how to write the number of threads to use with cut_up_fasta.py

[ShevchenkoAlla]

Hello)
I am sorry for bothering
I have a silly question, how can I write the number of threads to use?
According to the instructions there is an option -

-t THREADS, --threads THREADS
Number of threads to use

But when I have tried to use it, it didn't worked.
Unfortinatly I cant find information how many threads are by default.

Unfortinatly we have really strict rules on the server and if I run script than will take more than I allowed I will be banned, please clearify how can I add the number of threads, if it's possible.

I have tried:

cut_up_fasta.py --threads 16 contigs.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
usage: cut_up_fasta.py [-h] [-c CHUNK_SIZE] [-o OVERLAP_SIZE] [-m]
[-b BEDFILE]
contigs [contigs ...]
cut_up_fasta.py: error: unrecognized arguments: --threads

cut_up_fasta.py -t 16 contigs.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
usage: cut_up_fasta.py [-h] [-c CHUNK_SIZE] [-o OVERLAP_SIZE] [-m]
[-b BEDFILE]
contigs [contigs ...]
cut_up_fasta.py: error: unrecognized arguments: -t

I would appreciate any suggestions.
Than you for your time.
Best,
Alla

[alneberg]

Hello,

I am qiute sure that the cut_up_fasta.py is single-threaded and shouldn't use more than 1 thread at any point. Maybe there's some optimisation under the hood that could use more but I don't think so.

[ShevchenkoAlla]

Hello,

I am qiute sure that the cut_up_fasta.py is single-threaded and shouldn't use more than 1 thread at any point. Maybe there's some optimisation under the hood that could use more but I don't think so.

Thank you very much