# Pipeline started at 09-21 14:04:13 # pid hash cid runtime mem cmd lock 32206 969a85cc75 1 0:00:00.040000 0.0 ln lock.raw__tutorial1_R1.fastq.gz 32207 d75410cf13 2 0:00:00.020000 0.0 ln lock.raw__tutorial1_R2.fastq.gz 32208 8cff2171fe 3 0:00:00.020000 0.0 ln lock.fastq__tutorial1_R2.fastq.gz 32209 aa1746cdd7 4 0:00:00.020000 0.0 ln lock.fastq__tutorial1_R2.fastq.gz 32245 093d711023 5 0:00:25.060000 0.0034 skewer lock.fastq__tutorial1_R1_trim.fastq 32280 eaf2a8557d 6 0:00:00.100000 0.0 mv lock.fastq__tutorial1_R1_trim.fastq 32281 68fcd53692 7 0:00:00.030000 0.0003 mv lock.fastq__tutorial1_R1_trim.fastq 32286 75d56a3fe2 7f 0:00:07.190000 0.1639 fastqc lock.fastq__tutorial1_R1_trim_fastqc.html 32325 f0b94a8fb5 7f 0:00:06.410000 0.1722 fastqc lock.fastq__tutorial1_R2_trim_fastqc.html 32361 47f0c141e2 8 0:00:00.040000 0.0013 mkfifo lock.prealignments__rCRSd_bt2 32363 08fd08f509 10 0:00:14.430000 0.0676 bowtie2 lock.prealignments__tutorial1_rCRSd_unmap_R2.fq.gz 32545 c07faf9306 11 0:00:00.020000 0.0 mkfifo lock.prealignments__human_repeats_bt2 32547 9a7bdc412d 13 0:00:15.750000 0.0717 bowtie2 lock.prealignments__tutorial1_human_repeats_unmap_R2.fq.gz 32576 cab65f3e9f 14 0:00:07.790000 0.0032 pigz lock.prealignments__tutorial1_rCRSd_unmap_R1.fq.gz 32592 f7f8318007 15 0:00:06.220000 0.0032 pigz lock.prealignments__tutorial1_rCRSd_unmap_R2.fq.gz 32604 dcf6f46f79 16 0:00:07.700000 0.0032 pigz lock.prealignments__tutorial1_human_repeats_unmap_R1.fq.gz 32620 0637fca07b 17 0:00:05.910000 0.0032 pigz lock.prealignments__tutorial1_human_repeats_unmap_R2.fq.gz 32637 8104d6caaa 20 0:06:36.400000 0.2185 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 32635 8104d6caaa 18 0:06:36.410000 3.5437 bowtie2 lock.aligned_hg38__tutorial1_sort_dedup.bam 32636 8104d6caaa 19 0:06:36.430000 0.0037 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1500 3c04f88306 21 0:00:09.130000 0.0129 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1546 16ce5ccd7a 22 0:00:01.200000 0.0163 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam.bai 1551 b49401e168 23 0:00:01.280000 0.0171 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam.bai 1562 09d5603f82 27 0:00:00.150000 0.0 grep lock.aligned_hg38__tutorial1_noMT.bam 1559 09d5603f82 24 0:00:00.160000 0.0045 samtools lock.aligned_hg38__tutorial1_noMT.bam 1561 09d5603f82 26 0:00:00.210000 0.001 awk lock.aligned_hg38__tutorial1_noMT.bam 1560 09d5603f82 25 0:00:00.230000 0.0007 cut lock.aligned_hg38__tutorial1_noMT.bam 1564 106438406d 28 0:00:08.900000 0.0147 samtools lock.aligned_hg38__tutorial1_noMT.bam 1584 abae91eec9 29 0:00:00.040000 0.0002 mv lock.aligned_hg38__tutorial1_noMT.bam 1585 b49401e168 30 0:00:01.170000 0.0168 samtools lock.aligned_hg38__tutorial1_noMT.bam 1589 