SampCompDB error

[rezarahman12]

Dear Nanocomopore team,
Thanks again for this wonderful tool.
I have tried loading the nanocomopore SampComp output file outSampComp.db.dat
Below is my code-

Load database

db = SampCompDB (
db_fn = "/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/outSampComp.db",
fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa")

save the results

Reload DB

db = SampCompDB (db_fn = "/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/outSampComp.db",
fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa", log_level="warning")

Save report

db.save_report (output_fn="/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/nanocompore_report.tsv")

the log file is given below-
2022-11-01 15:49:07.853 | INFO | nanocompore.SampCompDB:init:55 - Loading SampCompDB
2022-11-01 15:49:07.891 | DEBUG | nanocompore.SampCompDB:init:62 - Reading Metadata
2022-11-01 15:49:07.906 | DEBUG | nanocompore.SampCompDB:init:68 - Loading list of reference ids
2022-11-01 15:49:07.915 | DEBUG | nanocompore.SampCompDB:init:82 - Checking files and arg values
2022-11-01 15:49:07.935 | INFO | nanocompore.SampCompDB:init:100 - Calculate results
Traceback (most recent call last):
File "nanocomopore_sampcompdb.py", line 26, in
fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa", log_level="warning")
TypeError: init() got an unexpected keyword argument 'log_level'

Could you please tell me how to fix this problem?

Kind regards
Reza

[lmulroney]

Dear rezarahman12,

Ttry again but after removeing:
, log_level="warning"
from your db instantiating line.

Logan