# Pipeline started at 06-15 07:17:12

# pid	hash	cid	runtime	mem	cmd	lock
380687	1a50217f9f	1	0:00:00.020000	 0.0	ln	lock.raw__HEK_PRO-seq_R1.fastq.gz
380691	27453967b5	2	0:00:00.020000	 0.0	ln	lock.raw__HEK_PRO-seq_R2.fastq.gz
380697	59a8d0b3dd	3	0:01:44.760000	 0.0025	pigz	lock.fastq__HEK_PRO-seq_R2.fastq
380803	aef6a7868a	4	0:00:58.640000	 0.0025	pigz	lock.fastq__HEK_PRO-seq_R2.fastq
381203	8dc2b9a1ee	5	0:00:39.590000	 1.7729	cutadapt	lock.fastq__HEK_PRO-seq_R1_processed.fastq
381274	36cb5b2c12	6	0:00:27.330000	 0.0008	seqtk	lock.fastq__HEK_PRO-seq_R1_processed.fastq
381275	36cb5b2c12	7	0:00:27.750000	 0.0023	seqtk	lock.fastq__HEK_PRO-seq_R1_processed.fastq
381328	4cb29161a5	7f	0:00:42.340000	 0.1563	fastqc	lock.trimmed_fastqc
381432	8d39730290	8	0:00:46.690000	 1.9862	seqkit	lock.fastq__HEK_PRO-seq_R1_trimmed.fastq
381515	d9eef89558	9	0:00:08.300000	 0.0008	seqtk	lock.fastq__HEK_PRO-seq_R1_trimmed.fastq
381516	d9eef89558	10	0:00:20.840000	 0.0023	seqtk	lock.fastq__HEK_PRO-seq_R1_trimmed.fastq
381619	2132d5c4fb	11	0:00:00.050000	 0.0004	touch	lock.fastq__processed_R1.flag
381621	48fa6608b5	12	0:01:12.270000	 1.9267	cutadapt	lock.fastq__HEK_PRO-seq_R2_trimmed.fastq
381919	12c0f5b284	13	0:00:16.590000	 0.0008	seqtk	lock.fastq__HEK_PRO-seq_R2_trimmed.fastq
381920	12c0f5b284	14	0:00:26.530000	 0.0023	seqtk	lock.fastq__HEK_PRO-seq_R2_trimmed.fastq
381983	4cb29161a5	14f	0:00:41.370000	 0.1546	fastqc	lock.trimmed_fastqc
382054	07784ad36c	14f	0:00:34.330000	 0.1533	fastqc	lock.trimmed_fastqc_R2
382246	7e33de5c60	15	0:01:41.550000	 2.4409	fastq_pair	lock.cutadapt__HEK_PRO-seq.histogram
382390	20edb23bd5	16	0:00:53.260000	 0.1333	flash	lock.cutadapt__HEK_PRO-seq.histogram
382583	4d52648dfd	17	0:00:05.130000	 0.2873	Rscript	lock.cutadapt__HEK_PRO-seq_adapter_insertion_distribution.pdf
382613	f4ccd297cc	18	0:00:21.980000	 0.002	cp	lock.fastq__HEK_PRO-seq_R2_trimmed_dups.fastq
382911	456b74305d	19	0:00:00.030000	 0.0	touch	lock.fastq__processed_R2.flag
382912	f647e68f51	20	0:01:45.600000	 2.0092	fastq_pair	lock.fastq__repaired.flag
383044	f6579f3a14	21	0:00:00.370000	 0.0008	mv	lock.fastq__repaired.flag
383045	ba12402ce8	22	0:00:00.370000	 0.0008	mv	lock.fastq__repaired.flag
383047	6c697add9c	23	0:00:00.040000	 0.0	touch	lock.fastq__repaired.flag
383048	79afae7e0c	24	0:01:18.070000	 2.5927	fastq_pair	lock.fastq__dups_repaired.flag
383175	85fdd82e90	25	0:00:00.450000	 0.0008	mv	lock.fastq__dups_repaired.flag
383182	549a9406bd	26	0:00:00.670000	 0.0008	mv	lock.fastq__dups_repaired.flag
383183	0d4e8e2cb5	27	0:00:00.040000	 0.0004	touch	lock.fastq__dups_repaired.flag
