unrecognized arguments - fasta file

[setshabaTaukobong]

Good day, I am trying to run the nanomonsv insert_classify command as follows:

nanomonsv: error: unrecognized arguments: GRCh38_latest_genomic.fa

However I am getting the following error: nanomonsv: error: unrecognized arguments: GRCh38_latest_genomic.fa

I am not sure why my fasta file is not being recognised. Could I please get some assistance on this. Thank you.

[friend1ws]

Thanks for using nanomonsv. Could you provide the exact command you used?

[setshabaTaukobong]

Hi there, thank you for getting back to me. The command:

nanomonsv insert_classify --grc False --genome_id hg38 --debug test_tumor.nanomonsv.result.txt output_file GRCh38_latest_genomic.fa

[setshabaTaukobong]

Hi there @friend1ws , I am still struggling with this issue and would appreciate some help. Thank you

[friend1ws]

Hi, could you try removing --grc False?

[setshabaTaukobong]

Hi @friend1ws I have tried using --grc False but I still get the same error (please see previous text with command).

[friend1ws]

Could you try the following command?

nanomonsv insert_classify --genome_id hg38 --debug test_tumor.nanomonsv.result.txt output_file GRCh38_latest_genomic.fa

[setshabaTaukobong]

@friend1ws
So I tried that and I get the following error:

Traceback (most recent call last): File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/bin/nanomonsv", line 10, in sys.exit(main()) File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/lib/python3.10/site-packages/nanomonsv/init.py", line 13, in main args.func(args) File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/lib/python3.10/site-packages/nanomonsv/run.py", line 524, in insert_classify_main import annot_utils.exon ModuleNotFoundError: No module named 'annot_utils' (nanomonsv) [staukobong@cnode0986 output]$ nanomonsv insert_classify --genome_id hg38 --debug test_tumor.nanomonsv.result.txt output_file GRCh38_latest_genomic.fa Traceback (most recent call last): File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/bin/nanomonsv", line 10, in sys.exit(main()) File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/lib/python3.10/site-packages/nanomonsv/init.py", line 13, in main args.func(args) File "/apps/chpc/bio/anaconda3-2020.02/envs/nanomonsv/lib/python3.10/site-packages/nanomonsv/run.py", line 524, in insert_classify_main import annot_utils.exon ModuleNotFoundError: No module named 'annot_utils'

[friend1ws]

nanomonsv insert_classify currently needs annot_utils pacakge. So please install it.

[friend1ws]

For using insert_classify, currently we do not recommend using conda. I'm trying to reduce the necessary packages and softwares. But currently I would use venv.

python -m venv nanomonsv_v0.7.2
source nanomonsv_v0.7.2/source/bin/activate
pip install nanomonsv
pip install annot_utils
pip install (other packages).

[setshabaTaukobong]

will do. Thank you @friend1ws