; network-interactions  -v 20 -title demo_01 -tfs $RSAT/public_html/demo_files/TFs_short.txt -cre $RSAT/public_html/demo_files/enhancers_short.bed -genome galGal4 -report_net -net $RSAT/public_html/demo_files/net_short.tsv -score 5 -pval 0.0005 -outdir ./Demo_01 -html
; Input files
;	TFs          	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/TFs_short.txt
;	network      	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/net_short.tsv
;	cres         	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/enhancers_short.bed
; Results files
;	network_intersection_onlyTFs	./Demo_01/ResultsFiles/network_intersection_onlyTFs_2022-03-03.092844.tsv
;	GRN_indirect_interactions	./Demo_01/ResultsFiles/GRN_indirect_interactions_2022-03-03.092844.tsv
;	archive      	./Demo_01/network-interactions_archive_2022-03-03.092844.zip
;	network_not_found_interactions	./Demo_01/ResultsFiles/network_not_found_interactions_2022-03-03.092844.tsv
;	err_log      	./Demo_01/ResultsFiles/_errors.txt
;	log          	./Demo_01/ResultsFiles/network-interactions_log_2022-03-03.092844.txt
;	network_intersection	./Demo_01/ResultsFiles/network_intersection_2022-03-03.092844.tsv
;	network_found_interactions	./Demo_01/ResultsFiles/network_found_interactions_2022-03-03.092844.tsv
;	summary      	./Demo_01/ResultsFiles/SUMMARY_2022-03-03.092844.html
;	GRN_direct_interactions	./Demo_01/ResultsFiles/GRN_direct_interactions_2022-03-03.092844.tsv
;	complete_direct_interactions	./Demo_01/ResultsFiles/complete_direct_interactions_2022-03-03.092844.tsv
; Intermediate files
;	used_regulatory_regions	./Demo_01/IntermediateFiles/network-interactions_used_regulatory_regions_2022-03-03.092844.bed
;	used_cre_seqs_geneheader	./Demo_01/IntermediateFiles/network-interactions_used_cre_seqs_geneheader_2022-03-03.092844.fa
;	used_matrixes	./Demo_01/IntermediateFiles/network-interactions_used_matrixes_2022-03-03.092844.tf
;	used_matrix_scan_results	./Demo_01/IntermediateFiles/network-interactions_used_matrix-scan_results_2022-03-03.092844.tsv
;	used_cre_seqs	./Demo_01/IntermediateFiles/network-interactions_used_cre_seqs_2022-03-03.092844.fa
# Interactions in common from:
#	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/net_short.tsv and ./Demo_01/ResultsFiles/complete_direct_interactions_2022-03-03.092844.tsv
#TFx	Geney	Coordinates	Positions	Scores
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71
; Host name	rsat-tagc
; Job started	2022-03-03.092844
; Job done	2022-03-03.092858
; Seconds	0.15
;	user	0.15
;	system	0.03
;	cuser	10.82
;	csystem	0.71