[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 3905 sequences (364869 bp)...
[M::mem_process_seqs] Processed 3905 reads in 1.451 CPU sec, 0.305 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada1 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/50_S50_ada1.fq
[main] Real time: 14.300 sec; CPU: 4.705 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 3905 sequences (291698 bp)...
[M::mem_process_seqs] Processed 3905 reads in 0.382 CPU sec, 0.081 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada2 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/50_S50_ada2.fq
[main] Real time: 2.724 sec; CPU: 2.629 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 7810 sequences (656567 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 3010, 283, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (55, 67, 132)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 286)
[M::mem_pestat] mean and std.dev: (85.94, 42.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 363)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (3, 3, 3)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 3)
[M::mem_pestat] mean and std.dev: (3.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (3, 3)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 7810 reads in 1.069 CPU sec, 0.221 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/50_S50_1.fq /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/50_S50_2.fq
[main] Real time: 2.542 sec; CPU: 3.333 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 159 sequences (14983 bp)...
[M::mem_process_seqs] Processed 159 reads in 0.026 CPU sec, 0.007 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada1 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/51_S51_ada1.fq
[main] Real time: 2.255 sec; CPU: 2.235 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 159 sequences (12135 bp)...
[M::mem_process_seqs] Processed 159 reads in 0.009 CPU sec, 0.005 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada2 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/51_S51_ada2.fq
[main] Real time: 2.270 sec; CPU: 2.243 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 318 sequences (27118 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 127, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (46, 46, 46)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (46, 46)
[M::mem_pestat] mean and std.dev: (46.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (46, 46)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 318 reads in 0.047 CPU sec, 0.014 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/51_S51_1.fq /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/51_S51_2.fq
[main] Real time: 2.245 sec; CPU: 2.249 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1324 sequences (125915 bp)...
[M::mem_process_seqs] Processed 1324 reads in 0.153 CPU sec, 0.034 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada1 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/52_S52_ada1.fq
[main] Real time: 2.287 sec; CPU: 2.375 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1324 sequences (102025 bp)...
[M::mem_process_seqs] Processed 1324 reads in 0.099 CPU sec, 0.024 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M -R @RG\tID:${file}_ada2 /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/52_S52_ada2.fq
[main] Real time: 2.299 sec; CPU: 2.337 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2648 sequences (227940 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1315, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (46, 66, 70)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 118)
[M::mem_pestat] mean and std.dev: (57.41, 11.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 142)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2648 reads in 0.285 CPU sec, 0.063 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 5 -M /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/52_S52_1.fq /mnt/storage/home/psbelokopytova/loxP_project/2021-10-11_rings//cutadapt/52_S52_2.fq
[main] Real time: 2.338 sec; CPU: 2.527 sec