/mnt/storage/home/vsfishman/Distr/3d-dna/run-asm-pipeline.sh -r 1 /mnt/storage/home/vsfishman/Distr/juicer-master/juicer-wd/references/sciara_merged_Prim_on_Gerbi_soft_WG.fasta /mnt/storage/home/vsfishman/tmp/sciara/aligned/merged_nodups.txt
version: 180922
 -r|--rounds flag was triggered, will run 1 round(s) of misjoin correction.
###############
Starting iterating scaffolding with editing:
...starting round 0 of scaffolding:
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to false.
:) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
...Using cprops file: sciara_merged_Prim_on_Gerbi_soft_WG.0.cprops
...Using merged_nodups file: sciara_merged_Prim_on_Gerbi_soft_WG.mnd.0.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
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:) DONE!
...visualizing round 0 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -q flag was triggered, starting calculations for 1 threshold mapping quality
:) -i flag was triggered, building mapq without
:) -c flag was triggered, will remove temporary files after completion
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

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