2021-09-16 15:23:18,382 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' --- 2021-09-16 15:23:18,382 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129109.sra 2021-09-16 15:23:18,382 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 15:23:18,387 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpg2s0ehyp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129109.sra" 2021-09-16 15:30:48,486 INFO SimpleSubprocess Sra2FastQ - 0:07:30 2021-09-16 15:30:48,487 DEBUG SimpleSubprocess gzip /tmp/tmpg2s0ehyp/* 2021-09-16 15:59:26,422 INFO SimpleSubprocess GZipFastQ - 0:28:37 2021-09-16 15:59:26,553 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmpg2s0ehyp/SRR6129109_1.fastq.gz /tmp/tmpg2s0ehyp/SRR6129109_R1.fastq.gz; mv /tmp/tmpg2s0ehyp/SRR6129109_2.fastq.gz /tmp/tmpg2s0ehyp/SRR6129109_R2.fastq.gz; cp /tmp/tmpg2s0ehyp/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 15:59:32,199 INFO SimpleSubprocess CopyFiles - 0:00:05 2021-09-16 15:59:33,022 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129110.sra 2021-09-16 15:59:33,022 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 15:59:33,076 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpxenw8uzh "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129110.sra" 2021-09-16 16:07:05,629 INFO SimpleSubprocess Sra2FastQ - 0:07:32 2021-09-16 16:07:05,629 DEBUG SimpleSubprocess gzip /tmp/tmpxenw8uzh/* 2021-09-16 16:36:02,063 INFO SimpleSubprocess GZipFastQ - 0:28:56 2021-09-16 16:36:02,088 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmpxenw8uzh/SRR6129110_1.fastq.gz /tmp/tmpxenw8uzh/SRR6129110_R1.fastq.gz; mv /tmp/tmpxenw8uzh/SRR6129110_2.fastq.gz /tmp/tmpxenw8uzh/SRR6129110_R2.fastq.gz; cp /tmp/tmpxenw8uzh/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 16:36:07,771 INFO SimpleSubprocess CopyFiles - 0:00:05 2021-09-16 16:36:08,634 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129111.sra 2021-09-16 16:36:08,634 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 16:36:08,634 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpzb49kbwv "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129111.sra" 2021-09-16 16:43:19,612 INFO SimpleSubprocess Sra2FastQ - 0:07:10 2021-09-16 16:43:19,613 DEBUG SimpleSubprocess gzip /tmp/tmpzb49kbwv/* 2021-09-16 17:12:26,453 INFO SimpleSubprocess GZipFastQ - 0:29:06 2021-09-16 17:12:26,454 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmpzb49kbwv/SRR6129111_1.fastq.gz /tmp/tmpzb49kbwv/SRR6129111_R1.fastq.gz; mv /tmp/tmpzb49kbwv/SRR6129111_2.fastq.gz /tmp/tmpzb49kbwv/SRR6129111_R2.fastq.gz; cp /tmp/tmpzb49kbwv/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 17:12:32,280 INFO SimpleSubprocess CopyFiles - 0:00:05 2021-09-16 17:12:33,138 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129112.sra 2021-09-16 17:12:33,138 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 17:12:33,216 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpibdzelkn "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129112.sra" 2021-09-16 17:17:59,686 INFO SimpleSubprocess Sra2FastQ - 0:05:26 2021-09-16 17:17:59,686 DEBUG SimpleSubprocess gzip /tmp/tmpibdzelkn/* 2021-09-16 17:42:18,682 INFO SimpleSubprocess GZipFastQ - 0:24:18 2021-09-16 17:42:18,682 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmpibdzelkn/SRR6129112_1.fastq.gz /tmp/tmpibdzelkn/SRR6129112_R1.fastq.gz; mv /tmp/tmpibdzelkn/SRR6129112_2.fastq.gz /tmp/tmpibdzelkn/SRR6129112_R2.fastq.gz; cp /tmp/tmpibdzelkn/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 17:42:23,350 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-16 17:42:24,060 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129113.sra 2021-09-16 17:42:24,060 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 17:42:24,060 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpvninic_p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129113.sra" 2021-09-16 17:47:52,939 INFO SimpleSubprocess Sra2FastQ - 0:05:28 2021-09-16 17:47:52,939 DEBUG SimpleSubprocess gzip /tmp/tmpvninic_p/* 2021-09-16 18:12:54,954 INFO SimpleSubprocess GZipFastQ - 0:25:02 2021-09-16 18:12:54,955 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmpvninic_p/SRR6129113_2.fastq.gz /tmp/tmpvninic_p/SRR6129113_R2.fastq.gz; mv /tmp/tmpvninic_p/SRR6129113_1.fastq.gz /tmp/tmpvninic_p/SRR6129113_R1.fastq.gz; cp /tmp/tmpvninic_p/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 18:12:59,618 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-16 18:13:00,250 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129114.sra 2021-09-16 18:13:00,250 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 18:13:00,250 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmphg3zhbwv "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129114.sra" 2021-09-16 18:18:32,413 INFO SimpleSubprocess Sra2FastQ - 0:05:32 2021-09-16 18:18:32,427 DEBUG SimpleSubprocess gzip /tmp/tmphg3zhbwv/* 2021-09-16 18:43:01,813 INFO SimpleSubprocess GZipFastQ - 0:24:29 2021-09-16 18:43:01,814 