# Pipeline started at 06-11 17:54:17 # pid hash cid runtime mem cmd lock 51553 43ff560a91 1 0:00:00.030000 0.0 ln lock.raw__H9_PRO-seq_20_R1.fastq.gz 51555 349b69326a 2 0:00:00.030000 0.0 ln lock.raw__H9_PRO-seq_20_R2.fastq.gz 51556 97d0661fbc 3 0:00:22.010000 0.0025 pigz lock.fastq__H9_PRO-seq_20_R2.fastq 52032 3be7217e35 4 0:00:19.530000 0.0025 pigz lock.fastq__H9_PRO-seq_20_R2.fastq 52485 8046e946ba 5 0:00:30.980000 0.9228 cutadapt lock.fastq__H9_PRO-seq_20_R1_processed.fastq 52688 c90f884dac 6 0:00:03.070000 0.0008 seqtk lock.fastq__H9_PRO-seq_20_R1_processed.fastq 52690 c90f884dac 7 0:00:12.500000 0.0023 seqtk lock.fastq__H9_PRO-seq_20_R1_processed.fastq 52772 07b330fb99 7f 0:00:15.470000 0.1793 fastqc lock.trimmed_fastqc 52955 9a73b66c1f 8 0:00:16.930000 0.4994 seqkit lock.fastq__H9_PRO-seq_20_R1_trimmed.fastq 53108 7de5729311 9 0:00:02.640000 0.0008 seqtk lock.fastq__H9_PRO-seq_20_R1_trimmed.fastq 53109 7de5729311 10 0:00:07.410000 0.0023 seqtk lock.fastq__H9_PRO-seq_20_R1_trimmed.fastq 53193 84d8cb87cf 11 0:00:00.030000 0.0 touch lock.fastq__processed_R1.flag 53198 dbdafc938c 12 0:00:35.510000 0.8892 cutadapt lock.fastq__H9_PRO-seq_20_R2_trimmed.fastq 53413 3d1b13bfba 13 0:00:02.730000 0.0008 seqtk lock.fastq__H9_PRO-seq_20_R2_trimmed.fastq 53414 3d1b13bfba 14 0:00:13.390000 0.0023 seqtk lock.fastq__H9_PRO-seq_20_R2_trimmed.fastq 53502 07b330fb99 14f 0:00:16.710000 0.1745 fastqc lock.trimmed_fastqc 53620 bd1f6132f2 14f 0:00:15.320000 0.1817 fastqc lock.trimmed_fastqc_R2 53727 9ffe003c6f 15 0:00:45.180000 1.0081 fastq_pair lock.cutadapt__H9_PRO-seq_20.histogram 53994 2c95421bc9 16 0:00:30.980000 0.0576 flash lock.cutadapt__H9_PRO-seq_20.histogram 54314 e1d396f26b 17 0:00:07.160000 0.2015 Rscript lock.cutadapt__H9_PRO-seq_20_adapter_insertion_distribution.pdf 54377 b545f3283d 18 0:00:06 0.0018 cp lock.fastq__H9_PRO-seq_20_R2_trimmed_dups.fastq 54414 5ab009603d 19 0:00:00.060000 0.0004 touch lock.fastq__processed_R2.flag 54416 895a4884bc 20 0:00:42 1.0563 fastq_pair lock.fastq__repaired.flag 55018 8c2d594812 21 0:00:00.220000 0.0015 mv lock.fastq__repaired.flag 55020 97b3046c61 22 0:00:00.140000 0.0008 mv lock.fastq__repaired.flag 55024 b8e0588ee4 23 0:00:00.230000 0.0004 touch lock.fastq__repaired.flag 55027 f72b07c6e4 24 0:00:36.190000 1.0465 fastq_pair lock.fastq__dups_repaired.flag 55246 f3f6951566 25 0:00:00.140000 0.0008 mv lock.fastq__dups_repaired.flag 55248 ced07e9d06 26 0:00:00.140000 0.0008 mv lock.fastq__dups_repaired.flag 55250 73b174b5a5 27 0:00:00.260000 0.0004 touch lock.fastq__dups_repaired.flag 55251 9a75d99abc 28 0:00:00.040000 0.0007 mkfifo lock.prealignments__human_rDNA_bt2 55654 3d90f3d74c 30 0:00:00.050000 0.0015 mkfifo lock.prealignments__human_rDNA_dups_bt2 56007 500688dc87 32 0:21:49.830000 3.5557 bowtie2 lock.aligned_hg38__H9_PRO-seq_20_sort.bam 56009 500688dc87 33 0:22:09.880000 0.0037 samtools lock.aligned_hg38__H9_PRO-seq_20_sort.bam 56010 500688dc87 34 