运行work_on_collection后，我得到了两个空的文件vsgv_example.csv和dsgv_example.csv

[sxg1027]

hello,
I built a database based on 600 microbial genomes, with the. fasta file size of 1.89GB. After running icra on 304 samples based on the database, each sample obtained 5 files, which are bam (15GB20GB),.jsdel (62Bytes15KB),.jspi (55Bytes),.pmp(1.5GB~2.0GB),.smp(5Bytes). But after running from SGVFinder2 import work_on_collection, the vsgv. csv and dsgv. csv obtained are empty. Here is my running code:
DATABASE = '/home/data/zhangcg/Metagenome/sgvfinder2/my_db/all_db'
from SGVFinder2 import work_on_collection
vsgv, dsgv = work_on_collection(
samp_to_map='/home/data/zhangcg/Metagenome/sgvfinder2/icra/',
max_spacing=10,
min_samp_cutoff=2,
delsdetectthresh=0.25,
real_del_thresh=0.95,
dels_cooc_thresh=0.25,
vsgv_dissim_thresh=0.125,
vsgv_clip_quantile=0.02,
vsgv_fit_interval=0.95,
vsgv_fit_method='betaprime',
x_coverage=0.01,
rate_param=10,
vsgv_dense_perc=85,
browser_path=None,
taxonomypath=DATABASE+'.taxonomy.df',
genepospath=DATABASE+'genepos.df',
frames_path=None
)
vsgv.to_csv('vsgv_example.csv')
dsgv.to_csv("dsgv_example.csv")
I would like to know if there is any way to obtain results that can be used for analysis. Is it due to my running error, or is there a problem with the data and database itself

[talkorem]

The size of your smp file and jspi file suggests that there was no sufficient / consistent coverage available for enough samples. Are you getting results with the default database?

[sxg1027]

The size of your smp file and jspi file suggests that there was no sufficient / consistent coverage available for enough samples. Are you getting results with the default database?

Thank you for your reply. My previous sample metagenome sequencing depth was 6g, and I obtained the results through the first generation version of SGVFinder, which is the default database. Now, for the same sample, my sequencing depth has been increased to 20g, but I did not obtain the results through SGVFinder2

[talkorem]

So it seems to point towards the 600 genomes database as the culprit.

[sxg1027]

It is possible that my database was built using the microorganisms from hungate1000 and the microorganisms from the default database downloaded from NCBI. Is there any way I can solve the database problem. Strangely, when I used data with a sequencing depth of 20G to run the first generation version of SGVFinder, I encountered the error ZeroDivisionError. So I would like to ask how I can obtain results for the sample with a sequencing depth of 20G. Can SGVFinder run on the default database? What should I do.

[zhangyu199711]

您好，请问您问题解决了吗，我也遇到可这个问题，两个文件都为空文件 #