# Pipeline started at 06-11 17:54:54 # pid hash cid runtime mem cmd lock 432526 d9b35b50f0 1 0:00:00.080000 0.0 ln lock.raw__H9_PRO-seq_30_R1.fastq.gz 432528 61b8bafffe 2 0:00:00.060000 0.0 ln lock.raw__H9_PRO-seq_30_R2.fastq.gz 432529 6181470dc8 3 0:00:20.910000 0.0025 pigz lock.fastq__H9_PRO-seq_30_R2.fastq 432753 775cf11d1c 4 0:00:22.470000 0.0025 pigz lock.fastq__H9_PRO-seq_30_R2.fastq 432826 a17e8d89e1 5 0:00:25.830000 1.588 cutadapt lock.fastq__H9_PRO-seq_30_R1_processed.fastq 432875 0d04e5cd23 6 0:00:04.700000 0.0008 seqtk lock.fastq__H9_PRO-seq_30_R1_processed.fastq 432877 0d04e5cd23 7 0:00:11.020000 0.0023 seqtk lock.fastq__H9_PRO-seq_30_R1_processed.fastq 432897 1c4988816c 7f 0:00:24.810000 0.1724 fastqc lock.trimmed_fastqc 432939 72dd995256 8 0:00:18.110000 1.0368 seqkit lock.fastq__H9_PRO-seq_30_R1_trimmed.fastq 433032 083c72fd9d 9 0:00:03.780000 0.0008 seqtk lock.fastq__H9_PRO-seq_30_R1_trimmed.fastq 433033 083c72fd9d 10 0:00:09.640000 0.0023 seqtk lock.fastq__H9_PRO-seq_30_R1_trimmed.fastq 433078 e0b57c82a1 11 0:00:00.060000 0.0 touch lock.fastq__processed_R1.flag 433080 847aead679 12 0:00:31.060000 1.561 cutadapt lock.fastq__H9_PRO-seq_30_R2_trimmed.fastq 433125 4dc063df4e 13 0:00:07.760000 0.0008 seqtk lock.fastq__H9_PRO-seq_30_R2_trimmed.fastq 433126 4dc063df4e 14 0:00:10.820000 0.0023 seqtk lock.fastq__H9_PRO-seq_30_R2_trimmed.fastq 433150 1c4988816c 14f 0:00:22.060000 0.1781 fastqc lock.trimmed_fastqc 433188 85efd5cbab 14f 0:00:21.100000 0.1683 fastqc lock.trimmed_fastqc_R2 433223 cbc650a455 15 0:00:42.690000 1.3463 fastq_pair lock.cutadapt__H9_PRO-seq_30.histogram 433269 9766c75994 16 0:00:31.120000 0.0723 flash lock.cutadapt__H9_PRO-seq_30.histogram 433707 2bf38e3d29 17 0:00:11.730000 0.1031 Rscript lock.cutadapt__H9_PRO-seq_30_adapter_insertion_distribution.pdf 433744 4e2d0881c7 18 0:00:06.180000 0.0018 cp lock.fastq__H9_PRO-seq_30_R2_trimmed_dups.fastq 433750 6e1de2dd9f 19 0:00:00.050000 0.0004 touch lock.fastq__processed_R2.flag 433751 1ee78bb3bd 20 0:00:52.280000 1.6695 fastq_pair lock.fastq__repaired.flag 433818 b73159b918 21 0:00:00.210000 0.0015 mv lock.fastq__repaired.flag 433819 ef9ca02cb9 22 0:00:00.100000 0.0008 mv lock.fastq__repaired.flag 433820 0b9cd2d387 23 0:00:00.030000 0.0 touch lock.fastq__repaired.flag 433821 0761078c89 24 0:01:00.080000 1.8728 fastq_pair lock.fastq__dups_repaired.flag 433884 a4804f9041 25 0:00:00.260000 0.0015 mv lock.fastq__dups_repaired.flag 433885 9ed36ff3d4 26 0:00:00.210000 0.0008 mv lock.fastq__dups_repaired.flag 433886 19e47c10de 27 0:00:00.040000 0.0 touch lock.fastq__dups_repaired.flag 433887 f912f3798a 28 0:00:00.050000 0.0007 mkfifo lock.prealignments__human_rDNA_bt2 433981 b158fec35f 30 0:00:00.080000 0.0015 mkfifo lock.prealignments__human_rDNA_dups_bt2 434060 3b44649c9b 32 0:19:53.230000 