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq"; mv /tmp/tmphg3zhbwv/SRR6129114_2.fastq.gz /tmp/tmphg3zhbwv/SRR6129114_R2.fastq.gz; mv /tmp/tmphg3zhbwv/SRR6129114_1.fastq.gz /tmp/tmphg3zhbwv/SRR6129114_R1.fastq.gz; cp /tmp/tmphg3zhbwv/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq" 2021-09-16 18:43:06,617 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-16 18:43:07,402 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__ 2021-09-16 18:43:07,402 INFO Juicer Genome assembly: mm10 2021-09-16 18:43:07,402 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-16 18:43:07,402 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-16 18:43:07,403 INFO Juicer Enzyme: HindIII 2021-09-16 18:43:07,403 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt 2021-09-16 18:43:07,403 INFO Juicer Threads: 10 2021-09-16 18:43:07,403 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/HIC_tmp" 2021-09-16 18:43:07,410 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-16 18:43:07,410 DEBUG SimpleSubprocess bash "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/juicer.sh" -t 10 -D "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer" -g mm10 -z "/Data/DataBases/mm10/mm10_canonic.fa" -p "/Data/DataBases/mm10/mm10_canonic.chrom.sizes" -s HindIII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__" 2021-09-17 10:40:32,795 INFO SimpleSubprocess Juicer - 15:57:25 2021-09-17 10:40:32,864 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/fastq/*_R*.fastq* to genome mm10 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129109_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129109_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129109.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129109.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129110_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129110_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129110.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129110.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129111_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129111_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129111.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129111.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129112_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129112_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129112.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129112.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129113_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129113_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129113.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129113.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129114_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129114_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129114.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/splits/SRR6129114.fastq.gz.sam done successfully (-: Finished sorting all sorted files into a single merge. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-09-17T05:13:48,992] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-09-17T08:29:38,525] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body ........................................................................................................................................................................................................................................ Writing footer Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Finished writing norms /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools is post-processing Hi-C for mm10 Data read from /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_30.hic. Motifs read from /Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/references/motif ARROWHEAD: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-09-17T10:40:31,713] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_30.hic Using 1 CPU thread(s) HiCCUPS: GPUs are not installed so HiCCUPs cannot be run (-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-: (-: Pipeline successfully completed (-: Run cleanup.sh to remove the splits directory Check /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned for results 2021-09-17 10:40:33,038 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/merged_nodups.txt 2021-09-17 10:40:33,038 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 10:40:33,092 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpst_ymtz8/inter.pairs.txt" 2021-09-17 10:45:27,620 INFO SimpleSubprocess MakeInterPairs - 0:04:54 2021-09-17 10:45:27,631 DEBUG SimpleSubprocess cp "/tmp/tmpst_ymtz8/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" 2021-09-17 10:45:37,537 INFO SimpleSubprocess CopyFiles - 0:00:09 2021-09-17 10:45:38,337 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 10:45:38,338 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-17 10:45:38,338 INFO Pairs2Cool