# Pipeline started at 06-11 16:59:46 # pid hash cid runtime mem cmd lock 170884 3c2c08f5fc 1 0:00:00.040000 0.0004 ln lock.raw__K562_PRO-seq_06.fastq.gz 170885 0e2956cce7 2 0:00:54.610000 0.0025 pigz lock.fastq__K562_PRO-seq_06_R1.fastq 171343 9d543b95f4 3 0:00:49.030000 3.9553 cutadapt lock.fastq__K562_PRO-seq_06_R1_processed.fastq 171415 282ce75152 4 0:00:30.700000 0.0008 seqtk lock.fastq__K562_PRO-seq_06_R1_processed.fastq 171416 282ce75152 5 0:00:36.210000 0.0023 seqtk lock.fastq__K562_PRO-seq_06_R1_processed.fastq 171938 78c13b97da 6 0:00:00.030000 0.0 echo lock.fastqc__K562_PRO-seq_06_R1_processed_fastqc.html 171956 bbb6885d9b 6f 0:01:39.590000 0.1966 fastqc lock.trimmed_fastqc 172162 cfdce44293 7 0:00:00.040000 0.0015 touch lock.fastq__processed_R1.flag 172163 c25ff6edd3 8 0:00:06.070000 0.2043 Rscript lock.cutadapt__K562_PRO-seq_06_R1_adapter_insertion_distribution.pdf 172819 f57a1f2d89 9 0:15:01.950000 3.7168 bowtie2 lock.aligned_hg38__K562_PRO-seq_06_sort.bam 172820 f57a1f2d89 10 0:15:22 0.0037 samtools lock.aligned_hg38__K562_PRO-seq_06_sort.bam 172821 f57a1f2d89 11 0:18:55.670000 0.8881 samtools lock.aligned_hg38__K562_PRO-seq_06_sort.bam 178942 fa6e2b7a15 12 0:00:55.640000 0.0184 samtools lock.aligned_hg38__K562_PRO-seq_06_sort.bam 182120 afb21c6653 13 0:00:49.550000 0.0092 pigz lock.prealignments__K562_PRO-seq_06_human_rDNA_unmap.fq.gz 182193 fa10895374 14 0:00:25.210000 0.0126 samtools lock.aligned_hg38__K562_PRO-seq_06_temp.bam.bai 182222 22a0b95772 15 0:00:22.630000 0.0118 samtools lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182255 bea238c71f 16 0:00:00.050000 0.0 samtools lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182257 bea238c71f 18 0:00:00.080000 0.0 awk lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182256 bea238c71f 17 0:00:00.110000 0.0 cut lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182258 bea238c71f 19 0:00:00.130000 0.0 grep lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182260 46f838d791 20 0:00:33.860000 0.0193 samtools lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182508 4c7b8f5993 21 0:00:00.260000 0.0008 mv lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182510 22a0b95772 22 0:00:23.590000 0.0113 samtools lock.aligned_hg38__K562_PRO-seq_06_noMT.bam 182754 da2c605edb 24 0:00:28.220000 1.4958 /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py lock.QC_hg38__K562_PRO-seq_06_bamQC.tsv 182825 96dbac361e 25 0:00:04.570000 0.0094 samtools lock.aligned_hg38__K562_PRO-seq_06_unmap.bam 182861 43a6af9359 26 0:01:53.450000 0.0063 samtools lock.aligned_hg38__K562_PRO-seq_06_minus.bam 182975 e59f5c9df8 27 0:01:50.160000 0.0063 samtools lock.aligned_hg38__K562_PRO-seq_06_minus.bam 183542 83d8b8dda5 28 0:00:00.500000 0.0015 sed lock.QC_hg38__minus_TSS.tsv 183544 13c34ceda5 29 0:00:05.540000 0.7091 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__K562_PRO-seq_06_plus_TssEnrichment.txt 183575 24e61b8cf4 30 0:00:04.980000 0.8142 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__K562_PRO-seq_06_minus_TssEnrichment.txt 183606 c3d784cd0b 31 0:00:07.590000 0.2221 Rscript lock.QC_hg38__K562_PRO-seq_06_TSSenrichment.pdf 183631 b96dc87a83 