651fe12c3d 31 0:00:09.250000 0.3544 /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamQC.py lock.QC_hg38__tutorial1_bamQC.tsv 1634 f8fce9f72f 32 0:00:01.120000 0.0046 samtools lock.aligned_hg38__tutorial1_unmap.bam 1655 f6853ea13f 33 0:00:23.030000 0.242 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1657 f6853ea13f 35 0:00:23.100000 0.0055 samblaster lock.aligned_hg38__tutorial1_sort_dedup.bam 1659 f6853ea13f 37 0:00:30.180000 0.2209 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1656 f6853ea13f 34 0:00:30.200000 0.0034 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1658 f6853ea13f 36 0:00:30.220000 0.0037 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1706 0f870831c9 38 0:00:01.160000 0.0171 samtools lock.aligned_hg38__tutorial1_sort_dedup.bam 1731 bd595c7b88 39 0:00:05.370000 0.0052 preseq lock.QC_hg38__tutorial1_preseq_out.txt 1740 02f725fd8a 40 0:00:05.730000 0.0051 preseq lock.QC_hg38__tutorial1_preseq_yield.txt 1746 5a6f2a4b2a 41 0:00:01.530000 0.0054 echo lock.QC_hg38__tutorial1_preseq_counts.txt 1755 6c6419c378 42 0:00:07.240000 0.2116 Rscript lock.QC_hg38__tutorial1_preseq_plot.png 1783 73b211f711 43 0:20:31.920000 1.8587 /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamSitesToWig.py lock.aligned_hg38__tutorial1_smooth.bw 6822 b507ebc288 44 0:00:14.960000 0.404 /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/pyTssEnrichment.py lock.QC_hg38__tutorial1_TSS_enrichment.txt 6862 804b5c664c 45 0:00:09.220000 0.2132 Rscript lock.QC_hg38__tutorial1_TSS_enrichment.pdf 6894 0dca1fed73 46 0:00:04.620000 0.0057 perl lock.QC_hg38__tutorial1_fragLenDistribution.pdf 6899 e1c49fc29e 47 0:00:01.040000 0.0185 sort lock.QC_hg38__tutorial1_fragLenDistribution.pdf 6900 e1c49fc29e 48 0:00:01.080000 0.0019 uniq lock.QC_hg38__tutorial1_fragLenDistribution.pdf 7061 46941d92ca 49 0:00:06.300000 0.2134 Rscript lock.QC_hg38__tutorial1_fragLenDistribution.pdf 7081 3ec343cd6d 50 0:00:00.050000 0.0013 ln lock.raw__hg38_annotations.bed 7082 3d8272d7b0 51 0:00:00.330000 0.0023 pigz lock.raw__hg38_annotations.bed 7088 302e12774b 52 0:04:03.800000 0.1203 macs2 lock.peak_calling_hg38__tutorial1_peaks.narrowPeak 8016 abf45a441f 53 0:00:01.570000 0.0047 pigz lock.aligned_hg38_exact__tutorial1_shift.bed.gz 8026 bd95ecf2d2 54 0:00:01.030000 0.0069 awk lock.peak_calling_hg38__tutorial1_peaks_fixedWidth.narrowPeak 8028 d0497d6551 55 0:00:15.230000 0.6707 Rscript lock.peak_calling_hg38__tutorial1_peaks_normalized.narrowPeak 8067 e0fdba11d1 56 0:00:00.020000 0.0 ln lock.raw__hg38_blacklist.bed 8068 0ded35e6bc 57 0:00:00.040000 0.0015 pigz lock.raw__hg38_blacklist.bed 8073 ca77d65369 58 0:00:00.840000 0.0045 bedtools lock.peak_calling_hg38__tutorial1_peaks_rmBlacklist.narrowPeak 8075 49efaee84d 59 