HLA-HD tool for genomic imputation

Question

[fra.r.silvestro]

Dear Biostars users,

I've followed this basic and clearly explained demo

After running the command bash bin/hlahd.1.7.0 t -4 ..., the terminal displays this message:

Error: Couldn't open split file. Could'nt open file. sh: estimation/$ID/pickup.sh: No such file or directory

Why does the tool requires this file or directory?

My output are inside the directory: estimation/$ID/mapfile/...

Thanks in advance,
F.R.Silvestro

Answer 1

[Spencer]

I think there are two problems here -- opening the split file and pickup.sh not being created. I have run into both of these. For the first one, I would check your path to the split file. It should look something like the following: ~/pathToHlahd/hlahd.1.7.0/HLA_gene.split.txt

For the other problem, have you tried changing the value of open files to 1024 using ulimit? Check the value using ulimit -Sa and if it is less than 1024 change it using ulimit -n 1024. This step is mentioned on the website but not on the pdf so it is easy to miss.

Answer 2

[Javier]

Hi, I just solved the same error. In my case, it was because I misunderstood the instructions.

hlahd.sh -t 4 
*-f ~/hlahd.1.7.0/freq_data* \
path_to_sample_1.fastq \
path_to_sample_2.fastq \
*~/hlahd.1.7.0/HLA_gene.split.txt* \
*~/hlahd.1.7.0/dictionary*  \
sample \
path_to_output_dir

Basically, I didn't get that 3 arguments ( the marked ones ) should be directed to directories and files within the program directory.