Apptainer Error: File existence/permissions problem in trying to open HMM file /usr/src/symcla/data/hmms_symcla/sy50.hmm #2
Description
Hi, thanks for making this great tool, I thought I would try it out through apptainer/singularity - however I get the following error message (see below).
Do you know what might be the cause of this? Perhaps it's possible I need to mount some directory to another? I don't think there should be much difference between singularity versions, though I'm using singularity version 3.6.0-rc.4+67-gca233ae. I'm running this on my university's computing cluster where I don't have root permissions.
Thanks a lot for your advice,
Best regards,
Will
p.s. probably beyond the scope of this software - but I was wondering if there's any way to link hosts with symbionts (in a metagenomic dataset), and secondarily, if this program would work on eukaryotes? Obviously the completeness/contamination data would not be correct, however I don't need that information as I can evaluate my genomes with e.g. EukCC/BUSCO.
$ singularity run ~/software/symcla/symcla_latest.sif symcla classify
[WARN tini (75927)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.
symcla: symbiont classifier
---------- Classifying genomes workflow ----------
Creating output dir
[OK] Output directory created at: /gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla
[OK] Genomes renamed
[OK] Proteins renamed
Merging genomes
[OK] Fasta files merged at: /gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla/tmp/merged_genomes.faa
Running hmmsearch on merged genomes for the hmm models file:
Error: File existence/permissions problem in trying to open HMM file /usr/src/symcla/data/hmms_symcla/sy50.hmm.
HMM file /usr/src/symcla/data/hmms_symcla/sy50.hmm not found (nor an .h3m binary of it)
[OK] Hmmsearch output saved at: /gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla/tmp/sy50_hmmsearch.tblout
Error: File existence/permissions problem in trying to open HMM file /usr/src/symcla/data/hmms_uni56/uni56.hmm.
HMM file /usr/src/symcla/data/hmms_uni56/uni56.hmm not found (nor an .h3m binary of it)
[OK] Hmmsearch output saved at: /gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla/tmp/uni56_hmmsearch.tblout
Saving list of models for each hmm model file
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /usr/src/symcla/symcla:648 in classify │
│ │
│ 645 │ merge_genomes(tmp_genomes_path) │
│ 646 │ run_hmmsearch(symcla_model=symcla_model, ncpus=ncpus) │
│ 647 │ run_hmmsearch_uni56(ncpus=ncpus) │
│ ❱ 648 │ save_list_of_models(symcla_model=symcla_model) │
│ 649 │ save_list_of_genomes(tmp_genomes_path=tmp_genomes_path) │
│ 650 │ hmmer_results_to_pandas_df() │
│ 651 │ classify_genomes(symcla_model=symcla_model, savedir=savedir) │
│ │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │ deltmp = True │ │
│ │ genomedir = '/gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/input_genomes' │ │
│ │ ncpus = 16 │ │
│ │ savedir = '/gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla' │ │
│ │ start_time = 1742232105.8948207 │ │
│ │ symcla_model = 'sy50' │ │
│ │ tmp_genomes_path = '/gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output_symcla/… │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│ │
│ /usr/src/symcla/symcla:244 in save_list_of_models │
│ │
│ 241 │ │ │ │ tmp_dir_path + "/" + hmmfile.split("/")[-1].split(".")[0] + "_models.lis │
│ 242 │ │ ) │
│ 243 │ │ with open(models_list_file_path, "w") as output_models_list_file: │
│ ❱ 244 │ │ │ with open(hmmfile, "r") as my_hmmfile: │
│ 245 │ │ │ │ for line in my_hmmfile: │
│ 246 │ │ │ │ │ if re.search("NAME", line): │
│ 247 │ │ │ │ │ │ output_models_list_file.write(line.replace("NAME ", "")) │
│ │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │ hmmfile = '/usr/src/symcla/data/hmms_symcla/sy50.hmm' │ │
│ │ list_of_hmm_models_files = [ │ │
│ │ │ '/usr/src/symcla/data/hmms_symcla/sy50.hmm', │ │
│ │ │ '/usr/src/symcla/data/hmms_uni56/uni56.hmm' │ │
│ │ ] │ │
│ │ models_list_file_path = '/gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/output… │ │
│ │ output_models_list_file = <_io.TextIOWrapper │ │
│ │ name='/gpfs/data/mock_lab/will/mosaic_tmp/mag_catalogue/symcla/o… │ │
│ │ mode='w' encoding='UTF-8'> │ │
│ │ symcla_model = 'sy50' │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
PermissionError: [Errno 13] Permission denied: '/usr/src/symcla/data/hmms_symcla/sy50.hmm'