0:22:54.220000 0.8958 samtools lock.aligned_hg38__H9_PRO-seq_20_sort.bam 63957 25801fefb7 35 0:00:30.520000 0.0112 samtools lock.aligned_hg38__H9_PRO-seq_20_sort.bam 65706 77303e270a 36 0:20:43.830000 3.5439 bowtie2 lock.aligned_hg38__H9_PRO-seq_20_sort_dups.bam 65707 77303e270a 37 0:21:03.890000 0.0037 samtools lock.aligned_hg38__H9_PRO-seq_20_sort_dups.bam 65708 77303e270a 38 0:21:25.460000 0.8957 samtools lock.aligned_hg38__H9_PRO-seq_20_sort_dups.bam 70827 25af7a8f8c 39 0:00:29.460000 0.0112 samtools lock.aligned_hg38__H9_PRO-seq_20_sort_dups.bam 70864 dafa160c46 40 0:00:11.440000 0.0038 pigz lock.prealignments__H9_PRO-seq_20_human_rDNA_unmap_R2.fq.gz 70880 9cf16b65dc 41 0:00:12.640000 0.0037 pigz lock.prealignments__H9_PRO-seq_20_human_rDNA_unmap_R1.fq.gz 70946 e3de92d0cd 42 0:00:07.840000 0.0121 samtools lock.aligned_hg38__H9_PRO-seq_20_temp.bam.bai 70961 3bc027aee8 43 0:00:05.900000 0.0123 samtools lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 70976 26b7fc8108 45 0:00:00.060000 0.0 cut lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 70978 26b7fc8108 47 0:00:00.090000 0.0 grep lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 70975 26b7fc8108 44 0:00:00.110000 0.0078 samtools lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 70977 26b7fc8108 46 0:00:00.120000 0.0 awk lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 70981 9de7fb3449 48 0:00:14.500000 0.0121 samtools lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 71004 04a69176d3 49 0:00:00.100000 0.0008 mv lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 71005 3bc027aee8 50 0:00:05.870000 0.0123 samtools lock.aligned_hg38__H9_PRO-seq_20_noMT.bam 71011 1d92858fad 51 0:00:27.680000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_20_PE2.bam 71012 1d92858fad 52 0:00:35.990000 1.043 samtools lock.aligned_hg38__H9_PRO-seq_20_PE2.bam 71157 4155dcefd8 53 0:00:27.370000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_20_PE2.bam 71158 4155dcefd8 54 0:00:29.820000 0.8385 samtools lock.aligned_hg38__H9_PRO-seq_20_PE2.bam 71219 8ebe37e332 55 0:00:07.470000 0.0126 samtools lock.aligned_hg38__H9_PRO-seq_20_temp_dups.bam.bai 55252 6120bc8e95 29 0:54:21.100000 0.0 perl None 55657 6055ab35a8 31 0:53:35.570000 0.0 perl None 71276 c734989573 63 0:00:26.790000 0.0038 samtools None 71277 c734989573 64 0:00:26.810000 0.0015 samtools None # Pipeline started at 06-11 19:13:07 # pid hash cid runtime mem cmd lock 21214 9a75d99abc 15 0:00:00.040000 0.0007 mkfifo lock.prealignments__human_rDNA_bt2 21215 3d90f3d74c 17 0:00:00.030000 0.0 mkfifo lock.prealignments__human_rDNA_dups_bt2 21221 c734989573 42 0:00:30.810000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_20_dups_PE2.bam 21222 c734989573 43 0:00:38.680000 1.0502 samtools lock.aligned_hg38__H9_PRO-seq_20_dups_PE2.bam 21271 d69a59f0d3 44 0:00:27.340000 0.0038 samtools lock.aligned_hg38__H9_PRO-seq_20_dups_PE2.bam 21272 d69a59f0d3 45 0:00:32.440000 0.8463 