0:00:12.650000 0.2956 Rscript lock.peak_calling_hg38__blacklist.flag 8112 c766851f9e 60 0:00:00.100000 0.0013 touch lock.peak_calling_hg38__blacklist.flag 8123 dac41f03d7 61 0:00:00.080000 0.0 samtools lock.peak_calling_hg38__chr_order.txt 8125 dac41f03d7 63 0:00:00.100000 0.0 awk lock.peak_calling_hg38__chr_order.txt 8124 dac41f03d7 62 0:00:00.120000 0.0 grep lock.peak_calling_hg38__chr_order.txt 8126 dac41f03d7 64 0:00:00.170000 0.0 awk lock.peak_calling_hg38__chr_order.txt 8129 bf4f5367f3 65 0:00:00.500000 0.0022 cut lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8131 dac41f03d7 66 0:00:00.090000 0.0 samtools lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8133 dac41f03d7 68 0:00:00.110000 0.0 awk lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8132 dac41f03d7 67 0:00:00.130000 0.0 grep lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8134 dac41f03d7 69 0:00:00.150000 0.0 awk lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8136 81a5547e0f 70 0:00:00.030000 0.0 cut lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8138 580bbb4c81 71 0:00:00.590000 0.0075 bedtools lock.peak_calling_hg38__tutorial1_peaks_sort.bed 8141 f263279407 72 0:00:03.390000 0.0114 bedtools lock.peak_calling_hg38__coverage.flag 8142 f263279407 73 0:00:03.420000 0.0022 uniq lock.peak_calling_hg38__coverage.flag 8147 a15ed5095f 74 0:00:01.010000 0.0111 awk lock.peak_calling_hg38__coverage.flag 8151 d044191698 75 0:00:00.040000 0.0008 mv lock.peak_calling_hg38__coverage.flag 8152 6cb47ecff4 76 0:00:00.050000 0.0004 touch lock.peak_calling_hg38__coverage.flag 8153 85dbf4460e 77 0:00:00.830000 0.0047 pigz lock.peak_calling_hg38__tutorial1_peaks_coverage.bed.gz 8176 cdfa369c35 78 0:00:00.030000 0.0 echo lock.peak_calling_hg38__bigNarrowPeak.as 8177 5eea0f44e9 79 0:00:01.300000 0.0038 bedToBigBed lock.peak_calling_hg38__tutorial1_peaks.bigBed 8179 beb1fc844b 80 0:00:41.110000 0.4591 Rscript lock.QC_hg38__tutorial1_peak_chromosome_distribution.pdf 8659 a577f63bee 81 0:00:16.620000 0.4965 Rscript lock.QC_hg38__tutorial1_peak_TSS_distribution.pdf 8724 1c842a6ffb 82 0:00:19.230000 0.5492 Rscript lock.QC_hg38__tutorial1_peak_genomic_distribution.pdf 8783 4ed4884b8e 83 0:00:01.580000 0.0054 awk lock.QC_hg38__3' UTR 8787 596b2ff2e2 84 0:00:00.030000 0.0 mv lock.QC_hg38__3_UTR 8788 4596e9b1df 85 0:00:00.050000 0.0 cut lock.QC_hg38__3_UTR_sort.bed 8789 4596e9b1df 86 0:00:00.990000 0.0026 grep lock.QC_hg38__3_UTR_sort.bed 8791 4596e9b1df 88 0:00:01.120000 0.0359 bedtools lock.QC_hg38__3_UTR_sort.bed 8790 4596e9b1df 87 0:00:01.140000 0.0007 cut lock.QC_hg38__3_UTR_sort.bed 8803 d79818a687 89 0:00:03.490000 0.007 bedtools lock.QC_hg38__tutorial1_3_UTR_coverage.bed 8822 4564ba3c1c 91 0:00:00.030000 0.0 mv lock.QC_hg38__5_UTR 