RSAT - peak-motifs result

Analysis: MEsalmon4_Up4_W2 (26/05/2025 03:44)

peak-motifs  -v 1 -title MEsalmon4_Up4_W2 -i $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/peak-motifscontrol_seq -markov auto -disco oligos,dyads,positions -nmotifs 10 -minol 6 -maxol 8 -no_merge_lengths -2str -origin end -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK

motif discovery
oligos_6nt_test_vs_ctrl	oligos_6nt_test_vs_ctrl_m1 assembly: aggcccaa (sig=1.45; e-value=0.035) RC: ttgggcct oligos_6nt_test_vs_ctrl_m2 assembly: atgagc (sig=0.82; e-value=0.15) RC: gctcat oligos_6nt_test_vs_ctrl_m3 assembly: atctta (sig=0.04; e-value=0.91) RC: taagat oligos_6nt_test_vs_ctrl_m4 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m5 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m6 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m7 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m8 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m9 : (sig=; e-value=1) RC: oligos_6nt_test_vs_ctrl_m10 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_7nt_test_vs_ctrl	oligos_7nt_test_vs_ctrl_m1 assembly: aggccca (sig=1.28; e-value=0.052) RC: tgggcct oligos_7nt_test_vs_ctrl_m2 assembly: attgggc (sig=0.77; e-value=0.17) RC: gcccaat oligos_7nt_test_vs_ctrl_m3 assembly: aattcta (sig=0.00; e-value=1) RC: tagaatt oligos_7nt_test_vs_ctrl_m4 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m5 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m6 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m7 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m8 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m9 : (sig=; e-value=1) RC: oligos_7nt_test_vs_ctrl_m10 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_8nt_test_vs_ctrl	oligos_8nt_test_vs_ctrl_m1 assembly: acttatac (sig=0.38; e-value=0.42) RC: gtataagt oligos_8nt_test_vs_ctrl_m2 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m3 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m4 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m5 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m6 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m7 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m8 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m9 : (sig=; e-value=1) RC: oligos_8nt_test_vs_ctrl_m10 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
dyads_test_vs_ctrl	dyads_test_vs_ctrl_m1 assembly: aggccca (sig=0.60; e-value=0.25) RC: tgggcct dyads_test_vs_ctrl_m2 assembly: aatnnnnnnnnnnnnnnnnnnatg (sig=0.60; e-value=0.25) RC: catnnnnnnnnnnnnnnnnnnatt dyads_test_vs_ctrl_m3 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m4 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m5 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m6 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m7 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m8 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m9 : (sig=; e-value=1) RC: dyads_test_vs_ctrl_m10 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]

Motif discovery
Motif 1   oligos_6nt_test_vs_ctrl_m1	k-mer sig=1.45; evalue=0.035 csaGGCCCAwcy RGWTGGGCCTSG	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor csaGGCCCAwcy ASR1:MA1812.1:JASPAR ASR1/MA1812.1/JASPAR D 12 0.8000 0.969 0.775 NA NA TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot R 12 0.8000 0.948 0.759 NA NA ASR1:MA1812.2:JASPAR ASR1/MA1812.2/JASPAR D 9 0.7500 0.974 0.730 NA NA Total matches= 14 (11 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 40 (11.49%) Max nb of predicted sites per peak: 4  (gene-Lalb_Chr23g0268801) Mean nb of predicted sites per peak: 1.45	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_test_vs_ctrl_m2	k-mer sig=0.82; evalue=0.15 ssatGaGCsr YSGCTCATSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssatGaGCsr HB-1:M0841_1.02:CISBP HB-1/M0841_1.02/CISBP R 8 0.8000 0.703 0.563 NA NA MYB88.ampDAP:M0516:AthalianaCistrome MYB88.ampDAP/M0516/AthalianaCistrome D 10 0.7692 0.703 0.540 NA NA OsLUX1:EEAD0074:EEADannot OsLUX1/EEAD0074/EEADannot R 7 0.5385 0.840 0.452 NA NA Total matches= 6 (3 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 44 (12.64%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr18g0057561) Mean nb of predicted sites per peak: 1.16	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_test_vs_ctrl_m3	k-mer sig=0.04; evalue=0.91 wcATCTTAry RYTAAGATGW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wcATCTTAry TOE2:TOE2_3:ArabidopsisPBM TOE2/TOE2_3/ArabidopsisPBM D 10 1.0000 0.728 0.728 NA NA TOE1:TOE1_3:ArabidopsisPBM TOE1/TOE1_3/ArabidopsisPBM D 10 1.0000 0.724 0.724 NA NA fgenesh1_pg.C_Chr_07.0001000042:M0808_1.02:CISBP fgenesh1_pg.C_Chr_07.0001000042/M0808_1.02/CISBP D 10 1.0000 0.719 0.719 NA NA Total matches= 83 (80 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 42 (12.07%) Max nb of predicted sites per peak: 2  (gene-Lalb_Chr20g0111721) Mean nb of predicted sites per peak: 1.10	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_8nt_test_vs_ctrl_m1	k-mer sig=0.38; evalue=0.42 ymaCtTaTaChy RDGTATAAGTKR	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ymaCtTaTaChy KUA1:MA1398.2:JASPAR KUA1/MA1398.2/JASPAR D 11 0.9167 0.718 0.659 NA NA AT5G04760:MA2031.1:JASPAR AT5G04760/MA2031.1/JASPAR D 11 0.9167 0.710 0.651 NA NA AtMYB63_I:AtMYB63_I:AthaMYB AtMYB63_I/AtMYB63_I/AthaMYB R 8 0.6667 0.825 0.550 NA NA Total matches= 24 (21 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 20 (5.75%) Max nb of predicted sites per peak: 1  (gene-Lalb_Chr25g0284521) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   dyads_test_vs_ctrl_m1	k-mer sig=0.60; evalue=0.25 csaGGCCCAwc GWTGGGCCTSG	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor csaGGCCCAwc ASR1:MA1812.2:JASPAR ASR1/MA1812.2/JASPAR D 9 0.8182 0.972 0.795 NA NA ASR1:MA1812.1:JASPAR ASR1/MA1812.1/JASPAR D 11 0.7333 0.968 0.710 NA NA TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot R 11 0.7333 0.947 0.695 NA NA Total matches= 16 (13 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 42 (12.07%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr23g0268801) Mean nb of predicted sites per peak: 1.40	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   dyads_test_vs_ctrl_m2	k-mer sig=0.60; evalue=0.25 vbaatGGSCCmmkssvmrmvyybrtsss SSSAYVRRBKYKBSSMKKGGSCCATTVB	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor vbaatGGSCCmmkssvmrmvyybrtsss TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot D 14 0.4828 0.888 0.429 NA NA ASR1:MA1812.1:JASPAR ASR1/MA1812.1/JASPAR R 14 0.4828 0.869 0.419 NA NA Total matches= 2		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 30 (8.62%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr23g0268801) Mean nb of predicted sites per peak: 1.47	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title MEsalmon4_Up4_W2 -i $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/peak-motifscontrol_seq -markov auto -disco oligos,dyads,positions -nmotifs 10 -minol 6 -maxol 8 -no_merge_lengths -2str -origin end -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK

Error: Cannot scale matrix with only null values
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_sig_matrices_rescaled.tf

Warning: Input file contained not a single matrix

Error: OpenInputFile: File tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_sig_sites.ft does not exist.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_count_matrices.tf

Warning: Input file contained not a single matrix

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.033512_2025-05-26.033512_JvU8AK/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_count_matrices.tf

Warning: Input file contained not a single matrix