Hi,
I have been attempting to explore some MHCII alleles for Balb-c mice.
I read in the file below with fread (from data.table) and ran garnish affinity on the data and got this error.
I was originally using an install on linux and then switched to the docker image and setup as per installation instructions.
Checking netMHC scripts in antigen.garnish data directory.
Running netMHC in parallel.
/usr/bin/sh: 1: netMHCII: not found
Error in run_netMHC(dtl[[2]]) :
netMHC errored on a command, check MHC syntax with list_mhc() and make sure netMHC is in path. Errored command was: netMHC -p -l 9 -a H-2-Dd -f netMHC_1d5ab905-0762-43d1.csv > netMHC_1d5ab905-0762-43d1_o.csv;netMHC -p -l 11 -a H-2-Dd -f netMHC_61829f34-dc4f-4dc7.csv > netMHC_61829f34-dc4f-4dc7_o.csv;netMHC -p -l 13 -a H-2-Dd -f netMHC_79007d33-e906-4a73.csv > netMHC_79007d33-e906-4a73_o.csv;netMHC -p -l 8 -a H-2-Kd -f netMHC_ad1efbc0-f2f8-44b2.csv > netMHC_ad1efbc0-f2f8-44b2_o.csv;netMHC -p -l 10 -a H-2-Kd -f netMHC_56595981-afb5-4a6d.csv > netMHC_56595981-afb5-4a6d_o.csv;netMHC -p -l 12 -a H-2-Kd -f netMHC_af7176fe-7f68-40df.csv > netMHC_af7176fe-7f68-40df_o.csv;netMHC -p -l 14 -a H-2-Kd -f netMHC_75f5dd77-a0a0-46e5.csv > netMHC_75f5dd77-a0a0-46e5_o.csv;netMHC -p -l 9 -a H-2-Ld -f netMHC_2cb1aa2d-0c46-4a97.csv > netMHC_2cb1aa2d-0c46-4a97_o.csv;netMHC -p -l 11 -a H-2-Ld -f netMHC_ad200b76-31d9-44e9.csv > netMHC_ad200b76-31d9-44e9_o.csv;netMHC -p -l 13 -a H-2-Ld -f netMHC_0b
In addition: Warning message:
In split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
data length is not a multiple of split variable
Removing temporary files.
Hi, I have been attempting to explore some MHCII alleles for Balb-c mice. I read in the file below with fread (from data.table) and ran garnish affinity on the data and got this error. I was originally using an install on linux and then switched to the docker image and setup as per installation instructions.
Any help would be appreciated. Thanks.
singlepep.csv
list_mhc()and make sure netMHC is in path. Errored command was: netMHC -p -l 9 -a H-2-Dd -f netMHC_1d5ab905-0762-43d1.csv > netMHC_1d5ab905-0762-43d1_o.csv;netMHC -p -l 11 -a H-2-Dd -f netMHC_61829f34-dc4f-4dc7.csv > netMHC_61829f34-dc4f-4dc7_o.csv;netMHC -p -l 13 -a H-2-Dd -f netMHC_79007d33-e906-4a73.csv > netMHC_79007d33-e906-4a73_o.csv;netMHC -p -l 8 -a H-2-Kd -f netMHC_ad1efbc0-f2f8-44b2.csv > netMHC_ad1efbc0-f2f8-44b2_o.csv;netMHC -p -l 10 -a H-2-Kd -f netMHC_56595981-afb5-4a6d.csv > netMHC_56595981-afb5-4a6d_o.csv;netMHC -p -l 12 -a H-2-Kd -f netMHC_af7176fe-7f68-40df.csv > netMHC_af7176fe-7f68-40df_o.csv;netMHC -p -l 14 -a H-2-Kd -f netMHC_75f5dd77-a0a0-46e5.csv > netMHC_75f5dd77-a0a0-46e5_o.csv;netMHC -p -l 9 -a H-2-Ld -f netMHC_2cb1aa2d-0c46-4a97.csv > netMHC_2cb1aa2d-0c46-4a97_o.csv;netMHC -p -l 11 -a H-2-Ld -f netMHC_ad200b76-31d9-44e9.csv > netMHC_ad200b76-31d9-44e9_o.csv;netMHC -p -l 13 -a H-2-Ld -f netMHC_0b In addition: Warning message: In split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) : data length is not a multiple of split variable Removing temporary files.