Closed hzauleibowen closed 10 months ago
lingfeiwang
commented
10 months ago Hi hzauleibowen,
Thank you for the question.
If you used macs2 to call peaks, can you follow the steps for bulk ATAC-seq at https://github.com/pinellolab/dictys/issues/23#issuecomment-1641035864? You can use either cell-type specific or tissue specific bulk ATAC-seq.
Let us know here if you have any issue.
Lingfei
hzauleibowen
commented
10 months ago Hi Lingfei,
Thanks so much for your timely reply.
I used macs2 to call peaks and mapped all the raw data,I will follow your advice to process the data in the coming days.
I hope that this approach will yield the results we desire.
Bowen
bioinformaticspcj
commented
9 months ago Dear Lingfei,
Thanks for your helpful software. I have tried the Dictys with bulk ATAC-seq data following https://github.com/pinellolab/dictys/issues/23#issuecomment-1641035864. However, I found the homer.tsv.gz and wellington.tsv.gz files were empty. I just do not know why. The the peaks generated from macs2 were formated 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
Could you be kind to help me?
Thanks again! Best, Bob
lingfeiwang
commented
9 months ago Hi Bob,
Happy to help. Did you run makefile_check.py as in the tutorial? Could you paste the output here?
Lingfei
bioinformaticspcj
commented
9 months ago Dear Lingfei,
Yes, I have tried the makefile_check.py as follows: dictys_helper makefile_check.py Joint profile: True Found 7047 cells with RNA profile Found 55095 genes with RNA profile 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 57, in <module> namec_atac=listdir(pjoin(dirdata,'bams')) FileNotFoundError: [Errno 2] No such file or directory: 'data/bams'
Of course, I have no bams and it returned the Errno. But, I have touched the bams in the corresponding directories according to the #23 (comment). Did I need the real bams?
Best, Bob
------------------ 原始邮件 ------------------ 发件人: "pinellolab/dictys" @.>; 发送时间: 2023年9月21日(星期四) 晚上10:23 @.>; @.**@.>; 主题: Re: [pinellolab/dictys] How to use Bulk ATAC to Run (Issue #28)
Hi Bob,
Happy to help. Did you run makefile_check.py as in the tutorial? Could you paste the output here?
Lingfei
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lingfeiwang
commented
9 months ago Hi Bob,
Could you update Dictys to the dev branch to perform more checks with this script? If you already have version 1.0.0, you can update with pip3 install --no-deps --force-reinstall git+https://github.com/pinellolab/dictys@dev in the right conda environment. After that, can you rerun makefile_check.py to see the output?
Lingfei
bioinformaticspcj
commented
9 months ago Dear Lingfei,
Thanks for your timely reply. I have tried the command that you provided. The output is as follows: Collecting @.*** Cloning https://github.com/pinellolab/dictys (to revision dev) to /data/backup/pcj/tmp/pip-req-build-bw92b6ie Running command git clone --quiet https://github.com/pinellolab/dictys /data/backup/pcj/tmp/pip-req-build-bw92b6ie Running command git checkout -b dev --track origin/dev branch dev 。 Resolved https://github.com/pinellolab/dictys to commit f5a31f6bc446fafdf86169dc18385d97de86fd54 Preparing metadata (setup.py) ... done Building wheels for collected packages: dictys Building wheel for dictys (setup.py) ... done Created wheel for dictys: filename=dictys-1.0.0-py3-none-any.whl size=142161 sha256=e08ef129eff9e4a336218864355addcd7c849235b5251f1e65254de2d68b0eca Stored in directory: /data/backup/pcj/tmp/pip-ephem-wheel-cache-1xfikw5p/wheels/3d/22/ac/b05f05973301e64b19e77fe84cd8c1358362f06b933caac8cd Successfully built dictys Installing collected packages: dictys Attempting uninstall: dictys Found existing installation: dictys 1.0.0 Uninstalling dictys-1.0.0: Successfully uninstalled dictys-1.0.0 Successfully installed dictys-1.0.0
And then, I tried the makefile_check.py again. It seems that the output is as the same as the before: Joint profile: True Found 7047 cells with RNA profile Found 55095 genes with RNA profile 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 90, in <module> raise e File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/helper/makefile_check.py", line 86, in <module> namec_atac=listdir(pjoin(dirdata,'bams')) FileNotFoundError: [Errno 2] No such file or directory: 'data/bams'
Best, Bob
------------------ 原始邮件 ------------------ 发件人: "pinellolab/dictys" @.>; 发送时间: 2023年9月22日(星期五) 凌晨2:24 @.>; @.**@.>; 主题: Re: [pinellolab/dictys] How to use Bulk ATAC to Run (Issue #28)
Hi Bob,
Could you update Dictys to the dev branch to perform more checks with this script? If you already have version 1.0.0, you can update with pip3 install --no-deps --force-reinstall @.*** in the right conda environment. After that, can you rerun makefile_check.py to see the output?
Lingfei
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lingfeiwang
commented
9 months ago Hi Bob,
Forgot to mention, could you run makefile_check.py -c instead for more tests please? I'm suspecting you have gene name mismatch in some of your input files.
Lingfei
bioinformaticspcj
commented
9 months ago Hi Lingfei,
Thanks for your suggestion. Yes, the makefile_check.py needs the "-c" option. You may need to added the option to the "Short tutorial" for I did not find it before. I have tried the command as you suggested as follows:
dictys_helper makefile_check.py -c 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 <module> raise RuntimeError(f'Found {nerr} error(s) in total.') RuntimeError: Found 1 error(s) in total.
The error "root:2" occurred and I do no know why. By the way, there are some TFs that are missed because of the gene symbol version. Do they affact the results a lot?
Best, Bob
------------------ 原始邮件 ------------------ 发件人: "pinellolab/dictys" @.>; 发送时间: 2023年9月25日(星期一) 中午1:42 @.>; @.**@.>; 主题: Re: [pinellolab/dictys] How to use Bulk ATAC to Run (Issue #28)
Hi Bob,
Forgot to mention, could you run makefile_check.py -c instead for more tests please? I'm suspecting you have gene name mismatch in some of your input files.
Lingfei
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lingfeiwang
commented
9 months ago Thank you, Bob.
The results suggest gene name mismatch is not a problem. There are quite some TFs recognized in the motif file. Can you paste the output of line !cd ..; dictys_helper network_inference.sh -j 32 -J 1 static in the notebook here?
Lingfei
bioinformaticspcj
commented
9 months ago Dear Lingfei,
I have tried the "!cd ..; dictys_helper network_inference.sh -j 32 -J 1 static" command. There is too much output here, thus I saved the output to a file (attacthed network.log.txt). Please find it.
Best, Bob
------------------ 原始邮件 ------------------ 发件人: "pinellolab/dictys" @.>; 发送时间: 2023年9月25日(星期一) 晚上11:55 @.>; @.**@.>; 主题: Re: [pinellolab/dictys] How to use Bulk ATAC to Run (Issue #28)
Thank you, Bob.
The results suggest gene name mismatch is not a problem. There are quite some TFs recognized in the motif file. Can you paste the output of line !cd ..; dictys_helper network_inference.sh -j 32 -J 1 static in the notebook here?
Lingfei
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lingfeiwang
commented
9 months ago Hi Bob. Unfortunately email attachments are not transferred to github issues. Can you upload it on github?
bioinformaticspcj
commented
9 months ago Hi Lingfei,
I just paste the output here:
OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset1/footprints.bed data/motifs.motif data/genome tmp_static/Subset1/expression.tsv.gz tmp_static/Subset1/motifs.bed tmp_static/Subset1/wellington.tsv.gz tmp_static/Subset1/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset10/footprints.bed data/motifs.motif data/genome tmp_static/Subset10/expression.tsv.gz tmp_static/Subset10/motifs.bed tmp_static/Subset10/wellington.tsv.gz tmp_static/Subset10/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset2/footprints.bed data/motifs.motif data/genome tmp_static/Subset2/expression.tsv.gz tmp_static/Subset2/motifs.bed tmp_static/Subset2/wellington.tsv.gz tmp_static/Subset2/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset3/footprints.bed data/motifs.motif data/genome tmp_static/Subset3/expression.tsv.gz tmp_static/Subset3/motifs.bed tmp_static/Subset3/wellington.tsv.gz tmp_static/Subset3/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset4/footprints.bed data/motifs.motif data/genome tmp_static/Subset4/expression.tsv.gz tmp_static/Subset4/motifs.bed tmp_static/Subset4/wellington.tsv.gz tmp_static/Subset4/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset5/footprints.bed data/motifs.motif data/genome tmp_static/Subset5/expression.tsv.gz tmp_static/Subset5/motifs.bed tmp_static/Subset5/wellington.tsv.gz tmp_static/Subset5/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset6/footprints.bed data/motifs.motif data/genome tmp_static/Subset6/expression.tsv.gz tmp_static/Subset6/motifs.bed tmp_static/Subset6/wellington.tsv.gz tmp_static/Subset6/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset7/footprints.bed data/motifs.motif data/genome tmp_static/Subset7/expression.tsv.gz tmp_static/Subset7/motifs.bed tmp_static/Subset7/wellington.tsv.gz tmp_static/Subset7/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset8/footprints.bed data/motifs.motif data/genome tmp_static/Subset8/expression.tsv.gz tmp_static/Subset8/motifs.bed tmp_static/Subset8/wellington.tsv.gz tmp_static/Subset8/homer.tsv.gz OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys chromatin homer --nth 4 tmp_static/Subset9/footprints.bed data/motifs.motif data/genome tmp_static/Subset9/expression.tsv.gz tmp_static/Subset9/motifs.bed tmp_static/Subset9/wellington.tsv.gz tmp_static/Subset9/homer.tsv.gz
Position file = 14-reform-split/aaaac
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaac
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 523 (avg size of targets)
Background files for 523 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1026 sequences from chr1
Extracting 1170 sequences from chr2
Extracting 923 sequences from chr3
Extracting 903 sequences from chr4
Extracting 805 sequences from chr5
Extracting 832 sequences from chr6
Extracting 763 sequences from chr7
Extracting 728 sequences from chr8
Extracting 696 sequences from chr9
Extracting 807 sequences from chr10
Extracting 814 sequences from chr11
Extracting 629 sequences from chr12
Extracting 666 sequences from chr13
Extracting 586 sequences from chr14
Extracting 578 sequences from chr15
Extracting 530 sequences from chr16
Extracting 523 sequences from chr17
Extracting 506 sequences from chr18
Extracting 392 sequences from chr19
Extracting 332 sequences from chrX
Extracting 2 sequences from chrY
Reading input files...
14211 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaad
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaad
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14217
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (avg size of targets)
Background files for 664 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1062 sequences from chr1
Extracting 1147 sequences from chr2
Extracting 887 sequences from chr3
Extracting 861 sequences from chr4
Extracting 824 sequences from chr5
Extracting 879 sequences from chr6
Extracting 770 sequences from chr7
Extracting 734 sequences from chr8
Extracting 767 sequences from chr9
Extracting 792 sequences from chr10
Extracting 798 sequences from chr11
Extracting 619 sequences from chr12
Extracting 668 sequences from chr13
Extracting 571 sequences from chr14
Extracting 586 sequences from chr15
Extracting 544 sequences from chr16
Extracting 546 sequences from chr17
Extracting 474 sequences from chr18
Extracting 366 sequences from chr19
Extracting 314 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14212 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaaa
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaaa
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 968 (avg size of targets)
Background files for 968 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 976 sequences from chr1
Extracting 1209 sequences from chr2
Extracting 874 sequences from chr3
Extracting 908 sequences from chr4
Extracting 821 sequences from chr5
Extracting 808 sequences from chr6
Extracting 960 sequences from chr7
Extracting 712 sequences from chr8
Extracting 774 sequences from chr9
Extracting 787 sequences from chr10
Extracting 820 sequences from chr11
Extracting 557 sequences from chr12
Extracting 636 sequences from chr13
Extracting 547 sequences from chr14
Extracting 517 sequences from chr15
Extracting 548 sequences from chr16
Extracting 547 sequences from chr17
Extracting 429 sequences from chr18
Extracting 382 sequences from chr19
Extracting 399 sequences from chrX
Extracting 4 sequences from chrY
Reading input files...
14215 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaac
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaac
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 523 (avg size of targets)
Background files for 523 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1026 sequences from chr1
Extracting 1170 sequences from chr2
Extracting 923 sequences from chr3
Extracting 903 sequences from chr4
Extracting 805 sequences from chr5
Extracting 832 sequences from chr6
Extracting 763 sequences from chr7
Extracting 728 sequences from chr8
Extracting 696 sequences from chr9
Extracting 807 sequences from chr10
Extracting 814 sequences from chr11
Extracting 629 sequences from chr12
Extracting 666 sequences from chr13
Extracting 586 sequences from chr14
Extracting 578 sequences from chr15
Extracting 530 sequences from chr16
Extracting 523 sequences from chr17
Extracting 506 sequences from chr18
Extracting 392 sequences from chr19
Extracting 332 sequences from chrX
Extracting 2 sequences from chrY
Reading input files...
14211 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaad
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaad
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14217
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (avg size of targets)
Background files for 664 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1062 sequences from chr1
Extracting 1147 sequences from chr2
Extracting 887 sequences from chr3
Extracting 861 sequences from chr4
Extracting 824 sequences from chr5
Extracting 879 sequences from chr6
Extracting 770 sequences from chr7
Extracting 734 sequences from chr8
Extracting 767 sequences from chr9
Extracting 792 sequences from chr10
Extracting 798 sequences from chr11
Extracting 619 sequences from chr12
Extracting 668 sequences from chr13
Extracting 571 sequences from chr14
Extracting 586 sequences from chr15
Extracting 544 sequences from chr16
Extracting 546 sequences from chr17
Extracting 474 sequences from chr18
Extracting 366 sequences from chr19
Extracting 314 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14212 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaaa
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaaa
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 968 (avg size of targets)
Background files for 968 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 976 sequences from chr1
Extracting 1209 sequences from chr2
Extracting 874 sequences from chr3
Extracting 908 sequences from chr4
Extracting 821 sequences from chr5
Extracting 808 sequences from chr6
Extracting 960 sequences from chr7
Extracting 712 sequences from chr8
Extracting 774 sequences from chr9
Extracting 787 sequences from chr10
Extracting 820 sequences from chr11
Extracting 557 sequences from chr12
Extracting 636 sequences from chr13
Extracting 547 sequences from chr14
Extracting 517 sequences from chr15
Extracting 548 sequences from chr16
Extracting 547 sequences from chr17
Extracting 429 sequences from chr18
Extracting 382 sequences from chr19
Extracting 399 sequences from chrX
Extracting 4 sequences from chrY
Reading input files...
14215 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaac
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaac
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 523 (avg size of targets)
Background files for 523 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1026 sequences from chr1
Extracting 1170 sequences from chr2
Extracting 923 sequences from chr3
Extracting 903 sequences from chr4
Extracting 805 sequences from chr5
Extracting 832 sequences from chr6
Extracting 763 sequences from chr7
Extracting 728 sequences from chr8
Extracting 696 sequences from chr9
Extracting 807 sequences from chr10
Extracting 814 sequences from chr11
Extracting 629 sequences from chr12
Extracting 666 sequences from chr13
Extracting 586 sequences from chr14
Extracting 578 sequences from chr15
Extracting 530 sequences from chr16
Extracting 523 sequences from chr17
Extracting 506 sequences from chr18
Extracting 392 sequences from chr19
Extracting 332 sequences from chrX
Extracting 2 sequences from chrY
Reading input files...
14211 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaad
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaad
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14217
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (avg size of targets)
Background files for 664 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1062 sequences from chr1
Extracting 1147 sequences from chr2
Extracting 887 sequences from chr3
Extracting 861 sequences from chr4
Extracting 824 sequences from chr5
Extracting 879 sequences from chr6
Extracting 770 sequences from chr7
Extracting 734 sequences from chr8
Extracting 767 sequences from chr9
Extracting 792 sequences from chr10
Extracting 798 sequences from chr11
Extracting 619 sequences from chr12
Extracting 668 sequences from chr13
Extracting 571 sequences from chr14
Extracting 586 sequences from chr15
Extracting 544 sequences from chr16
Extracting 546 sequences from chr17
Extracting 474 sequences from chr18
Extracting 366 sequences from chr19
Extracting 314 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14212 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaaa
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaaa
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 968 (avg size of targets)
Background files for 968 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 976 sequences from chr1
Extracting 1209 sequences from chr2
Extracting 874 sequences from chr3
Extracting 908 sequences from chr4
Extracting 821 sequences from chr5
Extracting 808 sequences from chr6
Extracting 960 sequences from chr7
Extracting 712 sequences from chr8
Extracting 774 sequences from chr9
Extracting 787 sequences from chr10
Extracting 820 sequences from chr11
Extracting 557 sequences from chr12
Extracting 636 sequences from chr13
Extracting 547 sequences from chr14
Extracting 517 sequences from chr15
Extracting 548 sequences from chr16
Extracting 547 sequences from chr17
Extracting 429 sequences from chr18
Extracting 382 sequences from chr19
Extracting 399 sequences from chrX
Extracting 4 sequences from chrY
Reading input files...
14215 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaad
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaad
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14217
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaac
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaac
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 523 (avg size of targets)
Background files for 523 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1026 sequences from chr1
Extracting 1170 sequences from chr2
Extracting 923 sequences from chr3
Extracting 903 sequences from chr4
Extracting 805 sequences from chr5
Extracting 832 sequences from chr6
Extracting 763 sequences from chr7
Extracting 728 sequences from chr8
Extracting 696 sequences from chr9
Extracting 807 sequences from chr10
Extracting 814 sequences from chr11
Extracting 629 sequences from chr12
Extracting 666 sequences from chr13
Extracting 586 sequences from chr14
Extracting 578 sequences from chr15
Extracting 530 sequences from chr16
Extracting 523 sequences from chr17
Extracting 506 sequences from chr18
Extracting 392 sequences from chr19
Extracting 332 sequences from chrX
Extracting 2 sequences from chrY
Reading input files...
14211 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (avg size of targets)
Background files for 664 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1062 sequences from chr1
Extracting 1147 sequences from chr2
Extracting 887 sequences from chr3
Extracting 861 sequences from chr4
Extracting 824 sequences from chr5
Extracting 879 sequences from chr6
Extracting 770 sequences from chr7
Extracting 734 sequences from chr8
Extracting 767 sequences from chr9
Extracting 792 sequences from chr10
Extracting 798 sequences from chr11
Extracting 619 sequences from chr12
Extracting 668 sequences from chr13
Extracting 571 sequences from chr14
Extracting 586 sequences from chr15
Extracting 544 sequences from chr16
Extracting 546 sequences from chr17
Extracting 474 sequences from chr18
Extracting 366 sequences from chr19
Extracting 314 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14212 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaaa
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaaa
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 968 (avg size of targets)
Background files for 968 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 976 sequences from chr1
Extracting 1209 sequences from chr2
Extracting 874 sequences from chr3
Extracting 908 sequences from chr4
Extracting 821 sequences from chr5
Extracting 808 sequences from chr6
Extracting 960 sequences from chr7
Extracting 712 sequences from chr8
Extracting 774 sequences from chr9
Extracting 787 sequences from chr10
Extracting 820 sequences from chr11
Extracting 557 sequences from chr12
Extracting 636 sequences from chr13
Extracting 547 sequences from chr14
Extracting 517 sequences from chr15
Extracting 548 sequences from chr16
Extracting 547 sequences from chr17
Extracting 429 sequences from chr18
Extracting 382 sequences from chr19
Extracting 399 sequences from chrX
Extracting 4 sequences from chrY
Reading input files...
14215 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaac
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaac
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 523 (avg size of targets)
Background files for 523 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1026 sequences from chr1
Extracting 1170 sequences from chr2
Extracting 923 sequences from chr3
Extracting 903 sequences from chr4
Extracting 805 sequences from chr5
Extracting 832 sequences from chr6
Extracting 763 sequences from chr7
Extracting 728 sequences from chr8
Extracting 696 sequences from chr9
Extracting 807 sequences from chr10
Extracting 814 sequences from chr11
Extracting 629 sequences from chr12
Extracting 666 sequences from chr13
Extracting 586 sequences from chr14
Extracting 578 sequences from chr15
Extracting 530 sequences from chr16
Extracting 523 sequences from chr17
Extracting 506 sequences from chr18
Extracting 392 sequences from chr19
Extracting 332 sequences from chrX
Extracting 2 sequences from chrY
Reading input files...
14211 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaad
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaad
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14217
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (avg size of targets)
Background files for 664 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1062 sequences from chr1
Extracting 1147 sequences from chr2
Extracting 887 sequences from chr3
Extracting 861 sequences from chr4
Extracting 824 sequences from chr5
Extracting 879 sequences from chr6
Extracting 770 sequences from chr7
Extracting 734 sequences from chr8
Extracting 767 sequences from chr9
Extracting 792 sequences from chr10
Extracting 798 sequences from chr11
Extracting 619 sequences from chr12
Extracting 668 sequences from chr13
Extracting 571 sequences from chr14
Extracting 586 sequences from chr15
Extracting 544 sequences from chr16
Extracting 546 sequences from chr17
Extracting 474 sequences from chr18
Extracting 366 sequences from chr19
Extracting 314 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14212 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaaa
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaaa
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 968 (avg size of targets)
Background files for 968 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 976 sequences from chr1
Extracting 1209 sequences from chr2
Extracting 874 sequences from chr3
Extracting 908 sequences from chr4
Extracting 821 sequences from chr5
Extracting 808 sequences from chr6
Extracting 960 sequences from chr7
Extracting 712 sequences from chr8
Extracting 774 sequences from chr9
Extracting 787 sequences from chr10
Extracting 820 sequences from chr11
Extracting 557 sequences from chr12
Extracting 636 sequences from chr13
Extracting 547 sequences from chr14
Extracting 517 sequences from chr15
Extracting 548 sequences from chr16
Extracting 547 sequences from chr17
Extracting 429 sequences from chr18
Extracting 382 sequences from chr19
Extracting 399 sequences from chrX
Extracting 4 sequences from chrY
Reading input files...
14215 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...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 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 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 <module> exec(code, run_globals) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in <module> docstringrunner(package) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner 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 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 248, in homer return func(*a,*ka) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 248, in homer return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer) return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.') ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix. raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.') ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix. make: [makefiles/common.mk:144: tmp_static/Subset4/motifs.bed] Error 1 make: [makefiles/common.mk:144: tmp_static/Subset9/motifs.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 <module> 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 248, in homer return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.') ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix. make: [makefiles/common.mk:144: tmp_static/Subset3/motifs.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 <module> 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 248, in homer return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.') ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix. make: [makefiles/common.mk:144: tmp_static/Subset8/motifs.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 <module> 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 248, in homer return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer) File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.') ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix. make: *** [makefiles/common.mk:144: tmp_static/Subset5/motifs.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 <module> docstringrunner(package) File "/data/nfs/OriginTools/pcj/python3/miniconda3/e Position file = 14-reform-split/aaaad Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome Output Directory = 15-motifscan/aaaad Using actual sizes of regions (-size given) Fragment size set to given Will use repeat masked sequences Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif Using Custom Genome Peak/BED file conversion summary: BED/Header formatted lines: 14217 peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14217
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 491 (avg size of targets)
Background files for 491 bp fragments found.
Custom genome sequence directory: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Extracting sequences from file: /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa
Looking for peak sequences in a single file (/data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome/genome.fa)
Extracting 1049 sequences from chr1
Extracting 1303 sequences from chr2
Extracting 938 sequences from chr3
Extracting 897 sequences from chr4
Extracting 828 sequences from chr5
Extracting 817 sequences from chr6
Extracting 679 sequences from chr7
Extracting 774 sequences from chr8
Extracting 720 sequences from chr9
Extracting 833 sequences from chr10
Extracting 676 sequences from chr11
Extracting 661 sequences from chr12
Extracting 716 sequences from chr13
Extracting 628 sequences from chr14
Extracting 553 sequences from chr15
Extracting 566 sequences from chr16
Extracting 482 sequences from chr17
Extracting 479 sequences from chr18
Extracting 333 sequences from chr19
Extracting 266 sequences from chrX
Extracting 3 sequences from chrY
Reading input files...
14201 total sequences read
356 motifs loaded
Finding instances of 356 motif(s)
|0% 50% 100%|
=================================================================================
Cleaning up tmp files...
Position file = 14-reform-split/aaaab
Genome = /data/share/pcj/CNE_analysis/single_Cell_GRN/data/genome
Output Directory = 15-motifscan/aaaab
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will find motif(s) in /data/share/pcj/CNE_analysis/single_Cell_GRN/data/motifs.motif
Using Custom Genome
Peak/BED file conversion summary:
BED/Header formatted lines: 14219
peakfile formatted lines: 0
Peak File Statistics:
Total Peaks: 14219
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 664 (aHi bioinformaticspcj,
I'm afraid your pasted reply was truncated. Is there any chance you can upload the full version as an attachment on github website or somewhere else? Or can you spot the error on your side?
Lingfei
bioinformaticspcj
commented
8 months ago Dear Lingfei,
Thanks for your suggestion. I have uploaded the output to https://figshare.com/articles/online_resource/Single_Cell_Log/24278206 in Figshare.
Hope you could find it !
Best, Bob
lingfeiwang
commented
8 months ago Hi Bob,
This appears to be the error:
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 <module>
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 248, in homer
return _motif_postproc(d2,fi_exp,fo_bed,fo_wellington,fo_homer)
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 192, in _motif_postproc
raise ValueError('Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.')
ValueError: Found non-unique motif name suffices. Each motif name is recommended to contain a unique suffix.As described above, the problem should be in your motif file. Could you add _0, _1, ... to the end of the name of each motif so each has a unique suffix? After that if the same error occurs, you can upload the motif file here so I can have a look.
Lingfei
lingfeiwang
commented
8 months ago Also, you can run makefile_check.py first as well. The new version should provide you with more information for diagnosis.
bioinformaticspcj
commented
8 months ago Dear Lingfei,
Thanks for your suggestion. I have tried to add the number to distinguish each motif name. 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
The motif file that I used has been uploaded to https://figshare.com/articles/dataset/Mouse_TF_motif/24333844 in figshare.
Could you help me to have a look to handle this issue?
Best, Bob
Checks before submitting the issue
Describe the error I have scRNA data and Bulk ATAC data from four samples. According to the paper, we can utilize bulk ATAC data to construct a network. However, in the tutorial provided at https://nbviewer.org/github/pinellolab/dictys/blob/master/doc/tutorials/short-multiome/notebooks/main.ipynb, the step "1. Preparation of individual input files in the data folder “the bam seems to be intended for scATAC data. How should I proceed to process my bulk ATAC data to get a network? Thank you for your guidance and advice.
Optional steps (may accelerate troubleshooting)