Support for MacOS

[padpadpadpad]

Describe the bug
Consistent errors trying to run on MacOS. I was running autocycler helper nextdenovo and getting consistent errors.

I ran it with an install of nextdenovo from GitHub and from conda.

Error message
[87287 INFO] 2025-07-02 07:47:26 NextDenovo start...
[87287 INFO] 2025-07-02 07:47:26 version:2.5.2 logfile:pid87287.log.info
[87287 WARNING] 2025-07-02 07:47:26 Re-write workdir
[87287 INFO] 2025-07-02 07:47:26 mkdir: /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo
[87287 INFO] 2025-07-02 07:47:26 mkdir: /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align
[87287 INFO] 2025-07-02 07:47:26 mkdir: /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/02.cns_align
[87287 INFO] 2025-07-02 07:47:26 mkdir: /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/03.ctg_graph
[87287 INFO] 2025-07-02 07:47:31 Total jobs: 1
[87287 INFO] 2025-07-02 07:47:31 Submitted jobID:[87293] jobCmd:[/Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle.
[87293 CRITICAL] 2025-07-02 07:47:31 Command '/bin/sh /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 126, error info: .
[87287 ERROR] 2025-07-02 07:47:37 db_stat failed: please check the following logs:
[87287 ERROR] 2025-07-02 07:47:37 /Users/dp415/google_drive/work_googledrive/zoltan/strain_data/sequencing/hybrid_assemblies/nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e

Genome characteristics
E. coli MG1655: ~4.6M bp

Config file
[General]
job_type = local
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
parallel_jobs = 1
input_type = raw
read_type = ont
input_fofn = input.fofn
workdir = nextdenovo

[correct_option]
read_cutoff = 1k
genome_size = 4000000
sort_options = -m 20g -t 6
minimap2_options_raw = -t 6
pa_correction = 1
correction_options = -p 6

[assemble_option]
minimap2_options_cns = -t 6
nextgraph_options = -a 1

Operating system
MacOS 15.4.1

GCC
Apple clang version 17.0.0 (clang-1700.0.13.3)

Python
Python 3.12.10

NextDenovo
nextdenovo 2.5.2

content of nextDenovo.sh.e

nextDenovo.sh.e.zip

[Artifice120]

Looks like the files have not been given executable permissions

line 5: /Users/dp415/Downloads/NextDenovo/bin/seq_stat: cannot execute binary file

a quick chmod might help

chmod -R +x  /Users/dp415/Downloads/NextDenovo/bin/