Dear Colleagues. I used the installation from conda. I get the following error on test data.
conda create -n maniac -c conda-forge mamba python=3.9
conda activate maniac
mamba install -c conda-forge -c bioconda snakemake pandas biopython=1.79 mmseqs2 r-base r-essentials r-arrow datamash pyopenssl=24.2 parallel=20240922
snakemake --cores 8 --quiet --snakefile MANIAC --configfile file.yml
Running MANIAC!
MODE: "FRAGMENTS_NT" [FRAGMENTS_NT | CDS_NT | CDS_AA]
FAST: False [True | False]
Processing input... Success!
PATHS:
Input file: /home/sergey/MANIAC_ANI_calculate/test/data/fragment-based.fasta
Output directory: /home/sergey/MANIAC_ANI_calculate/Output
Log directory: /home/sergey/MANIAC_ANI_calculate/Output/.log
Intermediate directory: /home/sergey/MANIAC_ANI_calculate/Output/intermediate
PARAMETERS (FRAGMENTS_NT):
Fragment size: 500
CDS based: False
DNA significant hits definition:
Minimum identity: 0.3
Minimum query & target coverage: 0.7
Available memory: 16G
MMSEQS CPU cores: 8
MMSEQS params: --search-type 3 -a --max-seqs 10000 --max-seq-len 65000 -s 7.5 --mask 0 -e 1e-15 -k 11 --zdrop 40 -c 0.7 --cov-mode 2 --seed-sub-mat "/home/sergey/MANIAC_ANI_calculate/scoring/blastn-scoring.out" --sub-mat "/home/sergey/MANIAC_ANI_calculate/scoring/blastn-scoring.out"
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count
--------------------- -------
best_hits 1
get_total_cds_lengths 1
make_db 1
make_query_db 1
mmseqs_qr_convert 1
mmseqs_qr_search 1
process_results 1
split_genomes 1
target 1
total 9
Select jobs to execute...
Select jobs to execute...
Select jobs to execute...
Traceback (most recent call last):
File "/home/sergey/MANIAC_ANI_calculate/.snakemake/scripts/tmpdxfdqarx.get_fasta_lengths.py", line 42, in <module>
length_table = pd.DataFrame({"genome": names, "length": lengths})
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/site-packages/pandas/core/frame.py", line 778, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/site-packages/pandas/core/internals/construction.py", line 480, in dict_to_mgr
columns = Index(keys) if keys else default_index(0)
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 565, in __new__
arr = sanitize_array(data, None, dtype=dtype, copy=copy)
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/site-packages/pandas/core/construction.py", line 654, in sanitize_array
subarr = maybe_convert_platform(data)
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 138, in maybe_convert_platform
arr = lib.maybe_convert_objects(arr)
File "lib.pyx", line 2538, in pandas._libs.lib.maybe_convert_objects
TypeError: Cannot convert numpy.ndarray to numpy.ndarray
[Wed Apr 30 09:18:59 2025]
Error in rule get_total_cds_lengths:
jobid: 8
input: /home/sergey/MANIAC_ANI_calculate/test/data/fragment-based.fasta
output: /home/sergey/MANIAC_ANI_calculate/Output/intermediate/phage_lengths.csv
RuleException:
CalledProcessError in file /home/sergey/MANIAC_ANI_calculate/MANIAC, line 75:
Command 'set -euo pipefail; /home/sergey/miniforge3/envs/maniac/bin/python3.9 /home/sergey/MANIAC_ANI_calculate/.snakemake/scripts/tmpdxfdqarx.get_fasta_lengths.py' returned non-zero exit status 1.
File "/home/sergey/MANIAC_ANI_calculate/MANIAC", line 75, in __rule_get_total_cds_lengths
File "/home/sergey/miniforge3/envs/maniac/lib/python3.9/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-04-30T091858.528939.snakemake.log
Dear Colleagues. I used the installation from conda. I get the following error on test data.