32 0:00:00.050000 0.0 samtools lock.QC_hg38__chr_order.txt 183633 b96dc87a83 34 0:00:00.080000 0.0 awk lock.QC_hg38__chr_order.txt 183632 b96dc87a83 33 0:00:00.100000 0.0 grep lock.QC_hg38__chr_order.txt 183634 b96dc87a83 35 0:00:00.130000 0.0 awk lock.QC_hg38__chr_order.txt 183636 352cd8eb87 36 0:00:00.040000 0.0022 cut lock.QC_hg38__chr_keep.txt 183639 77eeae4ab5 37 0:00:01.660000 0.0042 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 183640 77eeae4ab5 38 0:00:01.890000 0.0998 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 183643 04c26e88a9 39 0:00:00.320000 0.0026 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 183644 04c26e88a9 40 0:00:00.430000 0.0041 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 183647 1e1fb9ce6e 42 0:00:33.930000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_TSS_density.bed 183649 1e1fb9ce6e 44 0:00:34.610000 0.0025 sort lock.QC_hg38__K562_PRO-seq_06_TSS_density.bed 183646 1e1fb9ce6e 41 0:00:34.700000 0.011 bedtools lock.QC_hg38__K562_PRO-seq_06_TSS_density.bed 183648 1e1fb9ce6e 43 0:00:34.800000 0.005 sort lock.QC_hg38__K562_PRO-seq_06_TSS_density.bed 183682 281c77ddc0 45 0:00:42.440000 0.0843 bedtools lock.QC_hg38__K562_PRO-seq_06_gene_body_density.bed 183684 281c77ddc0 47 0:00:42.560000 0.0059 sort lock.QC_hg38__K562_PRO-seq_06_gene_body_density.bed 183683 281c77ddc0 46 0:00:42.590000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_gene_body_density.bed 183722 80f1372663 49 0:00:00.080000 0.0 awk lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 183723 80f1372663 50 0:00:00.890000 0.0 env lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 183721 80f1372663 48 1:02:52.740000 0.0007 join None # Pipeline started at 06-11 19:03:04 # pid hash cid runtime mem cmd lock 72731 9f49ab4671 28 0:00:00.100000 0.0007 join lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 72733 9f49ab4671 30 0:00:00.330000 0.0041 env lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 72732 9f49ab4671 29 0:00:00.350000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_pause_index.bed # Pipeline started at 06-14 21:06:13 # pid hash cid runtime mem cmd lock 1547 be24164ac3 28 0:00:00.130000 0.0007 join lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 1549 be24164ac3 30 0:00:00.360000 0.0041 env lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 1548 be24164ac3 29 0:00:00.370000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 1556 8128fedc89 31 0:00:00.040000 0.0015 awk lock.QC_hg38__K562_PRO-seq_06_pause_index.bed 1561 bdac3915c8 32 0:00:06.180000 0.2043 Rscript lock.QC_hg38__K562_PRO-seq_06_pause_index.pdf 1587 3282c6ea99 33 0:00:00.040000 0.0019 pigz lock.QC_hg38__K562_PRO-seq_06_pause_index.bed.gz 1640 902651bd31 34 0:00:00.750000 0.0042 grep lock.signal_hg38__K562_PRO-seq_06_gene_coverage.bed 1641 902651bd31 35 0:00:00.770000 0.0053 bedtools lock.signal_hg38__K562_PRO-seq_06_gene_coverage.bed 1644 5bd0ac80f4 36 0:00:48.800000 0.0824 bedtools lock.signal_hg38__K562_PRO-seq_06_gene_coverage.bed 1689 bac461a07b 37 0:00:00.050000 0.0015 ln lock.raw__hg38_annotations.bed 1690 3b23c95663 38 0:00:00.370000 0.0023 pigz lock.raw__hg38_annotations.bed 1699 