# Pipeline started at 06-11 17:31:59 # pid hash cid runtime mem cmd lock 51527 14ebc8c106 1 0:00:41.790000 0.003 cat lock.raw__HelaS3_GRO-seq.merged.fastq.gz 51577 6c3cb316b5 2 0:02:14.870000 0.0025 pigz lock.fastq__HelaS3_GRO-seq_R1.fastq 52260 4f73d38be2 3 0:03:24.640000 4.5859 cutadapt lock.fastq__HelaS3_GRO-seq_R1_processed.fastq 52745 0476d9033f 4 0:02:29.420000 0.0008 seqtk lock.fastq__HelaS3_GRO-seq_R1_processed.fastq 52746 0476d9033f 5 0:02:37.600000 0.0023 seqtk lock.fastq__HelaS3_GRO-seq_R1_processed.fastq 54520 78c13b97da 6 0:00:00.030000 0.0 echo lock.fastqc__HelaS3_GRO-seq_R1_processed_fastqc.html 55987 57adb2de9e 6f 0:03:56.940000 0.1921 fastqc lock.trimmed_fastqc 57324 537914eb16 7 0:00:00.220000 0.0004 touch lock.fastq__processed_R1.flag 57326 d804abfa8c 8 0:00:06.380000 0.2043 Rscript lock.cutadapt__HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf 59918 703bbe0069 9 0:08:57.240000 3.666 bowtie2 lock.aligned_hg38__HelaS3_GRO-seq_sort.bam 59923 703bbe0069 10 0:09:17.300000 0.0037 samtools lock.aligned_hg38__HelaS3_GRO-seq_sort.bam 59924 703bbe0069 11 0:12:23.350000 0.8988 samtools lock.aligned_hg38__HelaS3_GRO-seq_sort.bam 63877 7d7082e162 12 0:01:41.480000 0.0183 samtools lock.aligned_hg38__HelaS3_GRO-seq_sort.bam 67152 3b4ed8bca2 13 0:01:02.560000 0.0091 pigz lock.prealignments__HelaS3_GRO-seq_human_rDNA_unmap.fq.gz 67418 c25b4e5d31 14 0:00:23.710000 0.0161 samtools lock.aligned_hg38__HelaS3_GRO-seq_temp.bam.bai 67506 ffbfe5ef81 15 0:00:12.220000 0.0074 samtools lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67553 df4c07aa04 16 0:00:00.060000 0.0 samtools lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67555 df4c07aa04 18 0:00:00.080000 0.0 awk lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67554 df4c07aa04 17 0:00:00.090000 0.0 cut lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67556 df4c07aa04 19 0:00:00.120000 0.0 grep lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67558 5f0ff5e028 20 0:00:14.960000 0.019 samtools lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67633 91a58b7083 21 0:00:00.130000 0.0008 mv lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67637 ffbfe5ef81 22 0:00:11.750000 0.0074 samtools lock.aligned_hg38__HelaS3_GRO-seq_noMT.bam 67810 faf62bd0ab 24 0:00:21.320000 1.2674 /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py lock.QC_hg38__HelaS3_GRO-seq_bamQC.tsv 68140 2de6363881 25 0:00:11.830000 0.0167 samtools lock.aligned_hg38__HelaS3_GRO-seq_unmap.bam 68322 573c62f2c0 26 0:00:57.290000 0.0063 samtools lock.aligned_hg38__HelaS3_GRO-seq_minus.bam 68549 f18d1681ce 27 0:00:53.560000 0.0063 samtools lock.aligned_hg38__HelaS3_GRO-seq_minus.bam 68757 a05de91479 28 0:00:00.260000 0.0015 sed lock.QC_hg38__minus_TSS.tsv 68761 50e1c027e8 29 0:00:08.010000 0.5087 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__HelaS3_GRO-seq_plus_TssEnrichment.txt 68819 47ab5e5105 30 0:00:04.540000 0.8625 /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py lock.QC_hg38__HelaS3_GRO-seq_minus_TssEnrichment.txt 68863 655adc95f7 31 0:00:12.730000 0.0841 Rscript lock.QC_hg38__HelaS3_GRO-seq_TSSenrichment.pdf 68914 afb695e43d 32 0:00:00.050000 0.0 samtools lock.QC_hg38__chr_order.txt 68916 afb695e43d 34 0:00:00.060000 0.0 awk lock.QC_hg38__chr_order.txt 68915 afb695e43d 33 0:00:00.080000 0.0 grep lock.QC_hg38__chr_order.txt 68917 afb695e43d 35 0:00:00.100000 0.0 awk lock.QC_hg38__chr_order.txt 68922 879b107b7b 36 0:00:00.040000 0.0022 cut lock.QC_hg38__chr_keep.txt 68924 41e36b61c2 37 0:00:01.640000 0.0023 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 68925 41e36b61c2 38 0:00:02.090000 0.0927 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 68932 fe4cac0b81 39 0:00:00.330000 0.0026 grep lock.QC_hg38__hg38_ensembl_gene_body.bed 68933 fe4cac0b81 40 0:00:00.380000 0.0051 bedtools lock.QC_hg38__hg38_ensembl_gene_body.bed 68936 205c94b92d 41 0:00:19.240000 0.0558 bedtools lock.QC_hg38__HelaS3_GRO-seq_TSS_density.bed 68938 205c94b92d 43 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lock.QC_hg38__HelaS3_GRO-seq_mRNA_contamination.pdf 61409 b3e0bf7571 110 0:00:00.040000 0.0045 pigz lock.QC_hg38__HelaS3_GRO-seq_exon_intron_ratios.bed.gz 61417 39bb458e59 111 0:00:05.470000 0.0092 samtools lock.signal_hg38__HelaS3_GRO-seq_plus_smooth_body_0-mer.bw 61423 281cd9b341 112 0:05:23.130000 3.503 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__HelaS3_GRO-seq_plus_smooth_body_0-mer.bw 151408 13bb9862bd 113 0:00:04.950000 0.0096 samtools lock.signal_hg38__HelaS3_GRO-seq_minus_smooth_body_0-mer.bw 151418 204040626c 114 0:05:17.740000 3.524 /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py lock.signal_hg38__HelaS3_GRO-seq_minus_smooth_body_0-mer.bw