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
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fra.r.silvestro •
2 answers
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.
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.
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