/mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/*_R1*.f*q.gz
(-: Aligning files matching /mnt/storage/home/sykozyreva/Parus_Major/fastq_hic_inv/*_R*.f*q*
 to genome hg19 with site file /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.DpnII.juicer.txt
(-: Created /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits and /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned.
Running command bwa mem -t 23 /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.fasta /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R1.fastq.gz > /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R1.fastq.gz.sam
(-:  Align of /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R1.fastq.gz.sam done successfully
Running command bwa mem -t 23 /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.fasta /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R2.fastq.gz > /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R2.fastq.gz.sam
(-: Mem align of /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major_R2.fastq.gz.sam done successfully
(-: Sort read 1 aligned file by readname completed.
(-: Sort read 2 aligned file by readname completed.
(-: /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/splits/Parus_major.fastq.gz.sam created successfully.
(-: Finished sorting all sorted files into a single merge.
/mnt/storage/home/manuriddinov/Distributive/juicer-master/CPU/scripts/common/statistics.pl -s /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.DpnII.juicer.txt -l GATCGATC -o /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/Parus_Major_inv_new.txt -q 1 /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/merged_nodups.txt
/mnt/storage/home/manuriddinov/Distributive/juicer-master/CPU/scripts/common/juicer_tools pre -f /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.DpnII.juicer.txt -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000 -s /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/Parus_Major_inv_new.txt -g /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/Parus_Major_inv_new_hists.m -q 1 /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/merged_nodups.txt /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned/Parus_Major_inv_new.hic /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major1.1_HiC/new_fasta/Parus_major1.1_HiC.chrom.sizes
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
Writing expected
Writing norms
Finished writing norms
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
Writing expected
Writing norms
Finished writing norms
***! Error! Either inter.hic or inter_30.hic were not created
Either inter.hic or inter_30.hic were not created.  Check /mnt/scratch/ws/sykozyreva/202303161046data2/Parus_major_inv_HiC/new_map/PM_processed/aligned for results