The number of obtained marker genes is very low.

[bioinformaticspcj]

Dear Lingfei,

Thanks for your valuable suggestions in #37 . I have changed the motif file myself and the dictys works. However, only two marker genes were output. I got some error information as follows:

Traceback (most recent call last):
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in
docstringrunner(package)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner
run_args(pkgname,funcs,args)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 330, in run_args
return func(*a,**ka)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 129, in wellington
d2 = shell.cmdfile(cmd,[],quiet=False,cd=True)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/utils/shell.py", line 181, in cmdfile
raise RuntimeError('Command failed, possibly due to program error: ' + cmda)
RuntimeError: Command failed, possibly due to program error: /data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/chromatin_wellington.sh /data/share/pcj/CNE_analysis/single_Cell_GRN/tmp_static/Subset1/reads.bam /data/share
make: *** [makefiles/common.mk:141: tmp_static/Subset1/footprints.bed] Error 1
Traceback (most recent call last):
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in
docstringrunner(package)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner
run_args(pkgname,funcs,args)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 330, in run_args
return func(*a,**ka)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 791, in reconstruct
model.gen_params({'G_obs':model.tensor(dt0.astype(int),dtype=torch.int)})
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 635, in gen_params
super().gen_params(observations)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 530, in gen_params
t2=torch.pca_lowrank(t1,q=self.npc,center=False,niter=50)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/torch/_lowrank.py", line 274, in pca_lowrank
return _svd_lowrank(A, q, niter=niter, M=None)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/torch/_lowrank.py", line 170, in _svd_lowrank
U, S, Vh = torch.linalg.svd(B_t, full_matrices=False)
torch._C._LinAlgError: linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
make: *** [makefiles/common.mk:172: tmp_static/Subset7/net_weight.tsv.gz] Error 1
Traceback (most recent call last):
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in
docstringrunner(package)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner
run_args(pkgname,funcs,args)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 330, in run_args
return func(*a,**ka)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 791, in reconstruct
model.gen_params({'G_obs':model.tensor(dt0.astype(int),dtype=torch.int)})
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 635, in gen_params
super().gen_params(observations)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 530, in gen_params
t2=torch.pca_lowrank(t1,q=self.npc,center=False,niter=50)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/torch/_lowrank.py", line 274, in pca_lowrank
return _svd_lowrank(A, q, niter=niter, M=None)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/torch/_lowrank.py", line 170, in _svd_lowrank
U, S, Vh = torch.linalg.svd(B_t, full_matrices=False)
torch._C._LinAlgError: linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.

The format of input narrowPeak file (footprints.bed) is as follows:
chr1 24612366 24613560 peak1:chr1:24612366:24613560:172.29200
chr1 20819892 20820782 peak2:chr1:20819892:20820782:136.96100
chr14 54517060 54518015 peak3:chr14:54517060:54518015:135.39000
chr15 75085437 75087073 peak4:chr15:75085437:75087073:135.39000
chr14 119007166 119007934 peak5:chr14:119007166:119007934:134.67700
chr2 150362345 150363260 peak6:chr2:150362345:150363260:134.64800
chr2 148731571 148732731 peak7:chr2:148731571:148732731:133.37600
chr12 91383694 91384900 peak8:chr12:91383694:91384900:132.47700
chr13 119689853 119690996 peak9:chr13:119689853:119690996:131.85300
chr9 36767265 36768581 peak10:chr9:36767265:36768581:131.45500

Do I need to change the input narrowPeak files to run? If yes, could you give me some advice to change the files.

Many thanks!

Best,
Bob

[lingfeiwang]

Hi Bob,

Because you are using bulk ATAC-seq data, you are expected to find a weaker contrast, including fewer regulation marker genes. You can try to change the parameters in regulation marker gene discovery. The errors suggest something wrong with your input data but are unrelated to the number of marker genes here.

Lingfei