3.6603 bowtie2 lock.aligned_hg38__H9_PRO-seq_30_sort.bam 434061 3b44649c9b 33 0:20:13.420000 0.0037 samtools lock.aligned_hg38__H9_PRO-seq_30_sort.bam 434062 3b44649c9b 34 0:21:33.110000 0.9216 samtools lock.aligned_hg38__H9_PRO-seq_30_sort.bam 436644 2347d84776 35 0:00:29.610000 0.0146 samtools lock.aligned_hg38__H9_PRO-seq_30_sort.bam 437428 4d0478fd23 36 0:16:03.790000 3.6616 bowtie2 lock.aligned_hg38__H9_PRO-seq_30_sort_dups.bam 437434 4d0478fd23 37 0:16:23.880000 0.0037 samtools lock.aligned_hg38__H9_PRO-seq_30_sort_dups.bam 437435 4d0478fd23 38 0:17:37.880000 0.8959 samtools lock.aligned_hg38__H9_PRO-seq_30_sort_dups.bam 439839 add5a3f658 39 0:00:33.870000 0.0147 samtools lock.aligned_hg38__H9_PRO-seq_30_sort_dups.bam 439913 906adcdf07 40 0:00:10.420000 0.0079 pigz lock.prealignments__H9_PRO-seq_30_human_rDNA_unmap_R2.fq.gz 439953 46e78fa26e 41 0:00:13.250000 0.008 pigz lock.prealignments__H9_PRO-seq_30_human_rDNA_unmap_R1.fq.gz 440011 9ea72b8076 42 0:00:12.760000 0.0083 samtools lock.aligned_hg38__H9_PRO-seq_30_temp.bam.bai 440033 3f450f4a5b 43 0:00:09.590000 0.0091 samtools lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440048 7a02da1f16 45 0:00:00.060000 0.0 cut lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440050 7a02da1f16 47 0:00:00.080000 0.0 grep lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440047 7a02da1f16 44 0:00:00.090000 0.0081 samtools lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440049 7a02da1f16 46 0:00:00.110000 0.0 awk lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440052 b0cc99c487 48 0:00:13.370000 0.0153 samtools lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440075 9591be9c71 49 0:00:00.130000 0.0008 mv lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440076 3f450f4a5b 50 0:00:13.650000 0.008 samtools lock.aligned_hg38__H9_PRO-seq_30_noMT.bam 440088 5b537711e1 51 0:00:40.800000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_30_PE2.bam 440089 5b537711e1 52 0:00:48.060000 1.5615 samtools lock.aligned_hg38__H9_PRO-seq_30_PE2.bam 440167 33b370dba9 53 0:00:38.170000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_30_PE2.bam 440168 33b370dba9 54 0:00:44.550000 1.2529 samtools lock.aligned_hg38__H9_PRO-seq_30_PE2.bam 440272 cf1d3f902c 55 0:00:12.120000 0.0089 samtools lock.aligned_hg38__H9_PRO-seq_30_temp_dups.bam.bai 440287 17de3d0ab0 63 0:00:41.590000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 440288 17de3d0ab0 64 0:00:49.650000 1.5615 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 433888 b581d914ee 29 0:52:42.260000 0.0 perl None 433982 e751ae5fab 31 0:51:37.560000 0.0 perl None 440382 47795436bf 65 0:00:24.960000 0.0038 samtools None 440383 47795436bf 66 0:00:25.010000 0.0015 samtools None # Pipeline started at 06-11 19:13:38 # pid hash cid runtime mem cmd