383184	43293dbf56	28	0:00:00.030000	 0.0	mkfifo	lock.prealignments__human_rDNA_bt2
383576	2247948755	30	0:00:00.280000	 0.0015	mkfifo	lock.prealignments__human_rDNA_dups_bt2
383745	81a90c4302	33	0:30:12.260000	 0.0037	samtools	lock.aligned_hg38__HEK_PRO-seq_sort.bam
383744	81a90c4302	32	0:30:12.290000	 3.7719	bowtie2	lock.aligned_hg38__HEK_PRO-seq_sort.bam
383746	81a90c4302	34	0:33:26.410000	 0.9281	samtools	lock.aligned_hg38__HEK_PRO-seq_sort.bam
387133	73d76ba79d	35	0:00:50.820000	 0.0181	samtools	lock.aligned_hg38__HEK_PRO-seq_sort.bam
388990	732afb49db	36	0:26:51.270000	 3.7555	bowtie2	lock.aligned_hg38__HEK_PRO-seq_sort_dups.bam
388996	732afb49db	37	0:27:11.330000	 0.0037	samtools	lock.aligned_hg38__HEK_PRO-seq_sort_dups.bam
388997	732afb49db	38	0:30:01.320000	 0.9059	samtools	lock.aligned_hg38__HEK_PRO-seq_sort_dups.bam
393207	70ee0a9ad7	39	0:00:54.670000	 0.018	samtools	lock.aligned_hg38__HEK_PRO-seq_sort_dups.bam
393916	eb88b002c2	40	0:00:19.710000	 0.0108	pigz	lock.prealignments__HEK_PRO-seq_human_rDNA_unmap_R1.fq.gz
393975	492e6662de	41	0:00:22.600000	 0.013	pigz	lock.prealignments__HEK_PRO-seq_human_rDNA_unmap_R2.fq.gz
394034	0c7a94120c	42	0:00:24.350000	 0.0132	samtools	lock.aligned_hg38__HEK_PRO-seq_temp.bam.bai
394095	aa0ed2a354	43	0:00:20.080000	 0.0147	samtools	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394142	01612efdfb	45	0:00:00.060000	 0.0	cut	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394144	01612efdfb	47	0:00:00.080000	 0.0	grep	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394141	01612efdfb	44	0:00:00.090000	 0.0094	samtools	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394143	01612efdfb	46	0:00:00.110000	 0.0	awk	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394146	6851169dfe	48	0:00:27.960000	 0.0189	samtools	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394211	1e51cc8c97	49	0:00:00.170000	 0.0008	mv	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394213	aa0ed2a354	50	0:00:19.870000	 0.0146	samtools	lock.aligned_hg38__HEK_PRO-seq_noMT.bam
394562	0dc50e5f26	51	0:01:30.390000	 0.0038	samtools	lock.aligned_hg38__HEK_PRO-seq_PE2.bam
394563	0dc50e5f26	52	0:01:43.860000	 3.6411	samtools	lock.aligned_hg38__HEK_PRO-seq_PE2.bam
395221	2cf302203e	53	0:01:27.410000	 0.0038	samtools	lock.aligned_hg38__HEK_PRO-seq_PE2.bam
395222	2cf302203e	54	0:01:39.190000	 3.0764	samtools	lock.aligned_hg38__HEK_PRO-seq_PE2.bam
395571	70f574813e	55	0:00:22.940000	 0.0139	samtools	lock.aligned_hg38__HEK_PRO-seq_temp_dups.bam.bai
396181	2ed78c2e28	63	0:01:29.950000	 0.0038	samtools	lock.aligned_hg38__HEK_PRO-seq_dups_PE2.bam
396182	2ed78c2e28	64	0:01:52.510000	 3.5795	samtools	lock.aligned_hg38__HEK_PRO-seq_dups_PE2.bam
