Blast is required in the Bandage conda env.

[David-Mahoney]

sarand -i test/spade_output/assembly_graph_with_scaffolds.gfa -o test/test_output -a metaspades -k 55
2023-08-24 11:10:56,238 [INFO ]	Sarand initialised: output=test/test_output
2023-08-24 11:10:56,238 [INFO ]	Starting analysis...
2023-08-24 11:10:56,238 [INFO ]	Finding AMR genes in the assembly graph: /home/david/error_replication/sarandV0/test/spade_output/assembly_graph_with_scaffolds.gfa
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
           ^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/site-packages/sarand/full_pipeline.py", line 817, in process_amr_group_and_find
    p_find_amr_align = are_there_amrs_in_graph(
                       ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/site-packages/sarand/full_pipeline.py", line 770, in are_there_amrs_in_graph
    bandage_command = subprocess.run(
                      ^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mamba', 'run', '-n', 'bandage-0.8.1_err', 'Bandage', 'querypaths', PosixPath('/home/david/error_replication/sarandV0/test/spade_output/assembly_graph_with_scaffolds.gfa'), 'test/test_output/AMR_info/amr_group_0.fasta', 'test/test_output/AMR_info/alignments/amr_group_0_align_2023-08-24_11-10-56', '--pathnodes', '50', '--minpatcov', '0.94', '--minmeanid', '0.94', '--minhitcov', '0.94']' returned non-zero exit status 139.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/david/mambaforge/envs/sarand_err/bin/sarand", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/site-packages/sarand/sarand_main.py", line 178, in main
    full_pipeline_main(args)
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/site-packages/sarand/full_pipeline.py", line 1140, in full_pipeline_main
    unique_amr_files, unique_amr_path_list = find_all_amr_in_graph(
                                             ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/site-packages/sarand/full_pipeline.py", line 877, in find_all_amr_in_graph
    paths_info_group_list = p.map(p_find_amr, amr_objects)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/mambaforge/envs/sarand_err/lib/python3.11/multiprocessing/pool.py", line 774, in get
    raise self._value
subprocess.CalledProcessError: Command '['mamba', 'run', '-n', 'bandage-0.8.1_err', 'Bandage', 'querypaths', PosixPath('/home/david/error_replication/sarandV0/test/spade_output/assembly_graph_with_scaffolds.gfa'), 'test/test_output/AMR_info/amr_group_0.fasta', 'test/test_output/AMR_info/alignments/amr_group_0_align_2023-08-24_11-10-56', '--pathnodes', '50', '--minpatcov', '0.94', '--minmeanid', '0.94', '--minhitcov', '0.94']' returned non-zero exit status 139.

Bandage requires blast, adding it to the bandage conda env. solves the issue.

conda create -n bandage-0.8.1 -c conda-forge -c bioconda -c defaults -y bandage=0.8.1 blast