I have tried to add the number "_0, _1.." to distinguish each motif name as you suggested in https://github.com/pinellolab/dictys/issues/28. However the same error still occured. I also tried dictys_helper makefile_check.py -c command, the results are as follows:
Joint profile: True
Found 7047 cells with RNA profile
Found 55095 genes with RNA profile
ERROR:root:2
WARNING:root:Using RNA cell names for ATAC cell names for validations below.
Found 7047 cells with ATAC profile
Found 356 motifs
Found 356 TFs
Found 311 TFs in current dataset
Missing 45 TFs in current dataset: ANDR,AP2A,AP2C,ARI5B,BHA15,BHE40,BMAL1,BRAC,COE1,COT1,COT2,DMRTB,EVI1,GCR,HEN1,HNF6,HTF4,ITF2,KAISO,NDF1,NDF2,NGN2,NKX2-8,PEBB,PKNX1,PRD14,PRD16,PRGR,RORG,SUH,TF2L1,TF65,TF7L1,TF7L2,TFE2,THA,THA11,ZBT17,ZBT7A,ZKSC1,ZN143,ZN281,ZN322,ZN335,ZN431
Found 268 genes with TSS information
WARNING:root:Cannot find dynamic.mk or traj_node.h5. Skipping dynamic network inference checks.
Traceback (most recent call last):
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/helper/makefile_check.py", line 354, in
raise RuntimeError(f'Found {nerr} error(s) in total.')
RuntimeError: Found 1 error(s) in total.
Dear Lingfei,
I have tried to add the number "_0, _1.." to distinguish each motif name as you suggested in https://github.com/pinellolab/dictys/issues/28. However the same error still occured. I also tried dictys_helper makefile_check.py -c command, the results are as follows: Joint profile: True Found 7047 cells with RNA profile Found 55095 genes with RNA profile ERROR:root:2 WARNING:root:Using RNA cell names for ATAC cell names for validations below. Found 7047 cells with ATAC profile Found 356 motifs Found 356 TFs Found 311 TFs in current dataset Missing 45 TFs in current dataset: ANDR,AP2A,AP2C,ARI5B,BHA15,BHE40,BMAL1,BRAC,COE1,COT1,COT2,DMRTB,EVI1,GCR,HEN1,HNF6,HTF4,ITF2,KAISO,NDF1,NDF2,NGN2,NKX2-8,PEBB,PKNX1,PRD14,PRD16,PRGR,RORG,SUH,TF2L1,TF65,TF7L1,TF7L2,TFE2,THA,THA11,ZBT17,ZBT7A,ZKSC1,ZN143,ZN281,ZN322,ZN335,ZN431 Found 268 genes with TSS information WARNING:root:Cannot find dynamic.mk or traj_node.h5. Skipping dynamic network inference checks. Traceback (most recent call last): File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/helper/makefile_check.py", line 354, in
raise RuntimeError(f'Found {nerr} error(s) in total.')
RuntimeError: Found 1 error(s) in total.
The motif file that I used has been uploaded to https://figshare.com/articles/dataset/Mouse_TF_motif/24333844 in figshare.
Could you spare sometime to help me?
Thanks a lot.
Best, Bob