Genome assembly: mm10 2021-09-17 10:45:38,338 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-17 10:45:38,338 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-17 10:45:38,452 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":5000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/tmp/tmp4_4ey27y/inter_no_balanced.cool" 2021-09-17 10:51:58,680 INFO SimpleSubprocess MakeCool - 0:06:20 2021-09-17 10:51:58,680 DEBUG SimpleSubprocess cp "/tmp/tmp4_4ey27y/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-17 10:51:58,843 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 10:51:58,890 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 10:51:58,890 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-17 10:51:58,891 INFO Pairs2Cool Genome assembly: mm10 2021-09-17 10:51:58,891 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-17 10:51:58,891 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-17 10:51:58,891 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":10000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfz5bun9e/inter_no_balanced.cool" 2021-09-17 10:57:33,877 INFO SimpleSubprocess MakeCool - 0:05:34 2021-09-17 10:57:33,877 DEBUG SimpleSubprocess cp "/tmp/tmpfz5bun9e/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-17 10:57:34,012 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 10:57:34,060 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 10:57:34,060 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-17 10:57:34,060 INFO Pairs2Cool Genome assembly: mm10 2021-09-17 10:57:34,061 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-17 10:57:34,061 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-17 10:57:34,061 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":20000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfgq_bnoz/inter_no_balanced.cool" 2021-09-17 11:02:40,435 INFO SimpleSubprocess MakeCool - 0:05:06 2021-09-17 11:02:40,435 DEBUG SimpleSubprocess cp "/tmp/tmpfgq_bnoz/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-17 11:02:40,539 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:02:40,577 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 11:02:40,577 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-17 11:02:40,577 INFO Pairs2Cool Genome assembly: mm10 2021-09-17 11:02:40,577 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-17 11:02:40,577 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-17 11:02:40,607 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":25000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/tmp/tmp3xk8pu35/inter_no_balanced.cool" 2021-09-17 11:07:36,556 INFO SimpleSubprocess MakeCool - 0:04:55 2021-09-17 11:07:36,557 DEBUG SimpleSubprocess cp "/tmp/tmp3xk8pu35/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-17 11:07:36,651 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:07:36,687 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt 2021-09-17 11:07:36,687 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-17 11:07:36,687 INFO Pairs2Cool Genome assembly: mm10 2021-09-17 11:07:36,687 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-17 11:07:36,687 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-17 11:07:36,742 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":50000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/tmp/tmpxu5lrg2_/inter_no_balanced.cool" 2021-09-17 11:12:13,234 INFO SimpleSubprocess MakeCool - 0:04:36 2021-09-17 11:12:13,234 DEBUG SimpleSubprocess cp "/tmp/tmpxu5lrg2_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-17 11:12:13,310 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:13,322 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-17 11:12:13,322 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_5kb.cool 2021-09-17 11:12:13,322 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-17 11:12:13,355 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp6ief4fma/inter.cool" 2021-09-17 11:12:13,506 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-17 11:12:13,506 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6ief4fma/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-17 11:12:29,188 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-09-17 11:12:29,189 DEBUG SimpleSubprocess cp "/tmp/tmp6ief4fma/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_5kb.cool" 2021-09-17 11:12:29,339 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:29,381 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-17 11:12:29,381 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_10kb.cool 2021-09-17 11:12:29,381 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-17 11:12:29,382 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpuls8jajc/inter.cool" 2021-09-17 11:12:29,505 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-17 11:12:29,506 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpuls8jajc/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-17 11:12:32,506 