samtools lock.aligned_hg38__H9_PRO-seq_20_dups_PE2.bam 21318 274723711b 46 0:00:23.400000 0.0052 preseq lock.QC_hg38__H9_PRO-seq_20_preseq_out.txt 21337 f351203672 47 0:00:25.800000 0.0051 preseq lock.QC_hg38__H9_PRO-seq_20_preseq_yield.txt 21564 8876a004b9 48 0:00:06.660000 0.0054 echo lock.QC_hg38__H9_PRO-seq_20_preseq_counts.txt 21575 25d2c2b672 49 0:00:08.390000 0.1294 Rscript lock.QC_hg38__H9_PRO-seq_20_preseq_plot.png 21598 eba0d13d29 50 0:00:03.580000 0.0057 samtools lock.aligned_hg38__H9_PRO-seq_20_PE1.bam.bai 21602 acca0b03f1 51 0:00:11.310000 0.2849 /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py lock.QC_hg38__H9_PRO-seq_20_bamQC.tsv 21625 7be621dfdb 52 0:00:03.570000 0.006 samtools lock.aligned_hg38__H9_PRO-seq_20_unmap.bam 21644 d8e5c66f8c 53 0:00:16.470000 0.0063 samtools lock.aligned_hg38__H9_PRO-seq_20_minus.bam 21662 ed8b6c6809 54 0:00:15.940000 0.0063 samtools lock.aligned_hg38__H9_PRO-seq_20_minus.bam 21677 7729b16f8a 55 0:00:00.250000 0.0015 sed lock.QC_hg38__minus_TSS.tsv 21678 357d9447ad 56 0:00:05.450000 0.321 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__H9_PRO-seq_20_plus_TssEnrichment.txt 21694 88f5879ebd 57 0:00:04.850000 0.3539 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__H9_PRO-seq_20_minus_TssEnrichment.txt 21710 f3764ab751 58 0:00:06.980000 0.2848 Rscript lock.QC_hg38__H9_PRO-seq_20_TSSenrichment.pdf 21728 67102d7fe7 59 0:00:00.050000 0.0 samtools lock.QC_hg38__chr_order.txt 21730 67102d7fe7 61 0:00:00.060000 0.0 awk lock.QC_hg38__chr_order.txt 21729 67102d7fe7 60 0:00:00.080000 0.0 grep lock.QC_hg38__chr_order.txt 21731 67102d7fe7 62 0:00:00.100000 0.0 awk lock.QC_hg38__chr_order.txt 21733 44bd28eaee 63 0:00:00.020000 0.0 cut lock.QC_hg38__chr_keep.txt 21735 00bcd4dd55 64 0:00:01.810000 0.0026 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 21736 00bcd4dd55 65 0:00:02.080000 0.0986 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 21740 5e216a012f 66 0:00:00.350000 0.0026 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 21741 5e216a012f 67 0:00:00.420000 0.0041 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 21744 f915b5494d 69 0:00:06.890000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_TSS_density.bed 21746 f915b5494d 71 0:00:07.290000 0.0025 sort lock.QC_hg38__H9_PRO-seq_20_TSS_density.bed 21743 f915b5494d 68 0:00:07.310000 0.0062 bedtools lock.QC_hg38__H9_PRO-seq_20_TSS_density.bed 21745 f915b5494d 70 0:00:07.330000 0.0047 sort lock.QC_hg38__H9_PRO-seq_20_TSS_density.bed 21755 16a4c533e4 73 0:00:08.010000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_gene_body_density.bed 21754 16a4c533e4 72 0:00:08.030000 0.0266 bedtools lock.QC_hg38__H9_PRO-seq_20_gene_body_density.bed 21756 16a4c533e4 74 0:00:08.100000 0.0057 sort lock.QC_hg38__H9_PRO-seq_20_gene_body_density.bed 21768 60e66ebe83 75 0:00:00.120000 0.0007 join lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 21770 60e66ebe83 77 0:00:00.310000 