samtools: Permission denied

[parvathisudha]

Hi,
I’m trying to run a pipeline on our university’s HPC system. I’ve loaded the required modules (e.g., samtools, vcftools) using the module load command on the Linux system.
However, when I attempt to run preProcess, I receive the following warning:

sh: /N/project/Monopogen/apps/samtools: Permission denied

It seems the script is trying to access a version of samtools located in /N/project/Monopogen/apps/ as a result, the BAM index files are not being generated.
Is there something I need to change in the code or environment to ensure it uses the modules I’ve already loaded instead of the one in the apps directory?

Thank you!

Parvathi

[parvathisudha]

Hi, I have solved this issue by giving the samtools and bcftools path in Monopogen.py.
`global out, samtools, bcftools, bgzip, java, beagle
out = os.path.abspath(args.out)

#samtools  = os.path.abspath(args.app_path) + "/samtools"

samtools = "samtools"

#bcftools = "bcftools"`

In the germline.py I am getting similar error with vcftools.

[parkanha@i60 Monopogen]$ python ${path}/src/Monopogen.py germline -a ${path}/apps -t 1 -r /N/project/Monopogen/testMM/region.lst -p /N/project/Monopogen/example/ -g /N/project/Monopogen/example/chr20_2Mb.hg38.fa -s all -o out --norun TRUE
[2025-10-16 21:37:28,758] INFO Monopogen.py Performing germline variant calling...
[2025-10-16 21:37:28,758] INFO germline.py Parameters in effect:
[2025-10-16 21:37:28,758] INFO germline.py --subcommand = [germline]
[2025-10-16 21:37:28,758] INFO germline.py --region = [/N/project/Monopogen/testMM/region.lst]
[2025-10-16 21:37:28,758] INFO germline.py --step = [all]
[2025-10-16 21:37:28,758] INFO germline.py --out = [out]
[2025-10-16 21:37:28,758] INFO germline.py --reference = [/N/project/scmultiome_johnson/Monopogen/example/chr20_2Mb.hg38.fa]
[2025-10-16 21:37:28,758] INFO germline.py --imputation_panel = [/N/project/Monopogen/example/]
[2025-10-16 21:37:28,758] INFO germline.py --max_softClipped = [1]
[2025-10-16 21:37:28,758] INFO germline.py --app_path = [/N/project/Monopogen/apps]
[2025-10-16 21:37:28,758] INFO germline.py --nthreads = [1]
[2025-10-16 21:37:28,758] INFO germline.py --norun = [TRUE]
[2025-10-16 21:37:28,758] INFO Monopogen.py Checking existence of essenstial resource files...
[2025-10-16 21:37:28,782] INFO Monopogen.py Checking dependencies...
Traceback (most recent call last):
File "/N/project/Monopogen/src/Monopogen.py", line 343, in

main()

File "/N/project/Monopogen/src/Monopogen.py", line 336, in main
args.func(args)
File "/N/project/Monopogen/src/Monopogen.py", line 71, in germline
check_dependencies(args)
File "/N/project/Monopogen/src/germline.py", line 115, in check_dependencies
assert out != "", "Program {} cannot be found!".format(prog)
^^^^^^^^^
AssertionError: Program vcftools cannot be found!

After loading the module, I tried to solve the issue by similar way, which didn't work. Can you please tell me how to solve this issue?

Thanks!
Parvathi.