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openvax / mhctools

Python interface to running command-line and web-based MHC binding predictors
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Unable to open(r) file when running netMHCpan --version _MHCTOOLS_VERSION_SNIFFING #170

Open trevorpfiz opened 1 week ago

trevorpfiz commented 1 week ago

{"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
iskandr commented 1 week ago

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

— Reply to this email directly, view it on GitHub https://github.com/openvax/mhctools/issues/170, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

trevorpfiz commented 1 week ago

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 — Reply to this email directly, view it on GitHub <#170>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA . You are receiving this because you are subscribed to this thread.Message ID: @.>

I thought I did, but I will confirm. It doesn't list what file it is trying to open? Unable to open(r) file

iskandr commented 1 week ago

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? … <#m8121778983633458262> 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 — Reply to this email directly, view it on GitHub <#170 https://github.com/openvax/mhctools/issues/170>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA . You are receiving this because you are subscribed to this thread.Message ID: @.>

I made sure I did. It doesn't list what file it is trying to open? Unable to open(r) file

— Reply to this email directly, view it on GitHub https://github.com/openvax/mhctools/issues/170#issuecomment-2424148677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OKJM5BWE43Y4N5KN5DZ4KU2FAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRUGE2DQNRXG4 . You are receiving this because you commented.Message ID: @.***>

trevorpfiz commented 1 week ago

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? … <#m8121778983633458262> 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 — Reply to this email directly, view it on GitHub <#170 <#170>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA https://github.com/notifications/unsubscribe-auth/AAAL2OK6XH6RF33DFV3OLGDZ4IPETAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TQOJTGE2DMMA . You are receiving this because you are subscribed to this thread.Message ID: @.> I made sure I did. It doesn't list what file it is trying to open? Unable to open(r) file — Reply to this email directly, view it on GitHub <#170 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OKJM5BWE43Y4N5KN5DZ4KU2FAVCNFSM6AAAAABQHJUYZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRUGE2DQNRXG4 . You are receiving this because you commented.Message ID: @.>

[ec2-user@ip-xxx tools-fastapi]$ ls -ld /opt/netMHCpan-4.1/tmp/
drwxrwxrwx. 32 ec2-user ec2-user 16384 Oct 19 21:09 /opt/netMHCpan-4.1/tmp/

[ec2-user@ip-xxx tools-fastapi]$ umask
0022

[ec2-user@ip-xxx tools-fastapi]$ netMHCpan --version -v _MHCTOOLS_VERSION_SNIFFING
# Tmpdir made /opt/netMHCpan-4.1/tmp/netMHCpanzgThCT
Unable to open(r) file

[ec2-user@ip-xxx tools-fastapi]$ sudo netMHCpan --version _MHCTOOLS_VERSION_SNIFFING
# Tmpdir made /opt/netMHCpan-4.1/tmp/netMHCpaniy01Av
Unable to open(r) file

[ec2-user@ip-xxx tools-fastapi]$ /opt/netMHCpan-4.1/Linux_x86_64/bin/netMHCpan --version _MHCTOOLS_VERSION_SNIFFING
Unable to open(r) file $NETMHCpan/data/version

export NMHOME=/opt/netMHCpan-4.1
export TMPDIR=$NMHOME/tmp
export NETMHCpan=$NMHOME/Linux_x86_64

[ec2-user@ip-xxx tools-fastapi]$ /opt/netMHCpan-4.1/Linux_x86_64/bin/netMHCpan --version
# Tmpdir made /opt/netMHCpan-4.1/tmp/netMHCpan9K6hBq
Unable to open(r) file