Running the code given by developer as an example generates the error!

[Xiao-Zhong]

Dear the developers or other users,

Please take a look at the issue below (R version 4.4.0). Any suggestions are very welcome. Or Confirming antigen.garnish doesn't work nowadays is also very helpful! If that, I wouldn't waste too much time here, just because our legacy pipeline uses antigen.garnish. Thanks Thanks Thanks!

[Xiao-Zhong]

[andrewrech]

Please use the docker container.

[Xiao-Zhong]

Thank you, Andrew! Unfortunately, our HPC doesn't have Docker and we as users don't have permission to install it there.

[andrewrech]

This software has a brittle and complex dependency stack. We supply a Docker container to try to lock these things down. There are too many potential HPC deployments for me to support each, but if there is an issue with the Docker container, I am happy to fix it.

I understand not all HPCs support Docker; however, this software is not particularly computationally intensive, and you could run the software using Docker on almost any Mac, Windows, or Linux system you have admin access to, such as a laptop or personal workstation.

[Xiao-Zhong]

OK. I see. May I ask if it's possible to install antigen.garnish via Conda? Conda is allowed on our HPC.

If not, I'll have to run sequencing data processing, mapping and variant calling on the HPC, and then run antigen.garnish for the variants with Docker on my Mac as suggested. Not perfect, but looks good! Thank you!

[onbio]

Hi @andrewrech
I am trying to run antigen.garnish on my ubuntu wsl using docker as I was having the same issue as Xiao. I am getting the Segmentation fault (core dumped) with the example data.

library(magrittr)
library(data.table)

data.table 1.14.2 using 8 threads (see ?getDTthreads). Latest news: r-datatable.com

library(antigen.garnish)
file <- file.path("/root/src/inst/extdata/testdata/", "TUMOR.vcf")
dt <- garnish_variants(file)

Loading VCFs
Scanning file to determine attributes.
File attributes:
meta lines: 9
header_line: 10
variant count: 3
column count: 11
Meta line 9 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 3
Character matrix gt cols: 11
skip: 0
nrows: 3
row_num: 0
Processed variant: 3
All variants processed

Done loading variants.

dt[, MHC := c("HLA-A01:47 HLA-A02:01 HLA-DRB1*14:67")]
result <- dt %>% garnish_affinity(.)

Generating metadata.
Reading local transcript metadata.
Checking netMHC scripts in antigen.garnish data directory.
Extracting cDNA.
Make cDNA.
Generating mutant peptide index.
Generating variants
Generating nmers
Filtering WT peptide matches.
Checking netMHC scripts in antigen.garnish data directory.
Running blastp-short to find close matches for differential agretopicity calculation.
blastp -query Hu_ag_nmer_fasta.fa -task blastp-short -db /root/antigen.garnish/human.bdb -out Hud3286a98dcc34590_blastpout.csv -num_threads 16 -outfmt '10 qseqid sseqid qseq qstart qend sseq sstart send length mismatch pident evalue bitscore'
Calculating local alignment to WT peptides for proteome-wide differential agretopicity predictions.
[1] "Alignment subset 1 of 2"
[1] "Alignment subset 2 of 2"
Removing temporary fasta files.
Generating prediction commands.
Allele mapping to prediction tools:
MHC netMHCpan netMHC netMHCII netMHCIIpan
1: HLA-A01:47 HLA-A01:47
2: HLA-A02:01 HLA-A02:01 HLA-A0201
3: HLA-DRB1*14:67 DRB1_1467
Checking netMHC scripts in antigen.garnish data directory.
Running netMHC in parallel.
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Collating netMHC output...
Read 0 items
Error in data.table::setnames(., dt %>% names(), dtn) :
NA in 'new' at positions [1]
In addition: Warning message:
In .Call2("DNAStringSet_translate", x, skip_code, dna_codes[codon_alphabet], :
last 2 bases were ignored
Removing temporary files.

I tried reinstalling netMHC, but am still getting the same error on wsl.

root@150f390bdfae:~/antigen.garnish/netMHC/netMHC-4.0/test# ../netMHC test.fsa >test.fsa.myout
Segmentation fault (core dumped)

Do you have any experience resolving this issue?

[andrewrech]

This software has a brittle dependency stack with pinned versions. Could you please try the Docker image outside WSL?