lock 353510 f912f3798a 15 0:00:00.030000 0.0 mkfifo lock.prealignments__human_rDNA_bt2 353511 b158fec35f 17 0:00:00.030000 0.0 mkfifo lock.prealignments__human_rDNA_dups_bt2 353516 17de3d0ab0 42 0:00:42.590000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 353517 17de3d0ab0 43 0:00:50.140000 1.5553 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 353602 47795436bf 44 0:00:35.790000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 353603 47795436bf 45 0:00:41.920000 1.2459 samtools lock.aligned_hg38__H9_PRO-seq_30_dups_PE2.bam 353995 b65baa7d19 46 0:00:32.100000 0.0051 preseq lock.QC_hg38__H9_PRO-seq_30_preseq_out.txt 354032 b7fa43dfb7 47 0:00:34.310000 0.0051 preseq lock.QC_hg38__H9_PRO-seq_30_preseq_yield.txt 354174 1ba65f1a39 48 0:00:09.200000 0.0057 echo lock.QC_hg38__H9_PRO-seq_30_preseq_counts.txt 354187 abace19610 49 0:00:07.180000 0.2011 Rscript lock.QC_hg38__H9_PRO-seq_30_preseq_plot.png 354209 23aadcb5f2 50 0:00:04.980000 0.0118 samtools lock.aligned_hg38__H9_PRO-seq_30_PE1.bam.bai 354214 d2a02ae405 51 0:00:08.520000 0.7741 /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py lock.QC_hg38__H9_PRO-seq_30_bamQC.tsv 354244 1c48f6fa52 52 0:00:03.130000 0.0071 samtools lock.aligned_hg38__H9_PRO-seq_30_unmap.bam 354270 8f860217dc 53 0:00:22.350000 0.0063 samtools lock.aligned_hg38__H9_PRO-seq_30_minus.bam 354305 4a0ae09fd5 54 0:00:20.870000 0.0063 samtools lock.aligned_hg38__H9_PRO-seq_30_minus.bam 354324 2e8eb03106 55 0:00:00.210000 0.0015 sed lock.QC_hg38__minus_TSS.tsv 354325 ce9fc981e9 56 0:00:04.130000 0.6604 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__H9_PRO-seq_30_plus_TssEnrichment.txt 354347 90c257e2eb 57 0:00:03.890000 0.42 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__H9_PRO-seq_30_minus_TssEnrichment.txt 354369 50fbc30cd8 58 0:00:07.190000 0.2755 Rscript lock.QC_hg38__H9_PRO-seq_30_TSSenrichment.pdf 354390 f3c164a582 59 0:00:00.060000 0.0 samtools lock.QC_hg38__chr_order.txt 354392 f3c164a582 61 0:00:00.070000 0.0 awk lock.QC_hg38__chr_order.txt 354391 f3c164a582 60 0:00:00.090000 0.0 grep lock.QC_hg38__chr_order.txt 354393 f3c164a582 62 0:00:00.110000 0.0 awk lock.QC_hg38__chr_order.txt 354396 c70978e693 63 0:00:00.030000 0.0 cut lock.QC_hg38__chr_keep.txt 354398 46dd8e41be 64 0:00:01.740000 0.0042 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 354399 46dd8e41be 65 0:00:01.970000 0.0927 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 354403 27ec063a1a 66 0:00:00.320000 0.0026 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 354404 27ec063a1a 67 0:00:00.390000 0.0051 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 354407 5aa5ff6dc5 69 0:00:08.070000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_TSS_density.bed 354409 5aa5ff6dc5 71 0:00:09.390000 0.0025 sort