PICRTUST 2 No such file or directory: 'hmmalign'
kesava31 opened this issue · comments
Hi
I m running the PICRTUST 2 using fna file and tsv abundance file as a input. I m getting an error see below. Could you guide me how to fix it.
b-an01 [/proj/nobackup/hpc2nstor2023-021/Function/Prediction]$ picrust2_pipeline.py -s OTU.fna.fasta -i cleaned_OTU_table.tsv -o picrust4_out_pipeline -p 1
Error running this command:
place_seqs.py --study_fasta OTU.fna.fasta --ref_dir /hpc2n/eb/software/PICRUSt2/2.5.2-foss-2022b/lib/python3.10/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust4_out_pipeline/out.tre --processes 1 --intermediate picrust4_out_pipeline/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng
Standard error of the above failed command:
Traceback (most recent call last):
File "/hpc2n/eb/software/PICRUSt2/2.5.2-foss-2022b/bin/place_seqs.py", line 109, in
main()
File "/hpc2n/eb/software/PICRUSt2/2.5.2-foss-2022b/bin/place_seqs.py", line 85, in main
place_seqs_pipeline(study_fasta=args.study_fasta,
File "/hpc2n/eb/software/PICRUSt2/2.5.2-foss-2022b/lib/python3.10/site-packages/picrust2/place_seqs.py", line 45, in place_seqs_pipeline
system_call_check("hmmalign --trim --dna --mapali " +
File "/hpc2n/eb/software/PICRUSt2/2.5.2-foss-2022b/lib/python3.10/site-packages/picrust2/util.py", line 235, in system_call_check
return_value = call(cmd, stdout=stdout_fh,
File "/hpc2n/eb/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/subprocess.py", line 345, in call
with Popen(*popenargs, **kwargs) as p:
File "/hpc2n/eb/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/subprocess.py", line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/hpc2n/eb/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/subprocess.py", line 1847, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'hmmalign'
Hi there,
That issue would seem to be that it can't find the hmmalign program installed in your path. Can you try running which hmmalign in the environment you're using and see if that works/what the output is? If it says that this isn't installed, then you could try installing it following the instructions here and then re-running the PICRUSt2 command.
Robyn
Hi Wright
Thanks for your response. I installed now and it worked fine.