396694	054749e1df	65	0:01:27.400000	 0.0038	samtools	lock.aligned_hg38__HEK_PRO-seq_dups_PE2.bam
396695	054749e1df	66	0:01:38.240000	 3.0222	samtools	lock.aligned_hg38__HEK_PRO-seq_dups_PE2.bam
397460	4484fda57c	67	0:01:19.120000	 0.0052	preseq	lock.QC_hg38__HEK_PRO-seq_preseq_out.txt
397570	ccb4058645	68	0:01:24.320000	 0.0051	preseq	lock.QC_hg38__HEK_PRO-seq_preseq_yield.txt
397921	f7931d88fe	69	0:00:19.230000	 0.0057	echo	lock.QC_hg38__HEK_PRO-seq_preseq_counts.txt
397941	904fdde7f6	70	0:00:05.370000	 0.2677	Rscript	lock.QC_hg38__HEK_PRO-seq_preseq_plot.png
397960	c27c4adca2	71	0:00:10.230000	 0.0085	samtools	lock.aligned_hg38__HEK_PRO-seq_PE1.bam.bai
397979	248d33a455	72	0:00:14.480000	 1.0707	/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py	lock.QC_hg38__HEK_PRO-seq_bamQC.tsv
398020	50936e5332	73	0:00:05.200000	 0.0091	samtools	lock.aligned_hg38__HEK_PRO-seq_unmap.bam
398059	75313403d6	74	0:00:45.070000	 0.0063	samtools	lock.aligned_hg38__HEK_PRO-seq_minus.bam
398099	3e91d9ea7b	75	0:00:43.910000	 0.0063	samtools	lock.aligned_hg38__HEK_PRO-seq_minus.bam
398152	6aeb05a226	76	0:00:00.210000	 0.0015	sed	lock.QC_hg38__minus_TSS.tsv
398154	52ed5d8f4a	77	0:00:05.420000	 0.9874	/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py	lock.QC_hg38__HEK_PRO-seq_plus_TssEnrichment.txt
398185	d7d42f6aa1	78	0:00:05.330000	 0.9808	/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py	lock.QC_hg38__HEK_PRO-seq_minus_TssEnrichment.txt
398216	ed47e5f38f	79	0:00:06.090000	 0.3203	Rscript	lock.QC_hg38__HEK_PRO-seq_TSSenrichment.pdf
398238	6243e6bfde	80	0:00:00.040000	 0.0	samtools	lock.QC_hg38__chr_order.txt
398240	6243e6bfde	82	0:00:00.060000	 0.0	awk	lock.QC_hg38__chr_order.txt
398239	6243e6bfde	81	0:00:00.070000	 0.0	grep	lock.QC_hg38__chr_order.txt
398241	6243e6bfde	83	0:00:00.090000	 0.0	awk	lock.QC_hg38__chr_order.txt
398243	6bfc7993bc	84	0:00:00.020000	 0.0	cut	lock.QC_hg38__chr_keep.txt
398245	7a5ec487a6	85	0:00:01.630000	 0.0023	grep	lock.QC_hg38__hg38_ensembl_gene_body.bed
398246	7a5ec487a6	86	0:00:01.850000	 0.0985	bedtools	lock.QC_hg38__hg38_ensembl_gene_body.bed
398250	552098854f	87	0:00:00.270000	 0.0026	grep	lock.QC_hg38__hg38_ensembl_gene_body.bed
398251	552098854f	88	0:00:00.310000	 0.022	bedtools	lock.QC_hg38__hg38_ensembl_gene_body.bed
398254	6b29071e5c	89	0:00:17.810000	 0.0092	bedtools	lock.QC_hg38__HEK_PRO-seq_TSS_density.bed
398256	6b29071e5c	91	0:00:18.450000	 0.0117	sort	lock.QC_hg38__HEK_PRO-seq_TSS_density.bed
398255	6b29071e5c	90	0:00:18.460000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_TSS_density.bed