8823 085c5a0c92 92 0:00:00.060000 0.0 cut lock.QC_hg38__5_UTR_sort.bed 8824 085c5a0c92 93 0:00:00.900000 0.0026 grep lock.QC_hg38__5_UTR_sort.bed 8826 085c5a0c92 95 0:00:00.920000 0.0086 bedtools lock.QC_hg38__5_UTR_sort.bed 8825 085c5a0c92 94 0:00:00.940000 0.0007 cut lock.QC_hg38__5_UTR_sort.bed 8829 e9b6c0d076 96 0:00:01.690000 0.0075 bedtools lock.QC_hg38__tutorial1_5_UTR_coverage.bed 8839 8130859f4e 98 0:00:00.050000 0.0 cut lock.QC_hg38__Enhancer_sort.bed 8841 8130859f4e 100 0:00:01.240000 0.0007 cut lock.QC_hg38__Enhancer_sort.bed 8840 8130859f4e 99 0:00:01.260000 0.0023 grep lock.QC_hg38__Enhancer_sort.bed 8842 8130859f4e 101 0:00:01.330000 0.0467 bedtools lock.QC_hg38__Enhancer_sort.bed 8860 5f11ad2911 102 0:00:01.730000 0.0086 bedtools lock.QC_hg38__tutorial1_Enhancer_coverage.bed 8864 c7c9536168 104 0:00:00.060000 0.0 cut lock.QC_hg38__Exon_sort.bed 8865 c7c9536168 105 0:00:04.420000 0.0026 grep lock.QC_hg38__Exon_sort.bed 8867 c7c9536168 107 0:00:04.670000 0.1668 bedtools lock.QC_hg38__Exon_sort.bed 8866 c7c9536168 106 0:00:04.690000 0.0007 cut lock.QC_hg38__Exon_sort.bed 8878 9354c404a5 108 0:00:02.730000 0.0119 bedtools lock.QC_hg38__tutorial1_Exon_coverage.bed 8886 bc880729f3 110 0:00:00.050000 0.0 cut lock.QC_hg38__Intron_sort.bed 8889 bc880729f3 113 0:00:02.370000 0.0755 bedtools lock.QC_hg38__Intron_sort.bed 8887 bc880729f3 111 0:00:02.390000 0.0023 grep lock.QC_hg38__Intron_sort.bed 8888 bc880729f3 112 0:00:02.410000 0.0007 cut lock.QC_hg38__Intron_sort.bed 8894 4148d7bd1d 114 0:00:03.090000 0.0144 bedtools lock.QC_hg38__tutorial1_Intron_coverage.bed 8901 dbed94eaa8 116 0:00:00.050000 0.0 cut lock.QC_hg38__Promoter_sort.bed 8902 dbed94eaa8 117 0:00:00.470000 0.0026 grep lock.QC_hg38__Promoter_sort.bed 8904 dbed94eaa8 119 0:00:00.490000 0.0088 bedtools lock.QC_hg38__Promoter_sort.bed 8903 dbed94eaa8 118 0:00:00.510000 0.0007 cut lock.QC_hg38__Promoter_sort.bed 8906 e9a7157085 120 0:00:01.490000 0.007 bedtools lock.QC_hg38__tutorial1_Promoter_coverage.bed 8912 bc72f7b860 122 0:00:00.040000 0.0008 mv lock.QC_hg38__Promoter_Flanking_Region 8913 a1b5e9c983 123 0:00:00.080000 0.0 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 8915 a1b5e9c983 125 0:00:01.640000 0.0007 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 8914 a1b5e9c983 124 0:00:01.660000 0.0023 grep lock.QC_hg38__Promoter_Flanking_Region_sort.bed 8916 a1b5e9c983 126 0:00:01.740000 0.0502 bedtools lock.QC_hg38__Promoter_Flanking_Region_sort.bed 8921 acde1deca7 127 0:00:02.460000 0.0076 bedtools lock.QC_hg38__tutorial1_Promoter_Flanking_Region_coverage.bed 8933 95a39d1b32 128 0:00:39.570000 0.5363 Rscript lock.QC_hg38__tutorial1_cFRiF.pdf 9012 138e9400ce 129 0:00:35.030000 0.5399 Rscript lock.QC_hg38__tutorial1_FRiF.pdf