Hi! I'm trying to run pharokka.py on a contig and it always gets stuck in the same place after starting to run pyhmmer. None of my other contigs from the dataset return this error.
Traceback (most recent call last):
File "/home/ddawg/miniconda/bin/pharokka.py", line 499, in
main()
File "/home/ddawg/miniconda/bin/pharokka.py", line 364, in main
best_results_pyhmmer = run_pyhmmer(
^^^^^^^^^^^^
File "/home/ddawg/miniconda/bin/hmm.py", line 34, in run_pyhmmer
with pyhmmer.easel.SequenceFile(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pyhmmer/easel.pyx", line 6289, in pyhmmer.easel.SequenceFile.init
File "pyhmmer/easel.pyx", line 6283, in pyhmmer.easel.SequenceFile.init
ValueError: Could not determine alphabet of file: '8p5_11B_NODE_62_length_2252_cov_44.925878_pharokka/phanotate_aas_tmp.fasta'
Hi! I'm trying to run pharokka.py on a contig and it always gets stuck in the same place after starting to run pyhmmer. None of my other contigs from the dataset return this error.
$ pharokka.py -t 2 -d ~/pharokka_DB/ --skip_mash -i 8p5_11B_NODE_62_length_2252_cov_44.925878.fna -o 8p5_11B_NODE_62_length_2252_cov_44.925878_pharokka -f
Traceback (most recent call last): File "/home/ddawg/miniconda/bin/pharokka.py", line 499, in
main()
File "/home/ddawg/miniconda/bin/pharokka.py", line 364, in main
best_results_pyhmmer = run_pyhmmer(
^^^^^^^^^^^^
File "/home/ddawg/miniconda/bin/hmm.py", line 34, in run_pyhmmer
with pyhmmer.easel.SequenceFile(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pyhmmer/easel.pyx", line 6289, in pyhmmer.easel.SequenceFile.init
File "pyhmmer/easel.pyx", line 6283, in pyhmmer.easel.SequenceFile.init
ValueError: Could not determine alphabet of file: '8p5_11B_NODE_62_length_2252_cov_44.925878_pharokka/phanotate_aas_tmp.fasta'
Input fasta: 8p5_11B_NODE_62_length_2252_cov_44.925878.fna.txt