398257	6b29071e5c	92	0:00:18.530000	 0.0028	sort	lock.QC_hg38__HEK_PRO-seq_TSS_density.bed
398274	a5093f8a8b	93	0:00:20.450000	 0.0352	bedtools	lock.QC_hg38__HEK_PRO-seq_gene_body_density.bed
398276	a5093f8a8b	95	0:00:20.530000	 0.0065	sort	lock.QC_hg38__HEK_PRO-seq_gene_body_density.bed
398275	a5093f8a8b	94	0:00:20.540000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_gene_body_density.bed
398295	5181a0049f	96	0:00:00.100000	 0.0007	join	lock.QC_hg38__HEK_PRO-seq_pause_index.bed
398297	5181a0049f	98	0:00:00.330000	 0.0062	env	lock.QC_hg38__HEK_PRO-seq_pause_index.bed
398296	5181a0049f	97	0:00:00.350000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_pause_index.bed
398304	5f2c04646c	99	0:00:00.040000	 0.0015	awk	lock.QC_hg38__HEK_PRO-seq_pause_index.bed
398309	da39279199	100	0:00:05	 0.3163	Rscript	lock.QC_hg38__HEK_PRO-seq_pause_index.pdf
398330	cd37972198	101	0:00:00.040000	 0.0019	pigz	lock.QC_hg38__HEK_PRO-seq_pause_index.bed.gz
398370	9807a9d231	102	0:00:00.670000	 0.0042	grep	lock.signal_hg38__HEK_PRO-seq_gene_coverage.bed
398371	9807a9d231	103	0:00:00.700000	 0.0056	bedtools	lock.signal_hg38__HEK_PRO-seq_gene_coverage.bed
398373	1b3ddd3fb0	104	0:00:19.930000	 0.0357	bedtools	lock.signal_hg38__HEK_PRO-seq_gene_coverage.bed
398391	a3fa9386d0	105	0:00:00.020000	 0.0	ln	lock.raw__hg38_annotations.bed
398392	3a33412839	106	0:00:00.370000	 0.0023	pigz	lock.raw__hg38_annotations.bed
398401	39ec2a9e90	107	0:00:01.280000	 0.0023	awk	lock.QC_hg38__Enhancer
398403	824008fc7b	108	0:00:00.110000	 0.0	cut	lock.QC_hg38__Enhancer_sort.bed
398404	824008fc7b	109	0:00:00.770000	 0.0026	grep	lock.QC_hg38__Enhancer_sort.bed
398406	824008fc7b	111	0:00:00.840000	 0.0466	bedtools	lock.QC_hg38__Enhancer_sort.bed
398405	824008fc7b	110	0:00:00.850000	 0.0007	cut	lock.QC_hg38__Enhancer_sort.bed
398409	7b4f4338e0	112	0:00:08.570000	 0.0073	bedtools	lock.QC_hg38__HEK_PRO-seq_Enhancer_plus_coverage.bed
398417	7585fd387b	113	0:00:08.410000	 0.0074	bedtools	lock.QC_hg38__HEK_PRO-seq_Enhancer_minus_coverage.bed
398428	5f257628d5	115	0:00:00.040000	 0.0	cut	lock.QC_hg38__Promoter_sort.bed
398429	5f257628d5	116	0:00:00.250000	 0.0026	grep	lock.QC_hg38__Promoter_sort.bed
398431	5f257628d5	118	0:00:00.270000	 0.0083	bedtools	lock.QC_hg38__Promoter_sort.bed
398430	5f257628d5	117	0:00:00.280000	 0.0007	cut	lock.QC_hg38__Promoter_sort.bed
398433	1b50318f7f	119	0:00:08.850000	 0.0158	bedtools	lock.QC_hg38__HEK_PRO-seq_Promoter_plus_coverage.bed
398634	079bda1a52	120	0:00:08.460000	 0.0133	bedtools	lock.QC_hg38__HEK_PRO-seq_Promoter_minus_coverage.bed
398646	f013a32fa6	122	0:00:00.020000	 0.0	mv	lock.QC_hg38__Promoter_Flanking_Region