3b80a4a6cf 39 0:00:01.400000 0.0023 awk lock.QC_hg38__Enhancer 1702 2ef9e10e91 40 0:00:00.050000 0.0 cut lock.QC_hg38__Enhancer_sort.bed 1703 2ef9e10e91 41 0:00:00.710000 0.0023 grep lock.QC_hg38__Enhancer_sort.bed 1705 2ef9e10e91 43 0:00:00.770000 0.0443 bedtools lock.QC_hg38__Enhancer_sort.bed 1704 2ef9e10e91 42 0:00:00.790000 0.0007 cut lock.QC_hg38__Enhancer_sort.bed 1707 75c1337f08 44 0:00:17.550000 0.0089 bedtools lock.QC_hg38__K562_PRO-seq_06_Enhancer_plus_coverage.bed 1971 472cf47ef7 45 0:00:17.030000 0.0106 bedtools lock.QC_hg38__K562_PRO-seq_06_Enhancer_minus_coverage.bed 1990 1189a052af 47 0:00:00.050000 0.0 cut lock.QC_hg38__Promoter_sort.bed 1991 1189a052af 48 0:00:00.270000 0.0026 grep lock.QC_hg38__Promoter_sort.bed 1993 1189a052af 50 0:00:00.290000 0.0083 bedtools lock.QC_hg38__Promoter_sort.bed 1992 1189a052af 49 0:00:00.300000 0.0007 cut lock.QC_hg38__Promoter_sort.bed 1995 19f6287d11 51 0:00:19.530000 0.0395 bedtools lock.QC_hg38__K562_PRO-seq_06_Promoter_plus_coverage.bed 2014 3a53f78855 52 0:00:19.210000 0.034 bedtools lock.QC_hg38__K562_PRO-seq_06_Promoter_minus_coverage.bed 2032 288081ec00 54 0:00:00.290000 0.0015 mv lock.QC_hg38__Promoter_Flanking_Region 2034 af3c48374d 55 0:00:00.050000 0.0 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 2036 af3c48374d 57 0:00:01.060000 0.0007 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 2035 af3c48374d 56 0:00:01.070000 0.0023 grep lock.QC_hg38__Promoter_Flanking_Region_sort.bed 2037 af3c48374d 58 0:00:01.100000 0.0102 bedtools lock.QC_hg38__Promoter_Flanking_Region_sort.bed 2039 c215b32f55 59 0:00:18.920000 0.0125 bedtools lock.QC_hg38__K562_PRO-seq_06_Promoter_Flanking_Region_plus_coverage.bed 2060 01823ceddf 60 0:00:17.710000 0.0166 bedtools lock.QC_hg38__K562_PRO-seq_06_Promoter_Flanking_Region_minus_coverage.bed 2077 b9044f0e58 62 0:00:00.040000 0.0008 mv lock.QC_hg38__5_UTR 2078 8a39766a60 63 0:00:00.050000 0.0 cut lock.QC_hg38__5_UTR_sort.bed 2079 8a39766a60 64 0:00:00.550000 0.0026 grep lock.QC_hg38__5_UTR_sort.bed 2081 8a39766a60 66 0:00:00.620000 0.0295 bedtools lock.QC_hg38__5_UTR_sort.bed 2080 8a39766a60 65 0:00:00.640000 0.0007 cut lock.QC_hg38__5_UTR_sort.bed 2083 26bac59ec8 67 0:00:17.390000 0.0107 bedtools lock.QC_hg38__K562_PRO-seq_06_5_UTR_plus_coverage.bed 2100 bb16df40ed 68 0:00:16.860000 0.0091 bedtools lock.QC_hg38__K562_PRO-seq_06_5_UTR_minus_coverage.bed 2119 f6326d9b21 70 0:00:00.050000 0.0015 mv lock.QC_hg38__3_UTR 2120 5571df88c1 71 0:00:00.050000 0.0 cut lock.QC_hg38__3_UTR_sort.bed 2121 5571df88c1 72 0:00:00.630000 0.0026 grep lock.QC_hg38__3_UTR_sort.bed 2123 5571df88c1 74 0:00:00.660000 0.0108 bedtools lock.QC_hg38__3_UTR_sort.bed 2122 5571df88c1 73 0:00:00.680000 0.0007 cut lock.QC_hg38__3_UTR_sort.bed 2125 2e6cc8b46d 75 0:00:17.580000 0.0127 bedtools lock.QC_hg38__K562_PRO-seq_06_3_UTR_plus_coverage.bed 2141 191c659593 76 0:00:17.300000 0.0161 bedtools lock.QC_hg38__K562_PRO-seq_06_3_UTR_minus_coverage.bed 2157 e57abce387 78 0:00:00.060000 0.0 cut lock.QC_hg38__Exon_sort.bed 2158 e57abce387 79 0:00:02.770000 0.0027 grep lock.QC_hg38__Exon_sort.bed 2160 e57abce387 81 0:00:03.040000 0.158 bedtools lock.QC_hg38__Exon_sort.bed 