HMMSearchNotFound

[sly-cell]

Hi,

I have installed the vpf-class, but I had some problem when loading HMMER. It could not find HMMSearch, so I added --hmmer-prefix according to the usage( --hmmer-prefix HMMER Prefix to the HMMER installation (e.g. HMMER/bin/hmmsearch must exist)), and I got this error:

hmmsearch error: HMMSearchNotFound {hmmerConfig = HMMERConfig {hmmerPrefix = Just (Tagged "/lustre/software/hmmer/3.2.1/gcc/4.8.5/")}}

In fact, my hmmsearch in/lustre/software/hmmer/3.2.1/gcc/4.8.5/bin/hmmsearch is executable. I also tried other possible paths such as /lustre/software/hmmer/ or /lustre/software/hmmer/3.2.1/gcc/4.8.5/bin/hmmsearch, but they all failed. I wonder if I have missed something?

Best regards

[bielr]

Hi,

I haven't been able to reproduce this. Some ideas that came to my mind:

• Does the path /lustre/software/hmmer/3.2.1/gcc/4.8.5/bin/hmmsearch contain any broken symlinks?
• Does the command /lustre/software/hmmer/3.2.1/gcc/4.8.5/bin/hmmsearch -h work as expected? (no linker errors, etc)
• Are you using any special configuration (like a cluster) or is this a single machine?

Hope this helps

[sly-cell]

Hi, @bielr thank you for your reply. I have checked the path, it is a direct link, and the /lustre/software/hmmer/3.2.1/gcc/4.8.5/bin/hmmsearch -h also works well.

But it is worth noting that codes are run throughsbatch to Slurm rather than on a single machine. Normally I will usemodule load HAMMER/3.2.1-gcc-4.8.5 to load HMMER (of course did not work in this case). Maybe something is different on a cluster?

Here is my complete code:

singularity exec vpf-tools.sif stack exec -- vpf-class --data-index ../data/data-index.yaml -i ncl95_1kb.fasta -o test_classified --workers 28 --prodigal /lustre/software/prodigal/2.6.3/gcc/4.8.5/bin/prodigal --hmmer-prefix /lustre/software/hmmer/3.2.1/gcc/4.8.5/

(Here I used singularity for I once met some problem when installing vpf-class. It now works well except a WARNING: seccomp requested but not enabled, seccomp library is missing or too old. Hope more information would help solve this problem.)

[bielr]

Hi,

Unfortunately I do not have access to any cluster (or Slurm) currently, so these are just guesses.

• Make sure that hmmsearch is avaiable from the singularity container, no Slurm involved.
• Is hmmsearch automatically available in your PATH when module loading it? If so, vpf-class should be able to find it without further configuration.

After some research, I think it must be related to this. If /lustre is not your home directory, then it may not be accessible from your container by default.

[sly-cell]

Sorry for the delay. Installing HMM and Prodigal into the container did solve this problem. The reference helped me a lot. Thank you!