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-17 11:12:32,506 DEBUG SimpleSubprocess cp "/tmp/tmpuls8jajc/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_10kb.cool" 2021-09-17 11:12:32,627 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:32,645 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-17 11:12:32,645 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_20kb.cool 2021-09-17 11:12:32,645 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-17 11:12:32,646 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpuv10p0qw/inter.cool" 2021-09-17 11:12:32,750 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-17 11:12:32,750 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpuv10p0qw/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-17 11:12:35,054 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-17 11:12:35,054 DEBUG SimpleSubprocess cp "/tmp/tmpuv10p0qw/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_20kb.cool" 2021-09-17 11:12:35,178 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:35,193 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-17 11:12:35,193 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_25kb.cool 2021-09-17 11:12:35,193 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-17 11:12:35,218 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpcknsr51j/inter.cool" 2021-09-17 11:12:35,312 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-17 11:12:35,312 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpcknsr51j/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-17 11:12:37,756 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-17 11:12:37,756 DEBUG SimpleSubprocess cp "/tmp/tmpcknsr51j/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_25kb.cool" 2021-09-17 11:12:37,849 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:37,869 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-17 11:12:37,869 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_50kb.cool 2021-09-17 11:12:37,869 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-17 11:12:37,869 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpyc1sjej_/inter.cool" 2021-09-17 11:12:37,944 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-17 11:12:37,944 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpyc1sjej_/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-17 11:12:39,623 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-17 11:12:39,623 DEBUG SimpleSubprocess cp "/tmp/tmpyc1sjej_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_50kb.cool" 2021-09-17 11:12:39,698 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-17 11:12:39,893 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:39,899 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-17 11:12:39,928 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_5kb.cool 2021-09-17 11:12:39,928 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:39,928 INFO AddWeight Chromosome: chrX 2021-09-17 11:12:39,928 INFO AddWeight Resolution [bp]: 5000 2021-09-17 11:12:40,616 INFO AddWeight AddWeight successfully finished 2021-09-17 11:12:40,616 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_10kb.cool 2021-09-17 11:12:40,616 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:40,616 INFO AddWeight Chromosome: chrX 2021-09-17 11:12:40,616 INFO AddWeight Resolution [bp]: 10000 2021-09-17 11:12:40,752 INFO AddWeight AddWeight successfully finished 2021-09-17 11:12:40,752 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_20kb.cool 2021-09-17 11:12:40,752 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:40,752 INFO AddWeight Chromosome: chrX 2021-09-17 11:12:40,752 INFO AddWeight Resolution [bp]: 20000 2021-09-17 11:12:40,790 INFO AddWeight AddWeight successfully finished 2021-09-17 11:12:40,790 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_25kb.cool 2021-09-17 11:12:40,790 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:40,790 INFO AddWeight Chromosome: chrX 2021-09-17 11:12:40,791 INFO AddWeight Resolution [bp]: 25000 2021-09-17 11:12:40,829 INFO AddWeight AddWeight successfully finished 2021-09-17 11:12:40,829 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_50kb.cool 2021-09-17 11:12:40,829 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:40,829 INFO AddWeight Chromosome: chrX 2021-09-17 11:12:40,829 INFO AddWeight Resolution [bp]: 50000 2021-09-17 11:12:40,852 INFO AddWeight AddWeight successfully finished 2021-09-17 11:12:40,854 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.hic 2021-09-17 11:12:40,854 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_norm.hic 2021-09-17 11:12:40,854 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt 2021-09-17 11:12:40,854 INFO Vector2HiC Threads: 10 2021-09-17 11:12:41,176 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.hic" "/tmp/tmpt0fr2wuu/inter.hic" 2021-09-17 11:12:43,289 INFO SimpleSubprocess TempFiles - 0:00:02 2021-09-17 11:12:43,289 INFO Vector2HiC Vector: vector c-tale_normalization