lock.QC_hg38__H9_PRO-seq_30_TSS_density.bed 354406 5aa5ff6dc5 68 0:00:09.410000 0.006 bedtools lock.QC_hg38__H9_PRO-seq_30_TSS_density.bed 354408 5aa5ff6dc5 70 0:00:09.430000 0.0023 sort lock.QC_hg38__H9_PRO-seq_30_TSS_density.bed 354425 89691c8550 74 0:00:10.990000 0.0038 sort lock.QC_hg38__H9_PRO-seq_30_gene_body_density.bed 354423 89691c8550 72 0:00:11.010000 0.0306 bedtools lock.QC_hg38__H9_PRO-seq_30_gene_body_density.bed 354424 89691c8550 73 0:00:11.030000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_gene_body_density.bed 354436 2156ee45e9 75 0:00:00.120000 0.0007 join lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 354438 2156ee45e9 77 0:00:00.310000 0.0038 env lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 354437 2156ee45e9 76 0:00:00.330000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_pause_index.bed # Pipeline started at 06-14 21:18:33 # pid hash cid runtime mem cmd lock 287516 f912f3798a 15 0:00:00.040000 0.0007 mkfifo lock.prealignments__human_rDNA_bt2 287559 b158fec35f 17 0:00:00.030000 0.0 mkfifo lock.prealignments__human_rDNA_dups_bt2 287629 e1d929e68b 48 0:00:00.120000 0.0007 join lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 287642 e1d929e68b 50 0:00:00.310000 0.0038 env lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 287640 e1d929e68b 49 0:00:00.330000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 287832 6b9c9dba6a 51 0:00:00.050000 0.0015 awk lock.QC_hg38__H9_PRO-seq_30_pause_index.bed 287909 18a64318af 52 0:00:06.270000 0.2043 Rscript lock.QC_hg38__H9_PRO-seq_30_pause_index.pdf 289084 39e712ab57 53 0:00:00.070000 0.0016 pigz lock.QC_hg38__H9_PRO-seq_30_pause_index.bed.gz 289116 6eb5df8678 54 0:00:00.800000 0.0042 grep lock.signal_hg38__H9_PRO-seq_30_gene_coverage.bed 289117 6eb5df8678 55 0:00:00.820000 0.0061 bedtools lock.signal_hg38__H9_PRO-seq_30_gene_coverage.bed 289119 81fad49d6c 56 0:00:14.060000 0.0468 bedtools lock.signal_hg38__H9_PRO-seq_30_gene_coverage.bed 289137 326e7b1749 57 0:00:00.040000 0.0015 ln lock.raw__hg38_annotations.bed 289138 2c8386dc7e 58 0:00:00.310000 0.0023 pigz lock.raw__hg38_annotations.bed 289147 219c375093 59 0:00:01.530000 0.0023 awk lock.QC_hg38__Enhancer 289154 065cf3d8bc 60 0:00:00.050000 0.0 cut lock.QC_hg38__Enhancer_sort.bed 289155 065cf3d8bc 61 0:00:00.760000 0.0023 grep lock.QC_hg38__Enhancer_sort.bed 289157 065cf3d8bc 63 0:00:00.830000 0.0443 bedtools lock.QC_hg38__Enhancer_sort.bed 289156 065cf3d8bc 62 0:00:00.850000 0.0007 cut lock.QC_hg38__Enhancer_sort.bed 289159 ca42972811 64 0:00:04.340000 0.0074 bedtools lock.QC_hg38__H9_PRO-seq_30_Enhancer_plus_coverage.bed 289165 e54a14a0aa 65 0:00:04.260000 0.0081 bedtools lock.QC_hg38__H9_PRO-seq_30_Enhancer_minus_coverage.bed 289173 f77bac3957 67 0:00:00.060000 0.0 cut lock.QC_hg38__Promoter_sort.bed 289174 f77bac3957 68 