Hi,
After successfully creating the database based several MAG files, another error happened when I run the step 2 ICRA by python.
My code is
from SGVFinder2 import single_file, get_sample_map from pandas import to_pickle read1 = '/storage/public/home/2024110144/00.Project/Diet/Tan_rumenMeta/01.rmHost/clean_data/Unknown_BW368-003R0001_1_kneaddata_paired_1.fastq' read2 = '/storage/public/home/2024110144/00.Project/Diet/Tan_rumenMeta/01.rmHost/clean_data/Unknown_BW368-003R0001_1_kneaddata_paired_2.fastq' DATABASE = '/storage/public/home/2024110144/00.Project/Diet/Sheep_MAG/rename/Sheep_db' jspi_file, jsdel_file = single_file( ... fq1=read1, ... fq2=read2, ... outfol='/storage/public/home/2024110144/00.Project/Diet/Sheep_MAG/rename/output',dbpath=DATABASE)
The bam file have generated normally. And I generated the stat file of the bam file:
My error is as follows. As the error may be caused by the unpaired reads according to the error, then I have checked that the reads in bam are all paired and the fastq files are also paired. I am not sure what's wrong in my files. Hope for your reply. Thanks for your time and work.
Hi,
After successfully creating the database based several MAG files, another error happened when I run the step 2 ICRA by python.
My code is
from SGVFinder2 import single_file, get_sample_map from pandas import to_pickle read1 = '/storage/public/home/2024110144/00.Project/Diet/Tan_rumenMeta/01.rmHost/clean_data/Unknown_BW368-003R0001_1_kneaddata_paired_1.fastq' read2 = '/storage/public/home/2024110144/00.Project/Diet/Tan_rumenMeta/01.rmHost/clean_data/Unknown_BW368-003R0001_1_kneaddata_paired_2.fastq' DATABASE = '/storage/public/home/2024110144/00.Project/Diet/Sheep_MAG/rename/Sheep_db' jspi_file, jsdel_file = single_file( ... fq1=read1, ... fq2=read2, ... outfol='/storage/public/home/2024110144/00.Project/Diet/Sheep_MAG/rename/output',dbpath=DATABASE)The bam file have generated normally. And I generated the stat file of the bam file:
My error is as follows. As the error may be caused by the unpaired reads according to the error, then I have checked that the reads in bam are all paired and the fastq files are also paired. I am not sure what's wrong in my files. Hope for your reply. Thanks for your time and work.