chrX 5000 BP 2021-09-17 11:12:43,290 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0fr2wuu/inter.hic" "/tmp/tmpt0fr2wuu/vector.txt" 2021-09-17 11:12:49,727 INFO SimpleSubprocess NormalizeHiC - 0:00:06 2021-09-17 11:12:49,727 INFO Vector2HiC Vector: vector c-tale_normalization chrX 10000 BP 2021-09-17 11:12:49,728 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0fr2wuu/inter.hic" "/tmp/tmpt0fr2wuu/vector.txt" 2021-09-17 11:12:53,730 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-17 11:12:53,731 INFO Vector2HiC Vector: vector c-tale_normalization chrX 20000 BP 2021-09-17 11:12:53,732 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0fr2wuu/inter.hic" "/tmp/tmpt0fr2wuu/vector.txt" 2021-09-17 11:12:57,609 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-17 11:12:57,609 INFO Vector2HiC Vector: vector c-tale_normalization chrX 25000 BP 2021-09-17 11:12:57,610 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0fr2wuu/inter.hic" "/tmp/tmpt0fr2wuu/vector.txt" 2021-09-17 11:13:01,556 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-17 11:13:01,557 INFO Vector2HiC Vector: vector c-tale_normalization chrX 50000 BP 2021-09-17 11:13:01,557 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpt0fr2wuu/inter.hic" "/tmp/tmpt0fr2wuu/vector.txt" 2021-09-17 11:13:05,312 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-17 11:13:05,312 DEBUG SimpleSubprocess cp "/tmp/tmpt0fr2wuu/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_norm.hic" 2021-09-17 11:13:06,513 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-17 11:13:06,748 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/merged_nodups.txt" 2021-09-17 11:22:59,032 INFO SimpleSubprocess CopyResult - 0:09:52 2021-09-17 11:22:59,079 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter.pairs.txt" 2021-09-17 11:23:38,916 INFO SimpleSubprocess CopyResult - 0:00:39 2021-09-17 11:23:38,916 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/vector.txt" 2021-09-17 11:23:39,270 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:39,271 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter.hic" 2021-09-17 11:23:50,872 INFO SimpleSubprocess CopyResult - 0:00:11 2021-09-17 11:23:50,872 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_statistics.txt" 2021-09-17 11:23:50,880 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:50,880 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_no_balanced_5kb.cool" 2021-09-17 11:23:52,070 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-17 11:23:52,070 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_5kb.cool" 2021-09-17 11:23:54,202 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-17 11:23:54,202 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_no_balanced_10kb.cool" 2021-09-17 11:23:55,191 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:55,192 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_10kb.cool" 2021-09-17 11:23:56,125 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:56,125 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_no_balanced_20kb.cool" 2021-09-17 11:23:57,102 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:57,102 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_20kb.cool" 2021-09-17 11:23:58,088 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:23:58,089 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_no_balanced_25kb.cool" 2021-09-17 11:23:59,549 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-17 11:23:59,549 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_25kb.cool" 2021-09-17 11:24:00,618 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-17 11:24:00,619 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_no_balanced_50kb.cool" 2021-09-17 11:24:01,174 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:24:01,174 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/inter_50kb.cool" 2021-09-17 11:24:01,717 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-17 11:24:01,930 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__" 2021-09-17 11:24:31,770 INFO SimpleSubprocess RemoveTemp - 0:00:29 2021-09-17 11:24:31,770 INFO BenchmarkPipeline 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' FINISHED, SUMMARY TIME - 20:01:13 2021-09-20 11:27:07,191 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' --- 2021-09-20 11:27:07,211 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__" 2021-09-20 11:27:07,220 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-20 11:27:07,220 INFO BenchmarkPipeline 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' FINISHED, SUMMARY TIME - 0:00:00 2021-09-20 11:28:38,899 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' --- 2021-09-20 11:28:38,899 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114/__temp__" 2021-09-20 11:28:38,907 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-20 11:28:38,907 INFO BenchmarkPipeline 'SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114' FINISHED, SUMMARY TIME - 0:00:00