0.0054 env lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 21769 60e66ebe83 76 0:00:00.330000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_pause_index.bed # Pipeline started at 06-14 21:18:34 # pid hash cid runtime mem cmd lock 315045 9a75d99abc 15 0:00:00.050000 0.0 mkfifo lock.prealignments__human_rDNA_bt2 315138 3d90f3d74c 17 0:00:00.030000 0.0 mkfifo lock.prealignments__human_rDNA_dups_bt2 315371 0cf7372dd1 48 0:00:00.120000 0.0007 join lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 315420 0cf7372dd1 50 0:00:00.320000 0.0038 env lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 315391 0cf7372dd1 49 0:00:00.340000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 315958 8dfa2789f1 51 0:00:00.050000 0.0015 awk lock.QC_hg38__H9_PRO-seq_20_pause_index.bed 316144 c55dd9f231 52 0:00:06.440000 0.2043 Rscript lock.QC_hg38__H9_PRO-seq_20_pause_index.pdf 325365 5b8916e961 53 0:00:00.050000 0.0019 pigz lock.QC_hg38__H9_PRO-seq_20_pause_index.bed.gz 331058 5863f008bb 54 0:00:00.720000 0.0042 grep lock.signal_hg38__H9_PRO-seq_20_gene_coverage.bed 331060 5863f008bb 55 0:00:00.740000 0.0056 bedtools lock.signal_hg38__H9_PRO-seq_20_gene_coverage.bed 331425 6ae7355ba7 56 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332455 fbe1c605fc 119 0:00:06.610000 0.0292 bedtools lock.QC_hg38__H9_PRO-seq_20_introns_coverage.bed 332462 39280ea78e 120 0:00:00.510000 0.0088 awk lock.QC_hg38__H9_PRO-seq_20_exons_rpkm.bed 332464 39280ea78e 122 0:00:00.540000 0.0036 sort lock.QC_hg38__H9_PRO-seq_20_exons_rpkm.bed 332463 39280ea78e 121 0:00:00.560000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_exons_rpkm.bed 332467 68de76c96d 123 0:00:00.500000 0.0085 awk lock.QC_hg38__H9_PRO-seq_20_introns_rpkm.bed 332469 68de76c96d 125 0:00:00.550000 0.0038 sort lock.QC_hg38__H9_PRO-seq_20_introns_rpkm.bed 332468 68de76c96d 124 0:00:00.570000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_introns_rpkm.bed 332472 822062c227 126 0:00:00.090000 0.0007 join lock.QC_hg38__H9_PRO-seq_20_exon_intron_ratios.bed 332474 822062c227 128 0:00:00.200000 0.0033 sort lock.QC_hg38__H9_PRO-seq_20_exon_intron_ratios.bed 332473 822062c227 127 0:00:00.220000 0.001 awk lock.QC_hg38__H9_PRO-seq_20_exon_intron_ratios.bed 332480 5ee5a37c04 129 0:00:05.020000 0.3165 Rscript lock.QC_hg38__H9_PRO-seq_20_mRNA_contamination.pdf 332501 94aaae3339 130 0:00:00.070000 0.0021 pigz lock.QC_hg38__H9_PRO-seq_20_exon_intron_ratios.bed.gz 332509 e0cee4ef20 131 0:00:01.690000 0.0071 samtools lock.signal_hg38__H9_PRO-seq_20_plus_smooth_body_0-mer.bw 332515 06dbc82889 132 0:16:48.650000 1.3301 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__H9_PRO-seq_20_plus_smooth_body_0-mer.bw 135538 b1f236dd81 133 0:00:01.760000 0.0069 samtools lock.signal_hg38__H9_PRO-seq_20_minus_smooth_body_0-mer.bw 135541 86a832a1d8 134 0:16:35.160000 1.2811 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__H9_PRO-seq_20_minus_smooth_body_0-mer.bw