398647	26387128ef	123	0:00:00.040000	 0.0	cut	lock.QC_hg38__Promoter_Flanking_Region_sort.bed
398649	26387128ef	125	0:00:01	 0.0007	cut	lock.QC_hg38__Promoter_Flanking_Region_sort.bed
398648	26387128ef	124	0:00:01.020000	 0.0023	grep	lock.QC_hg38__Promoter_Flanking_Region_sort.bed
398650	26387128ef	126	0:00:01.040000	 0.0106	bedtools	lock.QC_hg38__Promoter_Flanking_Region_sort.bed
398653	3a6a612958	127	0:00:08.930000	 0.0093	bedtools	lock.QC_hg38__HEK_PRO-seq_Promoter_Flanking_Region_plus_coverage.bed
398662	3652cc8d76	128	0:00:08.730000	 0.0107	bedtools	lock.QC_hg38__HEK_PRO-seq_Promoter_Flanking_Region_minus_coverage.bed
398671	a47389d654	130	0:00:00.020000	 0.0	mv	lock.QC_hg38__5_UTR
398672	77522f056a	131	0:00:00.040000	 0.0	cut	lock.QC_hg38__5_UTR_sort.bed
398673	77522f056a	132	0:00:00.530000	 0.0026	grep	lock.QC_hg38__5_UTR_sort.bed
398675	77522f056a	134	0:00:00.550000	 0.0101	bedtools	lock.QC_hg38__5_UTR_sort.bed
398674	77522f056a	133	0:00:00.560000	 0.0007	cut	lock.QC_hg38__5_UTR_sort.bed
398678	2112c47371	135	0:00:08.610000	 0.0081	bedtools	lock.QC_hg38__HEK_PRO-seq_5_UTR_plus_coverage.bed
398687	b8aeac1e42	136	0:00:08.460000	 0.0087	bedtools	lock.QC_hg38__HEK_PRO-seq_5_UTR_minus_coverage.bed
398696	ff9e6dc6ee	138	0:00:00.040000	 0.0015	mv	lock.QC_hg38__3_UTR
398697	9d249ad63e	139	0:00:00.040000	 0.0	cut	lock.QC_hg38__3_UTR_sort.bed
398698	9d249ad63e	140	0:00:00.570000	 0.0026	grep	lock.QC_hg38__3_UTR_sort.bed
398700	9d249ad63e	142	0:00:00.640000	 0.0345	bedtools	lock.QC_hg38__3_UTR_sort.bed
398699	9d249ad63e	141	0:00:00.650000	 0.0007	cut	lock.QC_hg38__3_UTR_sort.bed
398702	2bbf4fab53	143	0:00:08.650000	 0.009	bedtools	lock.QC_hg38__HEK_PRO-seq_3_UTR_plus_coverage.bed
398711	2fcd217219	144	0:00:08.610000	 0.0104	bedtools	lock.QC_hg38__HEK_PRO-seq_3_UTR_minus_coverage.bed
398721	dec8903f34	146	0:00:00.040000	 0.0	cut	lock.QC_hg38__Exon_sort.bed
398722	dec8903f34	147	0:00:02.620000	 0.0041	grep	lock.QC_hg38__Exon_sort.bed
398724	dec8903f34	149	0:00:02.860000	 0.1699	bedtools	lock.QC_hg38__Exon_sort.bed
398723	dec8903f34	148	0:00:02.880000	 0.0007	cut	lock.QC_hg38__Exon_sort.bed
398728	d1c9889f08	150	0:00:09.990000	 0.0117	bedtools	lock.QC_hg38__HEK_PRO-seq_Exon_plus_coverage.bed
398738	649924fa6e	151	0:00:09.590000	 0.0119	bedtools	lock.QC_hg38__HEK_PRO-seq_Exon_minus_coverage.bed
398748	e435e35294	153	0:00:00.050000	 0.0	cut	lock.QC_hg38__Intron_sort.bed
398750	e435e35294	155	0:00:01.290000	 0.0007	cut	lock.QC_hg38__Intron_sort.bed
398749	e435e35294	154	0:00:01.320000	 0.0023	grep	lock.QC_hg38__Intron_sort.bed
398751	e435e35294	156	0:00:01.470000	 0.0822	bedtools	lock.QC_hg38__Intron_sort.bed