0:00:00.280000 0.0026 grep lock.QC_hg38__Promoter_sort.bed 289176 f77bac3957 70 0:00:00.300000 0.0089 bedtools lock.QC_hg38__Promoter_sort.bed 289175 f77bac3957 69 0:00:00.310000 0.0007 cut lock.QC_hg38__Promoter_sort.bed 289178 bcafce74c9 71 0:00:04.530000 0.0117 bedtools lock.QC_hg38__H9_PRO-seq_30_Promoter_plus_coverage.bed 289184 234de56f33 72 0:00:04.460000 0.0169 bedtools lock.QC_hg38__H9_PRO-seq_30_Promoter_minus_coverage.bed 289191 53211425da 74 0:00:00.070000 0.0015 mv lock.QC_hg38__Promoter_Flanking_Region 289192 cb36660b2b 75 0:00:00.050000 0.0 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 289194 cb36660b2b 77 0:00:01.110000 0.0007 cut lock.QC_hg38__Promoter_Flanking_Region_sort.bed 289193 cb36660b2b 76 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0:00:04.730000 0.0047 grep lock.QC_hg38__hg38_introns_sort.bed 289668 e93b438cf0 117 0:00:05.330000 0.0053 bedtools lock.QC_hg38__hg38_introns_sort.bed 289667 e93b438cf0 116 0:00:05.340000 0.0332 bedtools lock.QC_hg38__hg38_introns_sort.bed 289674 b2916930b6 118 0:00:08.640000 0.0081 bedtools lock.QC_hg38__H9_PRO-seq_30_introns_coverage.bed 292119 5006e017ca 119 0:00:11.660000 0.0184 bedtools lock.QC_hg38__H9_PRO-seq_30_introns_coverage.bed 301495 a0de4a49f7 120 0:00:00.570000 0.009 awk lock.QC_hg38__H9_PRO-seq_30_exons_rpkm.bed 301529 a0de4a49f7 122 0:00:00.590000 0.0025 sort lock.QC_hg38__H9_PRO-seq_30_exons_rpkm.bed 301517 a0de4a49f7 121 0:00:00.610000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_exons_rpkm.bed 302226 8bb2430743 123 0:00:00.600000 0.0088 awk lock.QC_hg38__H9_PRO-seq_30_introns_rpkm.bed 302240 8bb2430743 125 0:00:00.640000 0.0038 sort lock.QC_hg38__H9_PRO-seq_30_introns_rpkm.bed 302234 8bb2430743 124 0:00:00.660000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_introns_rpkm.bed 303039 2c4afa1e93 126 0:00:00.110000 0.0007 join lock.QC_hg38__H9_PRO-seq_30_exon_intron_ratios.bed 303062 2c4afa1e93 128 0:00:00.260000 0.0036 sort lock.QC_hg38__H9_PRO-seq_30_exon_intron_ratios.bed 303042 2c4afa1e93 127 0:00:00.280000 0.001 awk lock.QC_hg38__H9_PRO-seq_30_exon_intron_ratios.bed 303474 344889a37b 129 0:00:07.030000 0.2011 Rscript lock.QC_hg38__H9_PRO-seq_30_mRNA_contamination.pdf 312794 c975f6c1bf 130 0:00:00.060000 0.0024 pigz lock.QC_hg38__H9_PRO-seq_30_exon_intron_ratios.bed.gz 312929 d06d08ef3e 131 0:00:02.580000 0.0061 samtools lock.signal_hg38__H9_PRO-seq_30_plus_smooth_body_0-mer.bw 316552 01e679aae2 132 0:09:50.150000 2.2179 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__H9_PRO-seq_30_plus_smooth_body_0-mer.bw 9073 ab12d7983f 133 0:00:02.700000 0.006 samtools lock.signal_hg38__H9_PRO-seq_30_minus_smooth_body_0-mer.bw 9087 d10b4d3974 134 0:09:32.920000 1.8898 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__H9_PRO-seq_30_minus_smooth_body_0-mer.bw