2159 e57abce387 80 0:00:03.050000 0.0007 cut lock.QC_hg38__Exon_sort.bed 2165 2f495202f9 82 0:00:19.310000 0.0376 bedtools lock.QC_hg38__K562_PRO-seq_06_Exon_plus_coverage.bed 2186 d178c32e8f 83 0:00:18.870000 0.0205 bedtools lock.QC_hg38__K562_PRO-seq_06_Exon_minus_coverage.bed 2203 22502816a2 85 0:00:00.700000 0.0 cut lock.QC_hg38__Intron_sort.bed 2206 22502816a2 87 0:00:02.110000 0.0007 cut lock.QC_hg38__Intron_sort.bed 2205 22502816a2 86 0:00:02.130000 0.0023 grep lock.QC_hg38__Intron_sort.bed 2207 22502816a2 88 0:00:02.200000 0.0773 bedtools lock.QC_hg38__Intron_sort.bed 2210 39488730cd 89 0:00:22.810000 0.0291 bedtools lock.QC_hg38__K562_PRO-seq_06_Intron_plus_coverage.bed 2230 9fe6fa7756 90 0:00:20.260000 0.0386 bedtools lock.QC_hg38__K562_PRO-seq_06_Intron_minus_coverage.bed 2268 1d28a7d488 91 0:00:36.700000 0.4561 Rscript lock.QC_hg38__K562_PRO-seq_06_cFRiF.pdf 2501 5c5c6b3557 92 0:00:26.860000 0.4561 Rscript lock.QC_hg38__K562_PRO-seq_06_FRiF.pdf 2543 49fab98ff3 94 0:00:05.050000 0.0865 bedtools lock.QC_hg38__hg38_introns_sort.bed 2542 49fab98ff3 93 0:00:05.060000 0.0045 grep lock.QC_hg38__hg38_introns_sort.bed 2551 3e4f28dd02 95 0:00:04.750000 0.0046 grep lock.QC_hg38__hg38_introns_sort.bed 2553 3e4f28dd02 97 0:00:05.340000 0.0075 bedtools lock.QC_hg38__hg38_introns_sort.bed 2552 3e4f28dd02 96 0:00:05.350000 0.0333 bedtools lock.QC_hg38__hg38_introns_sort.bed 2560 f496c8b0d4 98 0:00:36.080000 0.0125 bedtools lock.QC_hg38__K562_PRO-seq_06_introns_coverage.bed 2595 032bab2f8c 99 0:00:39 0.0319 bedtools lock.QC_hg38__K562_PRO-seq_06_introns_coverage.bed 2629 fd76b0bce1 100 0:00:00.580000 0.0074 awk lock.QC_hg38__K562_PRO-seq_06_exons_rpkm.bed 2631 fd76b0bce1 102 0:00:00.590000 0.0025 sort lock.QC_hg38__K562_PRO-seq_06_exons_rpkm.bed 2630 fd76b0bce1 101 0:00:00.610000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_exons_rpkm.bed 2633 56800da2df 103 0:00:00.530000 0.0076 awk lock.QC_hg38__K562_PRO-seq_06_introns_rpkm.bed 2635 56800da2df 105 0:00:00.550000 0.0025 sort lock.QC_hg38__K562_PRO-seq_06_introns_rpkm.bed 2634 56800da2df 104 0:00:00.560000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_introns_rpkm.bed 2638 729f0ce0b8 106 0:00:00.080000 0.0007 join lock.QC_hg38__K562_PRO-seq_06_exon_intron_ratios.bed 2640 729f0ce0b8 108 0:00:00.270000 0.0036 sort lock.QC_hg38__K562_PRO-seq_06_exon_intron_ratios.bed 2639 729f0ce0b8 107 0:00:00.280000 0.001 awk lock.QC_hg38__K562_PRO-seq_06_exon_intron_ratios.bed 2646 2f256b70be 109 0:00:05 0.3163 Rscript lock.QC_hg38__K562_PRO-seq_06_mRNA_contamination.pdf 2667 9a1a9c49e0 110 0:00:00.050000 0.0027 pigz lock.QC_hg38__K562_PRO-seq_06_exon_intron_ratios.bed.gz 2675 bf3f79fb47 111 0:00:11.530000 0.0067 samtools lock.signal_hg38__K562_PRO-seq_06_plus_smooth_body_0-mer.bw 2685 6ab22f8183 112 0:08:08.540000 2.6208 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__K562_PRO-seq_06_plus_smooth_body_0-mer.bw 4340 ead23702d7 113 0:00:12.330000 0.0066 samtools lock.signal_hg38__K562_PRO-seq_06_minus_smooth_body_0-mer.bw 4355 8ffcb7e641 114 0:07:53.350000 2.6445 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__K562_PRO-seq_06_minus_smooth_body_0-mer.bw