398754	ba75803c3c	157	0:00:10.560000	 0.0189	bedtools	lock.QC_hg38__HEK_PRO-seq_Intron_plus_coverage.bed
398766	867d0d3834	158	0:00:10.360000	 0.0222	bedtools	lock.QC_hg38__HEK_PRO-seq_Intron_minus_coverage.bed
398791	713fdae854	159	0:00:34.160000	 0.5021	Rscript	lock.QC_hg38__HEK_PRO-seq_cFRiF.pdf
398831	5d708288cd	160	0:00:26.500000	 0.4721	Rscript	lock.QC_hg38__HEK_PRO-seq_FRiF.pdf
398864	fb97b936b3	161	0:00:04.620000	 0.0045	grep	lock.QC_hg38__hg38_introns_sort.bed
398865	fb97b936b3	162	0:00:04.810000	 0.0993	bedtools	lock.QC_hg38__hg38_introns_sort.bed
398871	76bdfd14c3	163	0:00:04.700000	 0.0046	grep	lock.QC_hg38__hg38_introns_sort.bed
398873	76bdfd14c3	165	0:00:05.300000	 0.0061	bedtools	lock.QC_hg38__hg38_introns_sort.bed
398872	76bdfd14c3	164	0:00:05.310000	 0.0362	bedtools	lock.QC_hg38__hg38_introns_sort.bed
398880	287dcc3514	166	0:00:17.010000	 0.0115	bedtools	lock.QC_hg38__HEK_PRO-seq_introns_coverage.bed
398896	ac9c7571f9	167	0:00:18.740000	 0.0264	bedtools	lock.QC_hg38__HEK_PRO-seq_introns_coverage.bed
398914	0a7deb9d92	168	0:00:00.490000	 0.0077	awk	lock.QC_hg38__HEK_PRO-seq_exons_rpkm.bed
398916	0a7deb9d92	170	0:00:00.510000	 0.0025	sort	lock.QC_hg38__HEK_PRO-seq_exons_rpkm.bed
398915	0a7deb9d92	169	0:00:00.530000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_exons_rpkm.bed
398919	9ed87135b8	171	0:00:00.450000	 0.0074	awk	lock.QC_hg38__HEK_PRO-seq_introns_rpkm.bed
398921	9ed87135b8	173	0:00:00.510000	 0.0054	sort	lock.QC_hg38__HEK_PRO-seq_introns_rpkm.bed
398920	9ed87135b8	172	0:00:00.530000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_introns_rpkm.bed
398923	3d00ac0406	174	0:00:00.090000	 0.0007	join	lock.QC_hg38__HEK_PRO-seq_exon_intron_ratios.bed
398925	3d00ac0406	176	0:00:00.240000	 0.0054	sort	lock.QC_hg38__HEK_PRO-seq_exon_intron_ratios.bed
398924	3d00ac0406	175	0:00:00.250000	 0.001	awk	lock.QC_hg38__HEK_PRO-seq_exon_intron_ratios.bed
398931	8cf28af5ec	177	0:00:05	 0.3163	Rscript	lock.QC_hg38__HEK_PRO-seq_mRNA_contamination.pdf
398952	764e4b74e6	178	0:00:00.040000	 0.0027	pigz	lock.QC_hg38__HEK_PRO-seq_exon_intron_ratios.bed.gz
398961	d2d6d735c3	179	0:00:05.160000	 0.0121	samtools	lock.signal_hg38__HEK_PRO-seq_plus_smooth_body_0-mer.bw
398966	5dad0f8724	180	0:06:15.310000	 3.4053	/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py	lock.signal_hg38__HEK_PRO-seq_plus_smooth_body_0-mer.bw
400419	977d28f6c9	181	0:00:05.040000	 0.0116	samtools	lock.signal_hg38__HEK_PRO-seq_minus_smooth_body_0-mer.bw
400428	5384b54190	182	0:06:16.420000	 3.4055	/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py	lock.signal_hg38__HEK_PRO-seq_minus_smooth_body_0-mer.bw
