900002 Threshold for output (%rank) [<0 print all]
# [-thrfmt filename] /opt/netMHCpan-4.1/Linux_x86_64/data/threshold/%s.thr.%s Format for threshold filenames
# [-expfix] 0 Exclude prefix from synlist
# [-version filename] /opt/netMHCpan-4.1/Linux_x86_64/data/version File with version information
# [-inptype int] 0 Input type [0] FASTA [1] Peptide
# [-listMHC] 0 Print list of alleles included in netMHCpan
# [-allname filename] /opt/netMHCpan-4.1/Linux_x86_64/data/allelenames File with print names for alleles
# [-BA] 0 Include Binding affinity prediction
# NetMHCpan version 4.1b
# Tmpdir made /opt/netMHCpan-4.1/tmp/netMHCpan9ynvog
Unable to open(r) file
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I thought I did, but I will confirm. It doesn't list what file it is trying to open? |
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NetMHCpan writes mysterious temp files, can you run it standalone from the
commandine?
On Sat, Oct 19, 2024 at 3:08 PM Trevor Pfizenmaier ***@***.***>
wrote:
… Sounds like you don’t have write permission in the tmp dir?
… <#m_8121778983633458262_>
On Sat, Oct 19, 2024 at 5:13 AM Trevor Pfizenmaier *@*.*> wrote:
{"detail":"Command '['netMHCpan', '--version',
'_MHCTOOLS_VERSION_SNIFFING']' returned non-zero exit status 1."} #
/opt/netMHCpan-4.1/Linux_x86_64/bin/netMHCpan --version
_MHCTOOLS_VERSION_SNIFFING # Sat Oct 19 09:11:42 2024 # User: ec2-user #
PWD : /opt/netMHCpan-4.1/test # Host: Linux ip-xxx.ec2.internal
xxx.amzn2023.x86_64 x86_64 # Command line parameters set to: # [-rdir
filename] /opt/netMHCpan-4.1/Linux_x86_64 Home directory for NetMHpan #
[-syn filename] /opt/netMHCpan-4.1/Linux_x86_64/data/synlist.bin Synaps
file # [-v] 0 Verbose mode # [-dirty] 0 Dirty mode, leave tmp dir+files #
[-tdir filename] /opt/netMHCpan-4.1/tmp/netMHCpanXXXXXX Temporary directory
(made with mkdtemp) # [-hlapseudo filename]
/opt/netMHCpan-4.1/Linux_x86_64/data/MHC_pseudo.dat File with MHC pseudo
sequences # [-hlaseq filename] File with full length MHC sequences # [-a
line] HLA-A02:01 MHC allele # [-f filename] File name with input # [-w] 0 w
option for webface # [-s] 0 Sort output on descending affinity # [-p] 0 Use
peptide input # [-rth float] 0.500000 Rank Threshold for high binding
peptides # [-rlt float] 2.000000 Rank Threshold for low binding peptides #
[-l string] 8,9,10,11 Peptide length [8-11] (multiple length with ,) #
[-xls] 0 Save output to xls file # [-xlsfile filename] NetMHCpan_out.xls
Filename for xls dump # [-t float] -99.900002 Threshold for output (%rank)
[<0 print all] # [-thrfmt filename]
/opt/netMHCpan-4.1/Linux_x86_64/data/threshold/%s.thr.%s Format for
threshold filenames # [-expfix] 0 Exclude prefix from synlist # [-version
filename] /opt/netMHCpan-4.1/Linux_x86_64/data/version File with version
information # [-inptype int] 0 Input type [0] FASTA [1] Peptide #
[-listMHC] 0 Print list of alleles included in netMHCpan # [-allname
filename] /opt/netMHCpan-4.1/Linux_x86_64/data/allelenames File with print
names for alleles # [-BA] 0 Include Binding affinity prediction # NetMHCpan
version 4.1b # Tmpdir made /opt/netMHCpan-4.1/tmp/netMHCpan9ynvog Unable to
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I made sure I did. It doesn't list what file it is trying to open? Unable
to open(r) file
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{"detail":"Command '['netMHCpan', '--version', '_MHCTOOLS_VERSION_SNIFFING']' returned non-zero exit status 1."}The text was updated successfully, but these errors were encountered: