RSAT - peak-motifs result

Analysis: ATACss (05/01/2025 23:46)

Command

peak-motifs  -v 1 -title ATACss -i $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/peak-motifscontrol_seq -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db cisBP_Mus_musculus tf $RSAT/public_html/motif_databases/cisBP2/cisBP_Mus_musculus_2019.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18

Sequence composition

Sequence composition (test sequences)

Nb of peaks: 43990
Total seq. size: 44 kb
Min length: 1 bp
Mean length: 1 bp
Max length: 1 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Sequence composition (ctrl sequences)

Nb of peaks: 11226
Total seq. size: 11 kb
Min length: 1 bp
Mean length: 1 bp
Max length: 1 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Discovered motifs (by algorithm)

motif discovery
oligos_6nt_test_vs_ctrl	Not a single significant pattern	[oligos_6nt_test_vs_ctrl]
oligos_7nt_test_vs_ctrl	Not a single significant pattern	[oligos_7nt_test_vs_ctrl]

Discovered motifs (with motif comparison)

Motif discovery

Motif comparisons

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]
Discovered motifs versus transcription factor databases
Motifs versus cisBP_Mus_musculus database		[ table: html txt ] [ alignments (logo): html text ] [ graph: gml (for CytoScape) ]

Command:  peak-motifs  -v 1 -title ATACss -i $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/peak-motifscontrol_seq -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db cisBP_Mus_musculus tf $RSAT/public_html/motif_databases/cisBP2/cisBP_Mus_musculus_2019.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18

Logs and parameter files

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

Publications

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

; Job started 2025_01_05.234621 ; Job done 2025_01_05.234621 ; Job started 2025_01_05.234621 ; Job done 2025_01_05.234621

Error: Error with the expected frequency file : the sum must be strictly positive 0
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Error: At least 2 rows and 2 columns are required
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Error: X axis data (column
1
) are not numeric.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

; Job started 2025_01_05.234625 ; Job done 2025_01_05.234625 ; Job started 2025_01_05.234625 ; Job done 2025_01_05.234625

Error: Error with the expected frequency file : the sum must be strictly positive 0
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Error: At least 2 rows and 2 columns are required
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Error: X axis data (column
1
) are not numeric.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Error: Error with the expected frequency file
tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab
Sum must be strictly positive
0
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Not a single pattern was found in file tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl.tab

Error: Error with the expected frequency file
tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab
Sum must be strictly positive
0
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Not a single pattern was found in file tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab

Warning: Discovered motif file does not exist tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/discovered_motifs/peak-motifs_motifs_discovered.tf

Error: OpenInputFile: File tmp/www-data/2025/01/05/peak-motifs.2025-01-05.234618_2025-01-05.234618_Mz6i18/results/discovered_motifs/peak-motifs_motifs_discovered.tf does not exist.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Not a single discovered motif. Reducing the order of the Markov model may increase sensitivity.